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What will be the research methodology if you are developing a generic software
I'm developing a generic software for the unorganised retail sector. The design is completely based on the literature review that has been conducted. The only problem is that since I'm not doing any interviews or surveys, what research methodology should I follow ? It can't be qualitative or quantitative. The end result is just the developed software.
The aim is to study why the unorganised retail is behind than the organised one. And the solution is to present a software for them to use to help in decision making. It's completely based on literature and no surveys or interviews were conducted.

Probably lacking context. Why do you need a research methodology for developing software? That being said, there's the design science methodology, which might be relevant for your purpose

Sounds like a good question for your instructor, alongside with "should I maybe do some interviews or surveys?".

@lighthouse keeper I'm doing this as a part of my dissertation. And I need to follow a specific methodology to design the software based on the literature review as I can't test the software in real time.

You need to ask your dissertation advisor  this question.

OK, that should probably be edited into in the question then. I gave you a pointer to a methodology above.

This is probably off-topic for academia, but my initial reaction is "what research are you doing?". Writing software is not research, although using it for something may be. By analogy, making a telescope is not research, but using it for something might be (and that thing might be "testing a better telescope design" - similarly for software, if you're a computer scientist). So figure out what the research aspect of your project is, and you'll be part way to the answer.

Writing software isn't research. Proving that a piece of software, written by yourself or others, can be research. How are you going to show that your software does what it set out to do? How are you going to show that it is better than the alternatives? For those questions you need methodology. Questionnaires? Observations? Objective measurements? Something.
But the software itself is just a tool. Showing it is valuable is the research part.
And, of course, if it is real research then you need to be prepared for the situation that you get evidence that the new tool isn't actually better. Research is a search for truth, not proof of a predefined statement.


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Should I quit my PhD, has anyone every done this and started over?
I have currently completed four years of my PhD.
My PhD supervisor was nice at first, and I actually thought I was lucky to get her. However, things quickly turned bad and have been bad for the last three years. There are three of us (pHD students) and together we ran and executed a rat model on a drug designed in our lab. However, numerous errors were made during the rat model (which I objected to at the time such as the concentration and mode of administration of the positive control) and after two years of analyzing the data, the drug did not have any affect and the positive control did not work at all.
Every time I brought my supervisor negative results based on these findings, she would say I am lazy or that there is something wrong with me for not doing the experiment correctly. During these meetings, I would defend myself and my technique, but I quickly learnt that the wrong thing to do. She started locking up reagents from me such as Trizol for RNA isolation and instead told me to make up my own from scratch (this included me going to another department and begging for chemicals such as phenol). This occurred for a year, in which every day I came in and tried to isolate RNA from expired reagents in a homemade Trizol solution. I had received external funding (Which I have to pay back if I leave), and every time I objected she threatened to write to my funders and tell them I was lazy as I hadn't made any progress.
During this time I thought I was the only one being affected in this way as the other PhDs (the two others who ran the model with me), looked fine. I only found at later that they were just as affected.
Anyway, during this time in meetings she called me lazy (I graduated top of my class in my MSc), selfish, and constantly threatened me with a bad reference to my funders. She called my PhD patchwork among other things, and said that it didn't make sense (even though she was the one who told me to do everything).
During meetings with my co-supervisor she would outright lie to make me look bad. I became very depressed, started to think of suicide and started to drink (I was never much of a drinker before the PhD).
I wrote up a paper and it kept on getting rejected due to the bad science (positive control not working), and when I told her we would have to correct this, she lost her mind and said that she has put too much money into the project and that I am wasteful. From that moment she cut me off reagents, I could not even get tips for my pippette or gloves, and had to go and buy some with my own money from the reps. During lab meetings she would repeatedly target me and crap on me for some small thing in front of everyone else. The humiliation was endless.
Every week we were having weekly meetings where she would offer no form of advice. During these weekly meetings she would again tell me that I am a failure, that she wishes she never took me on as a student and that I am wasting taxpayers money. During this time I managed to convince my co-supervisor to let me do some work in a lab in an adjacent campus. During this time all my experiments worked (because the lab was not toxic and didn't use expired reagents). Things went well, I thought my life was improving. The other PhDs were also working in that lab and slowly we began to open up and share our experiences.
However, as of November 2019 I am back in my original lab and as usual the experiments are not working.
For example most of the reagents are expired. In order to do protein assays we have to use re-washed plates which compromises the science. I worked straight through December and didn't take a break in order to try and finish my last remaining experiments, however, with a lack of resources, I was unable.
My funding has run dry and I am without money to register for this year. However, someone from another department has offered me a lecturing post that would keep me on campus and not force me to find work outside the university. I told my supervisor about it and she wrote me a long email noting how I am already behind on my PhD, and cc'd this person in on it, but still leaving the decision up to me. She also noted that my progress over December has not been good, even though I was sending her emails with my stuff every week which she never replied to.
I went to this person to go and take the position, only to find out that my supervisor had already contacted them and told them I was too behind and unable to do so, even though she knows I need the money. My supervisor and this person are friends outside of work so I didn't even bother raising my case.
I am at my wits end and feel like this will never end. Has anyone had any similar experiences? I have committed four years and lots of money to this, but I am seriously considering packing my bags and leaving. The only thing that is stopping me is giving her the satisfaction that she has ruined my life. However, I feel like she is trying to exhaust my resources and waste my time until I leave.
Any advice would be appreciated.

