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How do I best identify weak points in myself along a path to academia
I will be graduating from university (in the states) this semester with a bachelors in physics and mathematics. I applied for physics PhD programs (in the states) this cycle and obtained a few admissions. However, I am considering taking another year to improve my application and apply to physics PhD programs again, next cycle.
The problem is, I find it difficult to know what to focus on in terms of improving my application. Hence, I am asking how does one best judge what the weak points of their application is along a road to academia.
Clarification: Even though I am currently at the stage of entering graduate studies, I mean to ask this question for the more general setting of continuing on a path to academia.

Why did you apply to schools if you wouldn't go there when admitted? Were you offered funding? It sounds like your next step to improve in physics is to accept an offer and do a PhD.

Why do you need to improve your application and apply to physics PhD programs again next year, if you've already obtained a few admissions?

Does physics have a tradition of pre-doc RA jobs? That would be the way to get into a higher ranked program in my field, economics.

@BryanKrause There is also a 2-body problem involved, which makes it (for me) a serious option to apply another cycle.

@SillyGoose how would applying another cycle help? Are you planning to apply with your partner and only attending a university that accepts you both?

@Allure I would apply to more schools in the appropriate area and also hopefully improve my application so as to get better results.

How is it unacceptable that you got admitted already? Are any of those schools acceptable? Or all unacceptable?

So you didn't have a 2-body problem in November/December but do now that it's March? I know that's quite possible but do think carefully about decisions that will affect you for at least the next 5 years and possibly indefinitely.

"How do I best identify weak points in myself" – " what to focus on in terms of improving my application." These are two very different things. You can certainly do things to improve yourself (i.e., you can self-study). It is, however, highly doubtful that you can do anything to improve your application on your own (unless you have publications in the pipeline that can realistically be accepted before the next round of applications). What matters on PhD applications are tangible and verifiable facts, not your own assertion that you studied really hard all year to improve yourself.

@BryanKrause: it is not as simple as "schools I don't want to go" and "schools I want to go". There are "schools that are not great but would be acceptable". The OP is just pondering if improving his skills would land him in a better school. It is the same when you look for housing or for a job.

@Taladris Exactly: if they are acceptable then you go there when they admit you and other schools you rank higher don't.

@BryanKrause: you can rent/buy the first acceptable apartment you find. But if you can, you can also wait some time until you find your dream apartment. Same for a job, a PhD program, etc.

@Taladris You have to live somewhere, and there's an application calendar. So you apply to every apartment you might be willing to live in, and accept the best one that accepts you. If there's a dump you'd never live in even if they accepted you, you just don't apply. Grad school isn't like apartments where new ones open up from time to time: all the schools are there and they need you to apply at about the same time (typically in the US; of course there are some schools and some countries where rolling admissions happen, etc).

Now if something comes up that makes you decide a program you thought would be a good fit actually isn't (maybe you get a really bad one when visiting, maybe the professor(s) you hoped to work with aren't taking students) it's reasonable to not accept that offer, but OP described multiple accepted offers.

Your plan doesn’t sounds like a good idea. You can become better only by moving ahead in your academic journey as soon as you can, have PhD degree and start a faculty position. There is no definition of what is enough and what is not in your personal journey. It’s terrible idea to define “enough” looking at others when you are living your own journey by yourself. My suggestion is to accept position if you like and move ahead if you are already accepted.

@BryanKrause: you may live with your parents, stay at a friend's place, etc, until you find your dream apartment. If the OP does not choose to enroll in a program that accepts him, he will not be in a sort of limbo doing anything: he may choose to improve his skills, get a job (to get money to attend a better program?), etc

I think @Taladris 's original comment is what I had in mind. I also intended to do an RA in the interim year (for more research experience and a livable wage). I see it as: one extra year is really inconsequential in the big picture. I am surprised that more people do not see the perspective as presented by Taladris.

I agree with @Taladris (please write up your comment as an answer BTW), but I can understand the other perspectives as there is definitely an "age limit" for some stuff in academia, especially in more experimental disciplines. Universities also prefer to hire younger faculty for their first PI position.

There can be schools that you applied to as safeties with your partner, but since you both got into better schools, the safeties become a bad option that was only ever a back up to begin with. I think what OP might be thinking of is closer to "my partner and I applied to grad school together. I got into a few safeties, and they got into their top choice. I'm considering doing an RA in their region to apply to schools in that city so that I can both be near them and have a chance at getting into a better program", which is exponentially better than living alone at a safety school. @BryanKrause

You say that you "obtained a few [i.e., more that one] admissions"! Unless you deliberately applied only for schools that you thought were extremely weak in the belief that no stronger school would accept you, it is not at all clear what it would mean to "improve" your application. Clearly more than one school thought you were a good candidate.
My advice ... choose the school that seems like the best fit, and accept! It sounds (which might not reflect the reality of your experience, of course) as if the main problem is simply your self-confidence.

While I don't understand why you would give up acceptance and spend another year, likely without support, I'll try to answer your direct question and give a bit of advice.
You can identify weaknesses by asking one of your professors, who presumably has gone through the system to get a doctorate as well as experience in academia in your field to evaluate your application and give you general feedback on your suitability for both graduate study and academia.
You are unlikely, though it is possible, to have enough self awareness to be able to do it on your own. Someone who doesn't know you is less likely to be able to give more than general advice ("Take this course. Take that course."). Ask someone who knows you and your work. Someone you trust. Someone who will be honest.
The advice, which I think you've already taken if I read it correctly, is to accept the best offer you've gotten and live with that decision. Presumably you applied to institutions that would be acceptable to you for study. Taking a year away is likely to set you back, since it puts you a year out from close contact with faculty letter writers and leaves you with little, if any, actual guidance. Those letter writers are essential in the US and they are likely to be better when the memory of the writer is fresh.
Take a year away only if you have no other options. It seems, to me, to be the worst option of all. It would be different if you'd suggested that you had a way to keep in close contact and do some important work and get some important feedback and make some important contacts and, and, and.... But you aren't suggesting that.

Well, you are at such an early stage of your career that the weakest point in yourself is being "outside" of academia, and it seems you are deliberately putting yourself outside by rejecting PhD positions you were accepted for.
So that is the only point you can reasonably work on. Accept one of these positions and then work out your path from there.
If the biggest problem is a 2-body problem, as a PhD you will manage it by a mixture of strategically placed workshops, remote working hours... and living frugally to afford planes to move around (you are in the US, so you are bound to use these 20th century technological marvels, which is better than nothing).


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How to go about an unclear academic misconduct
In a lab I supposedly conducted academic misconduct by sharing my paper after the time was up. However, in the lab we are allowed to coordinate with our peers and ask questions about the processes of our work just not share the final answers. There are two TA’s in a lab of about 30 students who answer questions. My friend and I finished with about 10 minutes to spare and we started conversing with a neighbouring student. This student closed his computer (where his computations were) and handed in his paper to the TA at about 1 minute left. The lab included a cryptography decoding problem which we used matrix multiplication integers to get the corresponding letter to figure out the code (hence the computations). Out of goodness of his heart he came back in a rush saying the TA told him he needed the numbers. I knew he closed out his computer and I had my sheet in front of me and I could see he got the right answer as well as I did. So, I made the judgement that it is not sharing final answer but process especially because the TA told him to fix it with such little time. I hand him my paper and he is writing it down while the lab coordinator comes in and starts collecting papers saying “stop writing” he kept writing the code it was quite small and the coordinator saw I was without paper and my new friend has my paper beside him and declares 0’s. I politely questioned the fairness and he strictly said I have no right to argue. The TA didn’t say anything in our defence even though the situation was clearly not cheating. It’s a very flexible style- notes out, people walking all over the place to other parts of the lab for confirmations.
What is the best way to handle this situation?

Apologize, show that you understand what you did wrong, and let it go. Maybe ask for some way to make up the grade if it's critical/worth a lot.
Unless I'm misunderstanding something, this sounds an awful lot like cheating... A student handed in an assignment without "showing his work" and was asked to write out his process. You let him copy your work because you decided he had the right answer. Then, on top of that, he ignored instructions to stop writing and the lab coordinator saw that he was clearly copying your paper.
I think there is no way to defend this, even with the generous rules of the class. Just because you can talk and look through your notes doesn't mean you can just copy each other. I'll lay out the biggest issues:

I'm not sure that copying down someone else's work is following the spirit of the rules.
Even if they were inclined to let that part slide - your professor and the TA's have no way to know that he wasn't copy down your answers as well (which seems to be explicitly against the rules).
It isn't really your place to decide that "...he got the right answer..." and therefore could just copy your work.
He kept writing after being told not to.
You didn't have your paper/were obviously complicit.

The situation seems like it was impossible to ignore. So you both got 0's. Any attempt to fight this or escalate will probably not go well for you. I think that getting a 0 is one of the better outcomes here.

You would benefit from splitting your post into paragraphs

Like others have said, you let him copy your work which is explicitly against the rules of "no copying answers" so there really isn't much arguments to be made here.

I think this is a valuable lesson that helping someone cheats rarely ends well for you. There is a misconception that as long as you didn't cheat its okay. In most cases, the person who is helping someone cheat gets punished just as severely as the person who is cheating, if not more if it is a large-scale case.
To actually answer the question: Your best course of action is to literally just move on with your life. There is really nothing meaningful you can do aside from maybe apologising to the TA (but don't expect brownie points). Shit happens and we live and we learn. If this is any reassurance, it likely won't go on your official record/transcript (I mean the 0 score would but not the misconduct), so in the grand scheme of things this really is a pretty good outcome for academic misconduct

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Reference letter, personal vs prestigious?
I am currently seeking reference letters from professors for my masters application.  It struck me that the professors that I'm close with, who know me on a more personal level (through projects, work, etc.) are not as academically renowned as some other professors who may only know me as one of the many students who got an A in their course.
I would like to know how their reference letters fare when used to apply for masters in prestigious universities.  Is a more personal reference letter better, or a letter written by a more well known professor?

If you are applying for a job or position that requires you to justify that getting an 'A' in a subject or that you top the class in a subject, then the renowned professor's recommendation letter may be useful.  If it's about your research potential, then no.

A letter should highlight your skills, which usually only come out when working closely with somebody. Getting a letter from a renowned professor saying that you were sitting in his lecture is no more useful than listing this course on your CV. Hence, go for the "personal" (I guess it is work-oriented, rather than saying "Woofas is a nice chap who always entertains at our pub quiz night") letter, and highlight the course with the awesome professor elsewhere.

If the renowned scholar can give a good letter, highlighting your skills and achievements, you should opt for this option. Of course, if the renowned scholar writes a lukewarm letter, it is better to have the enthusiastic letter from a lesser known scholar.
Also, in contrast to common belief, a letter of recommendation does not necessarily have to come from someone who knows you personally. Letters come to highlight your professional achievements, not your persona.

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Is it possible not to have a hypothesis in your thesis?
I have been working on a research report in which forecasting is done on the basis of data, followed by an interpretation of the forecasted results.
Is it possible to have that kind of research without hypothesizing any statement?
If this question is off-topic kindly recommend a suitable community.

Would you please provide context for your thesis. For example, what is your area of study and what subfield are you in?

It would be answerable, if you could please add some more details as suggsted by @RichardErickson.

This question is not about academia but about statistics. It might be on-topic on crossvalidated.se

@henning I made it about statistics, but the question as it stands is about research protocol. On crossvalidated Ibn e Ashiq can ask how to do the statistics.

As a statistician, I'm inclined to say "no, you can't" as a short answer. Reason for this is simple: even in complete random datasets on average 5% of the correlations will be significant when tested in a model. So if you rely on only the data to make any kind of interpretation on association of variables, you're bound to publish false positives. This has been discussed for decades, eg this rather strong opinion of Ioannidis (2005) :
http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0020124
He says:

Bias can entail manipulation in the analysis or reporting of findings.
  Selective or distorted reporting is a typical form of such bias.

If you don't formulate a hypothesis and still interprete the data, you're -probably unintentionally- reporting selectively. You select from the analysis those results that tell a story, and in doing so, you're likely to report something that isn't a solid association or relation.
That said, you don't always have to formulate a specific hypothesis. For example, if you compare multiple methods on efficiency, you don't have to hypothesize beforehand which one is going to be the best. But the statistical test you use for comparison, will imply a "null hypothesis" that there is no real difference between all methods. Also this is "formulating a hypothesis" merely by the choice of analysis tools.
And this is even more important to realize: you might not formulate a hypothesis explicitly, but the nature of the statistical tools you use to come to your interpretation, will imply a set of rather rigid hypotheses and assumptions. You need to be aware of those hypotheses and also of those assumptions.
Because that's something I see far too often: people not explicitly formulating a hypothesis, still interpreting results from a statistical methodology, but failing to realize that their data does not meet the assumptions of that methodology. And that invalidates your entire interpretation.
This problem is even more stringent when forecasting. If you use regression models, you should be aware that predictions outside the boundaries of the original data cannot be interpreted. The uncertainty on those predictions is simply too big. If you use spline methods, you can even get into trouble at the edge of your original data. So definitely in the case of forecasting I would write out both the goal of the research and what you expect the predictions to show, including the scientific reason why. Only in those cases you can use forecasts as some form of evidence for or against the expected relation. If you don't do that, your forecasting model might as well be a fancy random number generator.
So in conclusion: even if your research goal isn't necessarily a defined hypothesis, you still need to formulate the hypotheses you want to test before carrying out the actual statistical tests.
And in all honesty, writing down what you expect to see is always a good idea, even if it's only to order your own thoughts.

+1 This is a really important point and a core principle of the scientific method, but for some reason many people either ignore it (out of convenience) or do not know about it.

There are fields - especially in Engineering - where results do not depend on a statistical analysis so as non-statistician, I would say, yes you can write a thesis without a hypothesis.

What if you split your data in half, do exploratory analysis on one half, and then use the resulting hypotheses to do significance testing with the other half?

As a non-statistician, how do I know how much knowledge in statistic I should learn before starting a research? Only my advisor knows, or is there any guide that I can rely on?

@o4tlulz explain to me how you draw any conclusion without formally testing it. I do work at an engineering department. A quick look in the literature shows me that about every engineering paper contains at least some T-tests or an ANOVA.

@Kevin That's using cross-validation, an often used statistical technique with its own assumptions. If you do that, you have to keep in mind that your training data and testing data have to be completely independent, or any hypothesis testing (yes, also there you test a hypothesis) is invalid. Independence is one of the most important assumptions in about every common statistical technique.

@Ooker I always tell my students to only use methods they know and understand. You can't know everything about statistics. But what you need to know, is all the details of the techniques you use yourself. And in any case every student should have the knowledge of the basic tests used in the majority of papers. Because if you don't understand those, there's no way you can evaluate yourself whether the conclusion in a paper actually makes sense.

@JorisMeys Here is an issue, here is a new method that can solve the issue, here is the a demonstrated solution. There is no formal hypothesis involved as in a medical or biology problem and certainly no statistical tests and validation. It either works or does not.

@o4tlulz and how do you assure me that it solves the issue? Can you prove that? Can you show me your "solution" isn't just random luck?

@JorisMeys Yes, with proper proofs and an experiment.

@o4tlulz well, there's your hypothesis. ;-)

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Austrian PhD without undergraduate degree?
The Austrian school system used to not have undergraduates. So when graduated from a high school, you just got in a Master's program for about 2 years and then PhD program for about 4 years. However, we called it "Master" and "PhD".  So it means that "it is a PhD degree in Austria", but by American standards, it is actually "a Master's degree". Should I still list as "PhD" degree on my CV?

However, we named as "master" and "PhD". – I fail to see the contrast here. I think you wanted to name it something else. Please [edit] your question to clarify. Also, please state in which country you want to use that CV.

Up to my knowledge, the old Austrian Master programmes were typically 4-5 years and not 2 years.

Christian is correct. A typical master in Austria always had the same length as a bachelor and master combined in most other countries (compared to the UK even longer), you just did not get a BSc in the middle. A phd in Austria, even in the fields where the Bachelor/Master/Phd system is not used, takes in total a minimum of 8 years, as in the US probably.

You're incorrect. The thing you did after school entitles you to use the title "Magister", not "Master". "Master" is what you get now, MA or MSc, after a Bachelor's. Analogously, you weren't awarded a PhD, you were awarded a Doktor. Austrian degrees PhD and Master are exactly the same as elsewhere, Dr. and Mag. are slightly different.

I would argue the opposite way. An Austrian PhD definitely qualifies as PhD internationally. The former master curricula were typically composed of two parts that resemble the undergrad and graduate master studies. So in essence, in order to get an Austrian PhD, you need to pass undergraduate, graduate master and a PhD curriculum, while in American standards, you just need an undergrad + a PhD program. I don't see, why this should be worth less. Besides, the PhD curriculum is distinct from the others in both cases since it typically involves research, publications and conference or workshop presentations. So a PhD degree in one country also matches a PhD degree in another just by the competence you gained in addition to exams.
I don't have the exact comparison in terms of credit/effort or something like that. Maybe someone else can clarify.

I tend to agree, however there used to be a "Doktoratsstudium" that did not require a previous "Magister " (MA equivalent), leading to a subtle distinction between Dr. and Mag. Dr., where it is sometimes assumed that the Mag. Dr. is equivalent to a PhD and the Dr. might be more like a MA with bells and whistles.

really? Isn't that only the case for medicine?

I may be wrong here, but I was of the opinion that even in medicine, you needed the M.D. (Dr. med. in Austria), which carries the name "doctor" but is in fact a master's degree. The PhD studies still requires a complete M.D. degree before, so there should be no difference to other studies. But I'm not the expert in this field.

Other than that, I'm not aware of any PhD program, which you could enter without a master's degree. I could imagine exceptions for arts related, but this is pure speculation. Any other - better - experts out there?

I agree with engineer, the Dr.med is basically a Masters, and I think you can do a phd in a more research related area afterwards

Before Bachelor and master was introduced at Austrian universities, the first
degree a student could get was a Magister- or Diplomgrad (master- or diploma-degree).
The titles broadly fall in three categories:

Magister/Magistra is awarded for studies in natural sciences (Mag.rer.nat),
pharmaceutics (Mag.pharm.), law (Mag.iur.), theology (Mag.theol.) and so on.
These studies typically last 8 to 10 semesters.
Diplom-Ingenieur/Diplom-Ingenieurin (Dipl.-Ing.) is the degree for technical
sciences. These studies typically last 10 semesters.
Doktor der Heilkunde (Dr.med.univ.) is actually the master degree for a medical
doctor. This one has a strange naming, because it is not a doctors degree.
Confusingly, a veterinarian finishes with Mag.med.vet. Medicine typically
has to be studied for 12 semesters.

Although the titles have different names depending on the type of university and
the type of studies, these are all considered the second highest degrees in Austria.
The English translation would be---depending on the studies---one of
master of art (MA), master of law (LLM), master of science (Msc), medical doctor (MD)
and so on.
Having one of the degrees above is usually a requirement for starting PhD studies.
PhD studies end with a doctor degree (Doktor of something). So there
is Dr.rer.nat., Dr.iur., Dr.theol., Dr.techn. (following a Dipl.-Ing.),
Dr.med.vet., and Dr.med.univ. et scient.med. (this one is the true doctor degree in
medicine). Those are commonly translated as PhD.
When the bachelor-master-system was introduced at my university, they would simply
split the studies into two parts. After 6 semester, one would get the bachelor degree
and after 4 more semesters they would get the Magister/Diplom (master). Having only
a bachelor is not enough for starting a PhD.
There is another type of university in Austria called Fachhochschule (Universities
of Applied Science). Their studies end with a Mag.(FH) or Dipl.-Ing.(FH) after 8 semesters.
These universities are not allowed to offer PhD studies. However, having such a degree
allows to start a PhD at a 'regular' university but one has to attend additional courses
(often for 2 semesters).
The Austrian Ministry of Education has published the degrees and their international equivalent (pdf).

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Masters w.o. thesis on the area I'm interested vs. masters w/ thesis on a different area
I am currently a graduate student and it's my first semester. My advisor is not assigned yet and it must be done soon. There is a prof. that I would like to work with on analytic number theory, however, he says that he is so busy and already have 3 students. So, he does not accepting me with a thesis program but instead, he says that he can only accept me if I choose not to write a thesis. If I decide to work with him, I will be alone on my research. I really want to make a research on analytic number theory and do not want to make a research on something different like probability or numerical analysis even if they are also a good research option.
In conclusion, should I accept him and try to write a thesis alone or look for a different advisor on a different area? Also, is it important to have a masters degree with thesis to apply for a phD program?
 Thank you for your valuable suggestions.

If I decide to work with him, I will be alone on my research. If that's the case what's the point of even working with him? And more importantly, how can you even learn analytic number theory (which he is good at) without working with him? That to me sounds like a perfect set up for those "I spent 10 years in this degree and still can't graduate" disasters.

@Penguin_Knight, I am accepted for masters degree with thesis program at one of the top national universities in my country and this is just my first semester. If that was my third or fourth semester which is the end of the programm then you may be right. However, I disagree with your answer, unfortunately. My problem is exactly like above.

Should I accept him and try to write a thesis alone or look for a different adviser on a different area?
This is up to you. You are pursuing a graduate degree and you have to take charge of your educational path. You have to weigh both options. A) Writing a thesis alone with no supervision and potentially having to struggle, B) Working under a different adviser who will supervise you, but it may be a boring/uninteresting topic.
Is it important to have a masters degree with thesis to apply for a PhD program?
This is dependent on the program. Some programs are more research heavy than others. I would scope out your future plans and tentatively look at what PhD programs you would like to apply for and see what their requirements are. I do believe that it is impossible to do "too much" work when applying for a PhD program, so a thesis may be in your favor.

First of all, thank you four your extensive answer. I looked up for some PhD programs but it is not mention that whether they want a masters degree with a thesis program or not. I think that this is because people start their PhD program after they graduate as a BSc. In my country, you usually apply for a masters program for 2 years, then, you apply for a PhD program for 4  years. In that case, can I assume that they do not care whether I graduated from a program with thesis or without thesis?


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How important is a grad school visit?
I need some grad school advice and I will try to be brief. School A and School B have invited me to a grad visit weekend on the same dates. I booked the trip with School B before I knew there was a schedule conflict. At School A I have secured an RA position and a good relationship with the professor offering the position. School A is also considering me for other scholarships. School B hasn't given me an indication of whether I will be admitted or not. I have spoken to a professor there who reviewed my application, but they did not say much more than I am a good candidate and they look forward to meeting me. School A is ranked higher than B in my field, but B is a top 20 overall while A is top 50. I'm interested in the research areas of both schools.
I asked the professor at School A if I should cancel my plane trip (I didn't mention the other visit conflict) and go to their visit to maximize my chances at the other scholarships that they are considering me for. They told me to email the visit coordinator and explain my situation: that I can't make it, but I want the scholarships and will visit the campus on my own to meet with everyone.
Even with that advice, I'm conflicted. I'm not sure how important this decision is or what the best choice is. Any advice would be greatly appreciated.

Comments are not for extended discussion; this conversation has been moved to chat.

The decision is probably not that important, so don't stress too much (or, which is basically the same, it's pretty much impossible to figure out what the effect it will have).  Remember that this feels very high stakes for you but for the people on the other end, it's just another day at the office.  I would focus on which trip will get you valuable information.  In an ideal world, I would say go to school A for the weekend, and try to visit school B some other time, but I don't know how much of an issue the expense of the tickets is for you.  It would be a different matter if school B had admitted you; you might want to push them a little harder on getting details (have they admitted anyone).

If you have already scheduled and booked a visit to School B, and that school remains of interest to you even after you have been admitted with an RAship to School A, then I would go ahead and attend School B's visitation day.
With regard to School A: I would go ahead and tell them the whole truth: that you have already booked travel to School B for their visitation day, but you remain very interested in School A and would like to attend at some other time.  In my mind (I am the graduate coordinator of my department, by the way) your reason for not attending their visitation day is the best possible one (both in terms of being understandable and reflecting well on you).  If you are active in scheduling an alternate visit, they will read you as being interested in their program.


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How to review a manuscript where the software is difficult to install?
I'm reviewing a manuscript that is protocol focussed. This protocol is a bioinformatics workflow that uses the author's own software that has already been published.
Part of the peer review requirements are to test the protocol to see if the instructions are accurate. I have no problems with this request. However, although their website suggests that the software should be installable on any OS, the installation package only includes an .exe file for a Windows system. I do not have a Windows system.
It is possible for me to figure out how to install their software, but these instructions are not included in the paper nor on the software website. This would also take me some time and this would be more than a normal amount of time that I should be spending reviewing this paper.
My question is: should I only review what I am able to easily complete from their protocol? In other words, should I only review what I can do from their given instructions and include the difficulties I had installing the software? Or should I contact the authors (without mentioning I am reviewing their new manuscript) and let them know that their installation package for their already published software is missing important files for unix-based systems?
I am still relatively new to the peer review process and think this paper is very interesting and don't want it to be rejected simply because I do not use Windows.

If the authors of the paper only use Windows, it seems totally unreasonable to expect them to port their software to a different OS and then re-validate it on that OS solely for the purpose of a review. And even if they did that, you are not actually reviewing what they did. There is a huge difference between "it should be installable (in principle) on a different OS" and "we claim that it works correctly on a different OS".

Is it really that hard for you to temporarily get access to a Windows machine and run their exe?  For instance, you could ask a colleague across the hall if you can borrow their computer, or you could spin up a vm (they are free).

if you're using a reasonably modern system, you could just install a Windows virtual machine using any of VMWare/VirtualBox/Qemu and run the exe in the Windows VM

Beside of a VM, wine (https://www.winehq.org/, applied e.g. for Ubuntu https://vitux.com/how-to-install-wine-on-ubuntu/) and PlayOnLinux (https://en.wikipedia.org/wiki/PlayOnLinux) or CrossOver for MacIntosh (https://en.wikipedia.org/wiki/CrossOver_(software)) equally allow to work with some orginally-Windows programs in your host OS, too.  Not all do fantastic for each application, of course, but for this you the different compatibility levels, e.g. silver/gold/platinum in wine.

I would not try a VM. I believe you should write the editor for advice. Emphasize how much time you have spent on this review.

Claiming that it is not dependent on Windows and then acting like no one uses anything else should be mentioned in the review.  And depending on the nature of the software, it may be wrong to assume most readers can do the VM tricks in these comments.

Of course I could use a VM, but this seems like I'd be putting in an extraordinary amount of effort to just review a paper. The whole protocol would take around 48 hours to run... far too long for me to just borrow someone's computer. The editor also wants to know if the protocol (including installation) could be followed by a grad student. In this case, the instructions could not be followed by a grad student using OSX or Linux because a file is missing.

Spinning up a VM is hardly "an extraordinary amount of effort".

"...their website suggests that the software should be installable on any OS" means a .exe is not sufficient. I develop these kinds of software and I think this is an unmistakable mistake. If I were the reviewer I would (probably) reject the paper.

@LightnessRaceswithMonica it is if you don't have access to the OS you're supposed to be emulating :)

@TasosPapastylianou True. Except, in this case, you do. They are freely available on the web from Microsoft. You literally just have to download it, then boot it. A link has already been provided. The problem could have been solved in far less time than the OP spent complaining about the situation on this question. :)

The IT people at my small maths department had a few laptops we could borrow when going to conferences (instead of using personal laptops). You may contact them to see if they have a computer you could borrow. That may be better than borrowing a colleague's computer, since you don't know exactly how long your review will take and they may need it.

You should ask your editor for advice on this. I doubt, however, that you should reach out to the authors in any way. But the editor can, on your behalf, ask the authors for specific instructions for installing the software on your OS. The editor can make this a condition of getting a review.
Moreover, the editor can communicate your concerns about missing files or whatever else is important to complete a review.

Yes, you should not lightly break the anonymity of the review process. That could lead to trouble down the road, for example if you find that you have to give a negative review for any other reason. Going through the editor is much better.

This might be too much work for the editor and for the OP.

This is exactly what I decided to do. I feel like the file omission was an oversight and I'd like to give the authors a chance to remedy it before I submit the actual review.

Come on. As much as I love Linux and as much as I like macOS, isn't it a bit ridiculous to contact the editor and authors asking for help because they "only" provided an exe for Windows?

Following up on this, I ended up contacting the editor who contacted the authors. They had accidentally left out essential files for installation for any operating system. BTW @EricDuminil, it was not "a bit ridiculous" because the review could not have been completed without it :)

@tinyteeth: Sure, if files are missing and cannot work on any OS, it makes sense to ask for clarification.

If the protocols/software implementation are a requirement for the journal rather than just the concepts, which sounds like the case, I would say there are two scenarios:
1.) Given a reasonable effort and appropriate background on your part, you were not able to get their software to run. All else in the paper seems fine. In this case, I might suggest "Reject and resubmit". Given that you are not able to test their code, you can't really give it a thumbs up or thumbs down, but it should be a relatively small step for them to meet this requirement and then you can adequately evaluate their software.
2.) You are able to use their software, but it took an unreasonable amount of effort or expertise on your part to get it done. In this case, you can evaluate their software, but ideally they should make it more readily available to the target audience. In this case, under the condition that you liked everything else about the paper, it may be reasonable to suggest "Accept with minor/major revisions", and you ask them to include the necessary instructions that will help guide other users of the code.

Comparing to replication in other sciences, which would require looking at the exact same live organisms, or unusual chemicals, or expensive specific hardware for the experimental setup, I'd assume that getting access to a computer with a somewhat popular OS version falls under "reasonable effort". If the software runs only on a weird, obsolete system that's not widely available, then running it would require unreasonable effort, but getting access to one of the 80%+ worldwide computers that run Windows definitely is not. I mean, Linux-only (2% marketshare) software gets reviewed as well.

@Peteris: I guess I didn't say it explicitly; I believe the OP's scenario is (2), so conditional on them being okay with the rest of the paper, I'd say "Accept with revisions" and ask them to give installation instructions for linux/unix as that doesn't seem like a huge request for the authors.

@Peteris let's not conflate marketshare for Facebook batteries with marketshare of people who do real work on their computers. That being said, yeah, OP should beg-borrow-steal a Windows PC for the test run.

It sounds from your description that the software is an essential part of the paper. Well, if the paper was missing one of its normal text sections due to sloppiness of the authors, would you be blaming yourself for that and going on a wild goose chase around the internet to find the missing section? I suspect not. The same should apply here. As referee, it is not your job to become an expert in compiling Linux binaries from source code (or whatever similar tasks you apparently need to do to get a working binary to test).
Similar to what @Buffy suggested, what I would do is write to the editor and inform them that I am unable to finish the refereeing assignment since not all parts of the work that need evaluation were provided to me. I would make clear that this is not a rejection, and that I am happy to finish the job once this situation has been remedied. It’s the editor’s job to communicate with the authors, so leave that part to them.

Saying the software cannot be run under linux is like the paper missing a part seems a bit over the top: Did the editor specify that the software should run on OP's OS? To me it reads more like OP speculates from the webpage that it should be installable on any OS, perhaps that's more a goal description and not the current state relevant for the paper? I do agree that the instructions should be clear so OP knows whether he can expect it to run on Linux or whether he would need a windows machine to run it. So, improvement suggestion: focus on the missing doc, not the missing OS support.

@FrankHopkins agreed. In fact, it certainly ought to be acceptable (and is acceptable AFAIK) for software that’s supplementary to a submitted paper to run on only one of the major OS platforms (assuming other conditions are met, particulary if the source code is available). However, that doesn’t mean the referee should have to tolerate misleading claims by the authors about which platforms are supported. And in any case, if OP does not have access to Windows computers then practically speaking they cannot referee a paper whose software component is Windows-only, and should let the editor know.

@DanRomik Which "misleading claims" are you referring to? I see no evidence that the author claimed the program would work on any platform besides Windows.

@LightnessRaceswithMonica The authors did not specify on which OS the software could run, but their primary manuscript and software website say it has been tested on both Windows and Linux and that their installation package should be including both an .exe and .sh file. However, the .sh file and separate .jar file is missing.

@tinyteeth Okay. It's just that, unless I'm missing something, you hadn't stated that when Dan made the claim.

@Lightness you’re missing something. This was stated in the question from the beginning.

In bioinformatics, it is quite common to have to install software from source., however they should also have good instructions such as vsearch.
Although vsearch also does have premade binaries, if this is early on in the softwares development and they are happy with how the algorithm works I don't think it is unfair to expect users to compile from source (again given good instructions).
If you actually can't install it to evaluate the content of their paper either ask for help from someone who might be able to or ask for good install instructions, if the software has not been released or is in beta then they might not be expecting a lot of people to install it yet. If you can install the software to evaluate the paper I would say yes but... and express your concerns about how the software isn't very beginner friendly.

One thing I haven't seen in any of the other answers so far, is to politely tell the editor that you cannot review this paper. The editor will send it to a different referee, who likely will be able to get access to a computer that had Windows.

I'm reviewing a manuscript that is protocol focussed...
  Part of the peer review requirements are to test the protocol to see
  if the instructions are accurate.

You have the option to test the protocol and review the paper (which seems like it will require a lot of effort), or you can choose not to review the paper at all (which will be very easy for you to do, in terms of the workload).
It all depends on how much effort you want to put into it, and whether or not you think that effort is worthwhile (for example building a good relationship with the editor by generously donating your time towards helping their journal, or having the chance to have your input considered before this paper is published). Sadly this referee task seems to be more time-consuming than the typical one, but again: no one is forcing you to referee this paper.

You did not make clear whether you made any attempt to install software on a Windows machine. If you did, then:
First:

Part of the peer review requirements are to test the protocol to see if the instructions are accurate.

Then:

It is possible for me to figure out how to install their software, but these instructions are not included in the paper nor on the software website.

Isn't this obvious? Instructions are incomplete/inaccurate/unavailable  and the paper should be assigned a major review round based on that fact alone.
If you don't and cannot get access to windows computer, then you cannot do the review, I am afraid, and you should let the editor know (without any penalty to authors).
Never contact authors directly!

.exe does not always mean a windows executable. .NET applications have the .exe extention by default, so your application may be executable with mono name.exe.
If it really is a Windows application, that's likely also fine. wine, installable on MacOS, Linux and FreeBSD is able to run most Windows applications just fine.

I guess this isn't necessarily the problem. The manuscript is basically a tutorial on how to use the software, and is not the primary manuscript for the tool. The tutorial should have these instructions.


text:
Is simplication of known results worth a publication?
I am an applied mathematician. A very simplified outline of my situation is as follows:
The leader of my research group is a "big wheel" in his specific research area. His contributions are considered both important and very demanding.
Recently I found a way to get a simplified access to one aspect of his work. I am very sure that no more than a few dozen people have ever made the effort to dig through this and understand it. The simplification is substantial, and even to my group leader it has not been known. Certainly it is not known to almost everybody else.
Other than an alternative simplified manner of setting up the theory, I can round out some things that have previously been done by hand-waving. That is only of theoretical interest.
So I wonder: finding this has been difficult, and it would help other researchers to know about it. But is it worth being published, with only a "sugar glaze" of actually -new- results? How can I determine this? How low for a journal should I aim?

I think this is so specific to your situation that you really have to ask several senior people whom you trust and who can appreciate the details.

It seems you are in discussion with your research group leader about this - wouldn't (s)he be able to judge well whether, and where, to publish this?

This sort of work is often publishable. I'd recommend making it obvious, even in the title of your paper, that its main contribution is simplification; for example, use a title like "A simplified proof of X".  You don't want inattentive referees complaining that your main result is already known.

It sounds exciting, and I can understand your itch to get your streamlined derivation out there.  The only thing that concerns me is the hand-waving part.  Could you find some usefuly application of the result that you re-derived?  This might give you a better way to package your theoretical work.

In general, this kind of result might be worth publishing, also in top journals. However, it is impossible to tell without knowing the specifics. It might well be something that has been known as a "folklore result" for long in your field.
Luckily, you say that the leader of your research group is the major expert on this. So, ask him and not a random bunch of people from other fields you found on the internet.
If you have already asked and he disagrees, chances are that he is right. But if you disagree and insist that it is a major breakthrough, you can still write everything up, put it on arXiv, and wait for feedback from other researchers.

Very much agree with this statement - the group leader seems in the best position to judge on this statement, and as long as there is no valid reason not to talk to him..

Let me add to this good answer an explicit example: Kleiner gave a new proof of a famous theorem of Gromov (that any group of polynomial growth is virtually nilpotent, but it does not matter here what this means) and published it in one of the very best mathematical journal, Journal of the AMS (about the equivalent to Science in mathematics, except it is a serious journal rather than a magazine). So, in some cases new proofs of known results are highly regarded. What is important in a paper is how it improves the reader's understanding of its subject, and that can be achieved by new proofs.

To avoid misunderstanding, I am not looking for a decision here on this site, but for "decision help", if you get what I mean.

You are not very specific in your question, so much of this is guesswork. However, since you say you are working in applied mathematics, there are two situations that would definitely lead to publishable results:

If you have a simplified proof of a significant theorem, that is worth publishing.
If you can find a simplified algorithm, especially with better complexity, that is of course also worth publishing.

The 'worth publishing' part is what the question is all about.


text:
How do researchers affect the funding opportunities of their department
I am mathematician, and I am interested how math departments view my activities.
Clearly, they view me as somebody who can carry teaching load. But I am also a researcher. What and how much I publish has an impact on my own career and my opportunities in getting grants and funding.
But what about the department? How does my work contribute to the department's possibilities when it comes research grants for individual researchers of the faculty, grants by several researchers on a project, or maybe huge grant schemes? Do I enter a statistics anywhere?
To be more concrete: when a researcher gets employed at a department, they not only do it for the sake of science. For example, they have keep an eye on their departments competitiveness. When I coauthor work with people at the department, then this certainly helps the individuals involved, e.g. in terms getting cited.
However, there are grants on a larger scale. For example, a department may apply to fund a huge center of research by the NSF. How does being productive at the department help in acquiring such a grant?

It's a little unclear what you're asking.  Maybe you could get more specific; a question like "Do I enter a [sic] statistics anywhere" encompasses a lot.

You know that the university (and the department) get a chunk of grant money for "administrative costs", plus part of your salary or grad students/post-doc salaries, equipment, etc., right? Well-funded professors also make the department attractive to prospective students, researchers elsewhere, etc.

A few quick points:

Many grants have evaluation criteria that incorporate the research environment of the investigators. Thus, the research ranking and status of researchers in the department and the university of the investigator can influence the chance of getting a grant.
Researchers within a department can help each other do good research in a wide range of ways. Senior researchers often mentor and teach more junior researchers. Researchers often collaborate within a department. This is both easy, because you are collocated. It also often aligns well. I.e., an academic is not only helping his own research track record, but he or she is helping the research output and capacity of the department.
If you do good research and increase the prestige of the school, this can have a range of other beneficial effects for the department and other researchers. Academic visitors may be more keen to visit. Good PhD students may be more attracted to the department. And so on.

So in general, the contribution of a single academic to a department's research status is often only modest, but it is still meaningful. And in extreme cases, where the department recruits a research superstar, the effects can be profound.


text:
Not answering questions during PhD interview
Recently I had a PhD interview for a very good university in Europe. The application was for the School of Mathematics, as I posses a Bachelor's and Master's degree in Pure Mathematics.
During the inteview I was quite nervous as it was a new experience for me and the questions posed were only of technical flavour. Questions about my thesis and a project that I concluded during my studies were asked. I was unable to answer most of the questions, as a lot of time had passed since I did my project and thesis, almost 6 months for the last one. After the interview though, as I calmed down, I realized that the answers to the questions were very easy to produce, though the questions were not at all trivial.
I should mention that a potential advisor commented on my thesis, saying that it was the first time he saw a master student write a thesis covering so much material and with such depth. Moreover, in my thesis I speculate about a potential connection between two theories. A thought that turned out to have some merit as some time later a publication appeared describing somewhat the same connection, (not by me).
Taking the above into consideration, I would like to ask wether the fact that I did not answer to the posed questions could be detrimental for my application. That is, if someone experienced a similar situation.
In case of rejection I would consider applying for US universities, though I will have to wait for a year. Do you think this will have a negative impact on such applications?

This is very hard to say as the role of the interview in decision making may vary strongly from country to country and place to place. In my university (Bologna, Italy) such decisions are usually made based on a previously agreed points system and typically there isn't much if anything on interview behaviour in the points system, so it may not harm you at all. However, in some places the impression that people get from the interview is quite important, although I cannot say anything about your specific situation; competitors may have been even worse or worse in other respects.

As stated in one of the comments, it really depends on the university policy. At some universities, the interview is just a pro forma step. In that is the case, your prospective advisor already has you admitted based on your thesis, or the department already admitted you based on a points system. At other universities, all the other stuff is pro forma and only the good word from a potential advisor will get you in. If that is the case, then yes of course your failure to answer questions will likely be detrimental to your application. But the deed is done and there's no point in fretting about it. Just wait to hear from them.
Putting that to the side, being nervous is natural and forgivable, but what is less forgivable is to come unprepared to an interview. I interview lots of candidates, and there's an obvious difference between a candidate who prepared but is shaking nervous, and a candidate that is nervous because they were caught off guard by a question we were obviously going to ask. I have my tricks to calm down prepared but nervous candidates and thus help them do better on the interview. After all, we all want the best candidate, not the best interviewee.
As for applying to the US, having been previously rejected by another university will have no effect on your candidacy. Being unprepared to interviews will have the same effect.

cheery.beach7701, thank you for your answer! To be honest, I did not expect questions concerning a project I completed one and a half year before graduation and has nothing to do with my thesis. Do you know though if a gap year affects applications to the US?

Every professor has his/her own criteria for what makes a good graduate student, so it's impossible to generalize. However, I think that a main cause of grad students failing is just personal immaturity. So I give points to those who have taken a gap year or years. Others might see a gap year as lack of focus.

@Prelude  Questions about my thesis and a project that I concluded during my studies were asked. I was unable to answer most of the questions, as a lot of time had passed since I did my project and thesis, almost 6 months for the last one. 6 months is not a lot of time, one can certainly read your thesis to evaluate your "research potential", but one is interested in understanding who is the wirter behind the thesis and if the writer of the thesis is the same person that appeared at the interview ... don't make yourself look like an homonymous of the thesis writer !

It could well negatively impact your current application. But it mostly speaks to lack of preparation for the interview and the fact that you haven't thought of those things for a while.
But for the future, it need not be an issue, provided that you spend some time preparing to answer questions that are likely to arise. That certainly includes your own work, but also general things in your field, including some recent developments.
You also need a way to deflect such questions if you aren't prepared. You can, at least, give the background required for an answer, or a framework in which to answer it. But, that, too, requires some preparation. Don't go in blind.

Buffy, thank you for your response! I am sure it will show some lack of preparation, but do you think it will be enough to diminish any research potential evidence?

I can't predict what others will think, but research isn't an on your feet quiz sort of thing. Certainly your application has indications of success in research.

Deflecting isn't quite the right approach, or maybe just not the right word.  8f you don't know the answer, showing that you know how to reason it out in finite time would be one rung down on the ladder, but I wouldn't call that deflection.

As others have said, this will depend on the country/university.
Let me offer a perspective from a position where the interview is directly related to whether you are offered a position or not. In those cases, you may be interested to know that quite often it is easy to discriminate between applicants who still know what they did a few months earlier and who can provide a coherent story with a bit of enthusiasm and those who cannot. The second category, I am sorry to say, is out.
This doesn't mean that the candidates themselves (or you in this case) would not be capable of doing a PhD or would even have been the right person for this position, but it does mean that these abilities and fit did not come across during the interview.
It's not a perfect selection mechanism (and suddenly shouldn't be - and typically isn't the only thing that is being evaluated), but what you are looking for in young researchers about to embark on a PhD is a spark and enthusiasm for research (which typically comes across when people talk about their prior work - or not) and their technical and conceptual comprehension of what they worked on before with the ability to also relay that to others - after all, this person will need to drive their own research project for the next few years which will require self-motivation and the ability to learn new things and integrate them over time into a larger scientific concept plus the ability to discuss science with others is at the core of doing science.
So if this was due to a lack of preparation from your end, do better next time to show that you've got the chops.

Why don't you contact them now via email stating that you were nervous/forgetful and provide an explanation to their questions? Irrespective of the outcome of the interview they might have been genuinly interested in your work. And they might still appreciate an answer. Also, it is always good to not leave any question marks around your research work.
Also a slight different perspective from the other answers: forgetting details about a project of yours or part of your work does not mean you were unprepared. People present in conferences very specific projects that they recently completed and forget details. It is still the work that you completed and maybe moved on to something else.
So, I would follow up via email, which is the expected behaviour if someone asks you a question that you can't answer on the spot. Again, irrespective of the outcome of the interview.

So by now, after interviewing other candidates, the comitee may have forgotten the candidate could not answer questions on their own thesis ... and you want to remind them this :) ?


text:
How should I respond to the professor who told me he has only a MSc student opening when I asked about PhD openings?
I have writen to a professor in Canada inquiring for a PhD position at his lab 6 months before in 2022. He requested
to write to him again in February and see.
I wrote to him today with resume, sop, and other documents. He replied to me by saying that, at this time, he only has funds for a MSc student and no funds for a PhD student. However, even though I already have a MSc in the same area from my home country, I am willing to take that MSc chance given the possibility of PhDs in my field in Canada in the future.
How to convince the professor and politely request to consider me for the MSc position?

A couple of questions: 1) are you trying to move to another country as part of your motivation, 2) was your MSc coursework based/thesis only/some hybrid. 3) Do you know what the project is, and is it something you really want to work on?
Also even assuming you were the best candidate for the job there may be some restrictions on who can be funded, perhaps the funding source may not allow for people with an equivalent level training to be funded. I've seen that for PhD funding (i.e. can only be given to people without a PhD). Though others might have a better grasp of this than I do.

I suggest that you look elsewhere in Canada or beyond. If they say that they don't have funds then you are at risk of winding up with a delay and no real advancement. There is no guarantee that funds will become available in a time frame useful to you.
If you really think that you need another masters then just ask to be considered. You don't need any special wording, other than expressing interest in the opportunity which you would do in any case.
Note that getting a masters in a country doesn't give you much of an advantage for getting a doctorate there. You will normally be considered along with any other candidate on the usual terms.


text:
2nd review round, referee did not accept the invitation - what are my options?
On a submission for a 2nd-round revise-and-resubmit in an Elsevier journal, one reviewer who did provide 2 rounds of positive feedback did not accept the invitation to re-review, 40 days after the invitation has been sent.
The editor is quite in-active. It takes them one month to send the revised draft to the reviewers. So far, the revised manuscript has been resubmitted 70 days ago, one reviewer's report is already in (thanks to the new status-track link provided by Elsevier) but one reviewer still has not accepted the invite to review...
Any suggestion on what should I do? Should I contact the editor or the editorial office? I am in the field of Economics/Finance. In these fields and for this particular journal, waiting 70 days for a report is not that long. But the speed should be much faster for the 3rd resubmission. For some career reason, I really need to have this paper published soon. I do not know if the editor can decide simply based on one report, or if they have to invite a new referee in case the old one keeps the status of "no response." (That could be a disaster.)

https://academia.stackexchange.com/questions/111996/what-happens-if-a-reviewer-withdraws-himself-from-peer-review-process related

Sorry, but there is not much you can do. As to timing, remember that it has been the holiday season in many countries, so you would expect things to slow down.

Just to second what @MaarenBuis said, i would not expect anything to go anywhere in any of December, and questionably in the first week of January in the Anglophone world.

There's not much you can do unfortunately. It's a problem for the editors of the journal to solve. Do they want to wait or not wait, whether their journal can make a decision based on only one reviewer or if they must have at least two, etc. - these are all things that the editor must decide, and you have no say in them.
About all you can do is write to the editor asking for a status update. You could tell them that you really need this paper published soon because of [reasons], and if they're sympathetic, they might proceed to a decision. But it's still their prerogative if they choose to invite new reviewers. If they do, the only thing you can do is wait.


text:
Is it possible to switch advisor if I am already behind in progress?
My professor has recently told me she might need to fire me because I am very behind in progress, unless I switch to a different lab and advisor. Because of the pandemic and everything, I've been struggling and made lots of mistakes. I am also behind in my progress. Eventually, my professor lost confidence in me.
I am thinking of trying one last time to see if I could switch to a different professor. My question is, as I am currently very behind (I am in my third year now but haven't even finished my second year project), is it even possible to switch professor? Will any professor be willing to take on astudent who's behind in progress?

Speak to the graduate co-ordinator in your school to discuss your options
Firstly, unless your university has some strange administrative processes, an individual professor/supervisor does not have the discretion to "fire" a PhD student.  Removal of a PhD candidate from their program is a decision made by the school after a formal process of milestone reviews and other review processes.  If a PhD candidate is significantly behind schedule they will typically receive an unsatisfactory rating in their milestone review and then there will be an opportunity to make a plan to catch up on progress and expectations will be set for minimum expected progress at the next milestone.  The decision to remove a PhD candidate from their candidature (e.g., downgrade them to a Masters program or remove them from the program completely) would usually be a decision made by a full panel of academics in the school after multiple unsatisfactory milestone outcomes.
Unless and until the school makes a decision to remove you from your program, your supervisor is under a professional obligation to assist you to try to make the most of your program and to assist you to complete successfully.  Rather than presenting you with an ultimatum of the kind you have described (move to another supervisor or I will fire you), she should be working with you to create a plan for successful completion of your candidature and to catch-up lost time to the extent that this is possible.  This should include milestones for completion of work and a coherent and feasible plan for completion.  Since you are significantly behind, this might include a requirement for applying for an extension of time, subject to having completed enough work to show progress.  Hopefully your supervisor is already doing this, but if she is not then she should be --- it is not acceptable professional practice to just give up on an enrolled PhD candidate because they are behind (though it is of course acceptable to go through formal review and remove them from the program under appropriate circumstances).
In principle, it is possible to switch supervisor at any point in your candidature, so long as it is okay with the school.  As to whether it is desirable to move supervisor, this might or might not be a worthwhile idea, and it depends on a lot of factors.  Moving to a new supervisor might mean that you have to shift your topic or focus area and this might put you further behind.  Alternatively, a new supervisor might be able to assist in helping you catch up (particularly in a case where your existing supervisor does not have a favourable view of your candidature).  You are correct that a third-year PhD candidate who is significantly behind in progress is not an attractive candidate for a new supervisor, but you should not let this dissuade you from making appropriate inquiries if this is an avenue you want to consider.  Some schools have particular academics who are good at taking over bad candidatures and getting them back on track, so you might get lucky.
The processes and expectations for a PhD candidature differ at different universities and schools, so you should speak to the graduate coordinator in charge of the PhD cohort in your school.  You should talk to them about a few things: (1) getting clarity on your obligations for progress and the processes for review/removal from your program; (2) your options in relation to getting assistance from your current supervisor to get back on track; (3) options for dealing with any interpersonal conflict or despondency from your existing supervisor; and (4) your options in relation to finding a new supervisor to help you get back on track.


text:
How should I mention to my supervisor that I have emailed his collaborator for a PhD position and would like him to write a reference letter directly
I intend to apply for a PhD in my summer research supervisor's collaborator's lab. I've informed my supervisor about this, and he's willing to reach out to his collaborator to directly recommend me to the lab.
However, I'm unsure about the best approach to making the first contact with the collaborator and notifying my supervisor. Should I cc my supervisor in the email to the collaborator, or should I email the collaborator directly, expecting him to contact my supervisor for additional information?

Your question seems a bit unclear. Will your supervisor make the first contact, or you?

I'll make the first contact

Again, having the supervisor make first contact can also work. See my other comment, below.

Email the collaborator directly, expressing your interest to join his group as a PhD student. Mention that your supervisor has recommended you doing so, and - depending on what your supervisor prefers - that he is happy to provide a recommendation, or that he will contact the collaborator directly with a recommendation. (Clarify the latter point with your supervisor first.)
More generally, it is advisable to ask your supervisor how to proceed, e.g. suggesting the protocol above, and asking whether he suggests/prefers a different way to proceed.

That works. You could also ask your supervisor to make first contact with an informal recommendation, saying you will soon follow up.

@Buffy ... though I think it is best to ask the supervisor openly how to proceed. Depending on the relation of supervisor and collaborator, and the collaborator's personality, it might make a better impression if the OP approaches the collaborator, rather than the supervisor writing "I have a student/intern who wants to do a PhD with you, whom I very much recommend", or the like -- or vice versa.

I offer my suggestion because it worked for me, actually. But yes, work with the supervisor on the approach.

@Buffy I think it depends on the people and their relation. Sending someone else as a "messenger" might look good, depending on the addressee and their relation to the messenger. I don't advise against it -- as I said I think it is best to ask the supervisor openly what he thinks would be the best way to proceed.


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Seeking Guidance on Comparing Algorithm Performance Metrics in Research Compilation
I am currently working on a research problem where the existing literature proposes an algorithm that is tested on data generating 100,000 integer values within the range of 0 to 20. The common practice in these papers is to present the frequency of each value in tabular form, along with the average of the 100,000 produced values as the sole performance metric—where a lower average is considered better.
In my research, I have developed a new algorithm that produces 100,000 values with a lower average compared to the algorithms discussed in the relevant literature. However, I would like to extend the comparison beyond the average and incorporate additional metrics such as variance, range, and others.
My question is whether it would be ethically acceptable to compile the frequency data from the existing literature, as presented in their papers, and use it to calculate additional metrics for comparison in my research. I want to ensure that my comparison is comprehensive and provides a more holistic view of algorithm performance.
Any guidance on the ethical considerations and best practices for such data compilation would be greatly appreciated.

Why do you think this would pose ethical issues? As long as you correctly cite where you took previous data from, you can absolutely do this. In a meta analysis, something like this is the whole point.

It is always ethical to extend existing research and to use publicly available information. If you avoid such things as copyright infringement (and plagiarism) then you should be fine. Just cite what you use, and perhaps acknowledge those who developed the earlier data (or whatever).
In fact, academia in general and science in particular advances specifically on the work of earlier people. Just provide context and cite those on whose shoulders you stand.

Note that speed for a given data size/implementation/system is, while common, quite useless. There are many factors influencing the performance including the quality of the implementation, platform etc. Much more interesting is performance characteristics (different n) or at least re-implementing/remeasuring to reduce irrelevant differences.


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Publishing with initial as first name & middle and last name spelled out in full
I guess this is not very common as I have not encountered it yet, but would it be to my disadvantage if I published as "Initial of the First Name - Middle Name - Surname". For context, I'm a graduate student and I'll be starting my PhD next month. So far I've always published using my name in full. However my first name sounds very obviously foreign to speakers of English and most European languages, while the same cannot be said for the second.
So I've been wondering the following:

Would publishing with my full name in local journals and only my middle name in other international publications create confusion in the future even with an ORCID account? Is it more advisable to be consistent?
Is it bad for citation purposes to publish under a name that starts with an initial?

How would you like to be introduced at a conference?  How would you like to be addressed by (potential) colleagues? My opinion is that a lack of consistency between the names you use in different academic situations could be the biggest downside.

Also I have a vague recollection of an eminent scientist who did this.  Dropping the first initial altogether is harder to spot, and reasonably common

I've seen it before, but the person is generally addressed by their middle name.

I'm not sure why an "obviously foreign sounding name" would be a problem.

FYI, I've seen this many times (e.g. example), but overall I guess it's not all that common.

@Buffy unconcious bias would be one potential problem.

Many databases of names are set up rigidly as "Firstname MiddleInitial Lastname". I use my middle name and I have exclusively all my life, but official records (where you must present identification) will not contain your middle name, only the initial. I have had an official and officious person tell me, "To us, you are Firstname, no matter what you prefer." I suggested that she should call me Mr. Lastname and she notified security. Mr. @ofthelake, your problem is going to haunt you unless you use your Firstname and don't care what others think. Good luck.

Thank you all for replying! @ChrisH that's a good point, I already go by my middle name in both my personal life and academic settings such as conferences so that's also another reason for me to want to use my middle name in publications.

Apart from some minor hurdles, the author of this article seemed to have quite an illustrious career https://www.jstor.org/stable/23912844

@Wastrel That being said, a rigid "Firstname MiddleInitial Lastname" structure in a database is of course a very bad idea - given that less than 20% of the world population live in countries with wide-spread middle-name traditions

@HagenvonEitzen It is indeed, but that's what the US government uses. I have had some cooperation with my name preference. It seems there are only 2 name fields on credit cards, and my bank was able to issue me a card saying "FirstInitial MiddleName LastName", I suppose by putting a space in the first field. Long ago I considered changing my name legally, but I'm too stubborn, I suppose.

J. Robert Oppenheimer comes to mind.

Actually, you can publish under any name you like as long as you don't engage in fraud by, for example, using the name of some prominent person implying you are them. However...
I urge you to choose a name, whether your given name or not, and stick with it through your career. This will avoid confusion, though there are solutions. An ORCID identifier is helpful, but still (IMO) a bit awkward in practice.
However, since you have already published under your given name I suggest you just keep doing that. My (personal) advice is to celebrate who you are, whether your name "sounds" foreign to others or not. I find some joy, actually, in names that aren't boring/common as my given name is.

Thank you! I guess I was correct to worry about lack of consistency. As for worrying about my first name sounding "foreign", I am mostly concerned about implicit and unconscious bias that unfortunately exist in academia, but that's a good point.

Or legally change your name? I would if I thought my name had any probability whatsoever of impacting my bottom line. Except it loosely translates to foreman and I do construction, so.... - Where would someone be from that an implicit and unconscious bias exists in academia against them? India? China? Not AFAIC if you want to be a doctor. You wanna teach? Then no, sorry; can't understand you. - It sucks that this is a thing, but to ignore it outright would be a silly way to play the hand.

@Mazura My mother published under her maiden name, even after getting married and legally changing her last name.  If she were to publish today, she would probably still publish under that maiden name (indeed, she produced an illustration for my phd thesis several years ago, which was signed with her maiden name).  Even if a person changes their legal name, they often continue to publish under their old name.  If you want to be recognized, it is generally best to pick a name and stick with it.

Idk, Buffy is a pretty cool name ;)

If I see two papers in the same area by people with the same initials and surname, I assume they are the same person unless there is evidence to the contrary. Most people will routinely abbreviate names to initials + surname in bibliographies anyway, with the same outcome in both cases. So IMO this shouldn't cause a problem as long as you publish as F. Middlename Lastname (and not just Middlename Lastname, which looks like a different person). As always, the more authors there are with your surname, the more likely it is to cause a problem. An ORCID should help with anything that indexes you automatically, provided the journal has a space for it.
As for 2, no I don't see that this is a problem at all. Indeed, many people publish routinely as F. M. Lastname. It's difficult to find people who publish mainly as F. Middlename Lastname, although I found some examples where this is one of several forms the person has used. (These are people known by their middle name in everyday life, such as Timothy Gowers; see references in that article.)
In my experience, the main danger here already exists in the form you have previously been using: for both F. Middlename Lastname and Firstname Middlename Lastname, it might be unclear where your surname begins. You might find some people put you in a bibliography under M rather than L. If Middlename is something commonly used as a given name, this is probably less likely to happen.

F. Scott Fitzgerald is an author who immediately springs to mind using this convention, but it's pretty uncommon, I can't really think of another

I suspect it was more common a century or more ago than it is now — but you probably know some of W. Somerset Maugham, L. Frank Baum, H. Rider Haggard, L. Ron Hubbard, F. Paul Wilson, L. Sprague de Camp, etc. (I expect many authors used it as a way to reserve their first name for personal acquaintance, separate from their public persona.) If OP had started out using a name in that form, then it would be fine as you say; it's the change of professional name that could be problematic.

More recently, but not an author (at least, I don't know if he has published texts), there's M. Night Shyamalan, though I have yet another caveat that "Night" isn't his original middle name.

There's a bunch of surnames that are also given names in Germany. Friedrich Martin and Martin Friedrich are two separate people! Germany also does not account given names significance - all your given names together make your given name, and you use any combo of them (unless they are hyphenated, then you use those two in conjunction as a single entry)

@Trish Yes, it often happens that something could easily be a given name or a surname. Particularly unfortunate when it happens for Hungarian names, where it might not be clear which name order is being used! But if the choice is "it's a middle name" versus "it's part of a two-word surname", the former is much more likely.

In mathematics, Brian Conrey is a well-known analytic number theorist. His first name is John, and he publishes under J. B. Conrey (57x), Brian Conrey (23x), J. Brian Conrey (17x), John Brian Conrey (5x), or B. Conrey (2x), per MathSciNet.

Speaking as someone who publishes under "F. Middlename Surname", I have never had any issue with publishing papers with my name formatted in this manner (in maths, if it makes any difference). So I think 2. will not be a problem for you.
Overall, I would just second the advice of several other commenters, to pick a format that you like for your name and stick with it. This applies not just to your name on papers, but also to name badges for conferences and the name you use in academic life: people will want to be able to connect your papers to you, and this is much harder if you introduce yourself as "Firstname" while you publish under "F. Middlename Surname". (If I see someone publish under "F. Middlename Surname", my first assumption is that they -- like me -- are to be called by their middle name.) So decide first how you want your academic colleagues to actually call you, and then choose how to write your name based on that.

Some notable examples of F. Middlename Surname include F. William Lawvere, H. Floris Cohen, I. Bernard Cohen, and J. Robert Oppenheimer.

@GaiusPetronius: Regarding I. Bernard Cohen, although his father's first name is Isador, I think 'I' is not an abbreviation for Isador or any other name. See the footnote 1 on pp. 4-5 of Seven Decades of History of Science. I. Bernard Cohen (1914–2003), Second Editor of Isis by Dauben/Gleason/Smith (2009).

There are two risks to your strategy, and they are sort of opposites.
Firstly, people may assume that the two different versions of your name refer to different people. ORCID can help a little bit in this regard, but you can't expect everyone who encounters your name to look at your ORCID.
Secondly, people may be aware that the two names refer to the same person, and try to "correct" one to the other. The most likely "correction" is that people who are aware of your full name will refer to you by that name (in citations and in other places) even when they mean your "international persona".
There is considerable debate about whether the people "correcting" your name would be wrong to do so (see, for example, the answers to this question). Regardless of whether it is appropriate to do so, however, you should keep in mind that people likely will do it, at least some of the time.
I would therefore recommend against using different names in the way you suggest.
To explicitly answer your questions:

Yes, publishing under different names is still likely to cause confusion.
It is not necessarily bad to publish with a starting initial, but be aware that people will sometimes attempt to replace the initial by the name it stands for when citing you.

I have published with several colleagues who use their first initial and their whole middle name, ie, P. Middle Familyname.
You can use OrcID to make sure that your works are properly attributed, but if you're publishing in the same area and your first two initials are the same in all your pairs, people will likely assume those papers are published by the same person.

The problem with names is that there's so many of them people.
There is a good reason why Donald Ervin Knuth has spent probably thousands of hours tracking down the full name of every author in the bibliographies of his books, including names in native alphabets in addition to Latin transliterations - e.g. Japanese names in a Japanese alphabet next to Latin.
Ideally, always use the full name for disambiguation, and criticize citation styles that insist on initials only (if someone insists on that silliness).
That also means that you should use your full name.

However my first name sounds very obviously foreign to speakers of English

That's a "them" problem, not a "you" problem. We live in a global society. Non-English names are way, way more common on Earth than English ones. That's also the case in academia I'd bet.
Of course, nowadays with DOI global identifiers, it's easier to at least unambiguously refer to a publication. But whether the data associated with that DOI has enough to fully disambiguate the author is another story.

This is a great question.  My recommendation would be for you to look ahead into the future after you have a lot of papers published and then think about how many papers have different names that you have used.  This is a standardization issue, for which the variability of your author name should not be "all over the map."  On the downside, the worst that could happen during a future faculty job interview could be that you are asked e.g.: "your publications seem to use a different name a lot, so can you explain that?"

In my experience academia is generally fine with this name format, the problems usually come with the edge cases where academia interacts with the rest of the world.
For example, suppose you're J. Edgar Hoover and known as Ed Hoover.  That's all fine, until you go to a conference and the hotel registration insists you are John E. Hoover.  Maybe the conference reserved the hotel room for you as Ed Hoover but that's not what's on your passport.  Perhaps you need to apply for a visa but the letter of invitation to J. Edgar Hoover doesn't match the embassy system which expects Firstname Lastname (no middle name, because that's the way $country thinks everyone does their names).  Maybe an industry conference asks for your full name for the visa and then prints your badge as John Hoover.
These are all tolerable minor annoyances.  But it helps to develop a strategy for filling in academia-adjacent forms like this to head off potential glitches.


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How to propose alteration of study subjects in college?
I've been studying and working with Game Development for quite a while and I can't help to notice that I'm not using anything that was presented to me in college.
My college is focused in gaming programming, BUT all that is taught is basic programming like basic loops, conditions or object oriented programming. Most of the teachers don't even know how to build a game or what a game engine is.
I believe it's taught this way because there's no teacher with experience in the area and the topics are very wide, like "programming class" without specifying a programming language and what's going to be learned.
Is there a way I could propose a change of the subjects we study in class? Or even bring attention to the matter, so that someone could take action?

Do you still keep in touch with any of your old profs? You could drop them a nice email and mention new methods you use. Or, you could offer to give a seminar or guest lecture for your profs. Another option would be to speak for a student group (e.g., a student SIAM chapter).

Are you still in that college, or are you well past it?

I'm afraid I don't understand the question - is it that you're now teaching at a college and they are making you teach a syllabus which you don't think is suitable or that you're studying at a new college and it's not as good as your previous one?

See Approach the professors about making the course more “relevant”

You might want to compare your school's program of study with that of another school with a strong program in your field, and then contact the accrediting body.

Needs more detail: Are you a current student, ex-student, something else? When you say "working with Game Development" are you talking about: class assignments, hobby work, or professional work?

@RichardErickson there are my current teachers.

@svavil still in the college

@Retro actually I dont agree with the content teacher are teaching in my current college

Can you more specifically describe what work you're doing: It sounds like you're using a prepackaged game engine. What engine is it? What work are you doing with it? How large is the team that you're working with? Have they successfully shipped a product in the past?

@DanielR.Collins yep, we use Unity Engine (which btw is free for academic use), we use it to put all together (sound, models, etc) and program the game and its dependences, the team is not large, about 6 people, yep they succeeded in inumerous projects.

I'll ask again: "What work are you doing with it?" Are you creating graphics? 3D models? Scripts? Shaders? Testing? Programming?

@DanielR.Collins ohhh ok, didn't get it that way, well Im programming it

This is very hard to parse. You say in the question "I'm not using anything that was presented to me in college.... all that is taught is basic programming like basic loops, conditions or object oriented programming." But now you say that you are programming. Are you scripting gameplay in C#, or Javascript, or do you mean something else?

@DanielR.Collins Im using C# and yeah, im using basic loops and conditions in the coding that is needed, but 99% of the coding in the game demands knowledge a little bit deeper then normal business programming. I feel that in college teachers focuses too much in the normal business programming and in diferent programming languages that have just some details that makes em different.

In the comments, you explained that you are currently a student. I would suggest you have a friendly conversation with your professors. Perhaps you know your advisor a little bit, or one of your professors from your class and you're comfortable talking to her or him.
For example, let's say you decide to talk with Professor Smith. I would go up to Professor Smith (e.g., during office hours) and say: "Hi. I had a cool internship at Gaming, Inc. I learned some interesting programing methods X, Y, and Z" (follow their interest in their methods here, you might end up deep in details or your professor may not care). Then ask something like "We haven't covered the methods in my classes. I think they would help other students in our program. Are they included anywhere in our curriculum?"
This will start a conversation with your Professor about the curriculum. Most reasonable professor will be open to your conversation, just don't put them on the defensive. For example, avoid saying something like "our program sucks..." or "you should do...". Also, keep your suggestions positive and avoid being arrogant. Perhaps your program is revising their curriculum now and you do not know about it.
As an aside, I had a similar experience as an undergrad wildlife biology student. During a summer internship, I worked for a government agency using management approaches not covered in class. I asked a friendly professor why we were not learning the topic during an informal office hour. The friendly prof said a couple of reasons (basically their curriculum had not been updated) and then another, crotchety old professor jumped in and though my idea was stupid (he was dinosaur who did not like change). The friendly professor actually changed his view point and started defending my question/view-point. In my case, I was not able to change the curriculum, but I did learn why it was what it was.


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Is it ok to have a paper with no academic citation but just think tank and investigative journalism?
I'm writing my first paper for a conference about an issue enquired just by think tank, investigative journalism, ONG and United Nation Agencies but not directly from academic research.
So, is it correct to present that paper with only collateral academic writing?

I'm not sure I understand, are you saying there exists no research at all on this topic?

Not that directly concerns the issue

Well, if it doesn't exist you can't cite it. Someone has to be the first. Just make sure it really is you.

everything can be put in scientific or social science perspective.

If your research concerns a specific subject for which all presently published material comes from think-tanks and news articles, then it is perfectly legitimate to cite those sources as your main source of literature.  However, while this may be true of the specific issue you are investigating, it would be extremely unusual for that issue to be so unique that it cannot be put into any broader scholarly context in any field of academic inquiry.
For example, suppose you take some extremely specific topic -- e.g., you want to investigate the effect of fluctuating prices of bananas on the eating habits of rural families in Peru.  Perhaps there is not yet any academic literature on that topic, but there might be news articles from time to time that talk about farmers when banana prices go up or down.  Even so, if you were writing about that topic, you would probably discuss the specifics within a broader academic context with some economic theory, social science, etc.  So you might augment your discussion of the specific topic by noting that shortages of bananas in other parts of the world cause consumer prices to increase, and this increases profits to banana growers, which gives them more disposable income, etc.  There would be plenty of general academic literature (e.g., general economics literature) on those phenomena that are not specific to banana-growing in Peru.  By citing literature on these general phenomena you would augment your specific topic by placing it in a broader context.
If you are unable to find any scholarly literature that could put your issue into an academic context, you are implicitly telling your reader that your issue falls outside the scope of all historic scientific and academic inquiry, and there is no avenue of academic research that could shed any light on your topic.  Are you sure that is the case?

+1 for your excellent example. When I read the question my main thought was that I don't think I could come up with ANYTHING that one could write about and for which no reasonable literature references could be given. (Perhaps someone else might be able to do this, but it'd probably be in a general field that I know nothing about. But I doubt someone else could do this in mathematics (my general field), even areas which I know next to nothing about.)

It it okay? My answer is "Yes, but..."
Yes: The purpose of citations is to point the the information you used in creating your own work, to source your ideas and link your work with the larger body of thought on a topic. For example, it's entirely possible that your paper will primarily/exclusively have citations to non-academic literature. To use one of my papers as an example, in it's 11 citations it has:

One Blog
One National Public Radio transcript
Two popular press articles
One fan-maintained Wiki
One fan-maintained data scraping website
One software documentation document
One semi-popular press book
Three academic citations, three of which appear at the end of the document

Clearly that's not exclusively non-academic citations, but there's a lot there that's not a conventional citation, and that's okay.
But... : It is highly unusual for there to be nothing that touches on your topic, even in the broadest form - a review, a paper that suggests this as a way forward, a paper identifying a gap that might be filled with your work, etc.
I would take a long, hard look at your paper and topic and make sure you haven't missed anything. But if the answer, after that self-examination, is "No, this is it" then that is what it is.