Related, yet not the exact same situation : https://academia.stackexchange.com/questions/141199/i-wasted-six-years-of-my-life-getting-a-phd-degree-what-should-i-do-and-how-wi

"I am seriously considering packing my bags and leaving" it is wonderful to hear.
I feel so depressed for the hundreds of PhD that cannot even think that choice. The system is deeply rotten.

Many people have quitted PhD studies before, some of them have asked about it on this site.
If the situation is as bad as you describe it, it is probably best for you to to try to switch to a different advisor, either at your university or at a different one. Maybe you can talk with the people in the other lab you worked. If you did well there, they might be interested in your work. You might also ask your co-supervisor about this, if you feel they will be more supportive.
If you cannot find any advisor to switch to, you will have to decide whether you want to stay and try to finish as soon as possible, start a new PhD somewhere else, or quit and go to industry. Whether the first option is possible will partially depend on your current supervisor. None of the two latter options are impossible, and many people have done them before. If the current situation is negatively affecting your health as you describe, you should seriously consider them. But it needs to be your decision.
Finally, and importantly, you say

The only thing that is stopping me is giving her the satisfaction that she has ruined my life.

This is not a factor to consider. At all. You should care about your own career and well-being. The fact that you "give her satisfaction by quitting" should matter exactly zero in your decision.

Definitely agree with the last point and, ultimately, while you may think it would reflect poorly on you to quit after four years, it also  reflects poorly on your advisor. If their behavior persists and is similar with other students, no doubt they will quickly have a very poor mentoring track record.

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What are the computer science skills used (if any) in HEP experimental or observational cosmology programmes?
I am currently an undergrad junior majoring in physics and mathematics and will likely apply for a high energy experiment or observational cosmology PhD programme after graduation. I have heard quite a few times that many people who studied physics and mathematics in undergrad wished they had studied more computer science; especially if their graduate research is related to high energy experiment. Since CS skills are needed everywhere, even if I were to quit academia, I am trying to take some CS courses before I graduate.
Question: How much data analysis and what sort of analysis do you do in high energy experimental/observational cosmology programmes?
As of right now I am planning on taking a few courses on basic programming (data structures etc.),
a course on statistical analysis for data science, and a course on machine learning.

Learn source control concepts and practices, how to develop and interact with core components such as relational and noSQL databases, continuous integration in practice, service-based architectures, etc., though all this can be done effectively outside of the classroom. If the opportunity to take a numerical analysis course presents itself, that's probably worthwhile. Similar for algorithms and data structures.

I'll answer from the cosmology perspective, though probably a lot of this applies to hep-ex as well.
You should aim to have a good working knowledge of Python as that is the lingua franca in cosmology. Additionally, it's useful to be familiar with either Fortran or C, as some of the larger numerical cosmology codes such as CAMB and CLASS are written in those.
For observational cosmology specifically, you should learn how to handle large datasets and image files, especially FITS files. If you're going to be using existing databases of images, spectra etc, then learning SQL will also be useful.
Finally, the vast majority of statistical analysis in cosmology follows a Bayesian rather than frequentist framework, so understanding the basic concepts of that, as well as methods such as MCMC parameter inference will be useful.
Machine learning methods are becoming increasingly popular, though there is little true expertise in the field. Any knowledge and experience you have of using machine learning, especially classification and regression methods, will be a bonus.
If I were you, I would take a look at some recent papers in your specific field of interest to get an idea of the specific data analysis and computing methods used, as it will differ quite a lot from project to project even within cosmology. You can find relevant papers on the astro-ph.co section of arXiv.

Thanks for the clear answer! I gather that C and python are very important and data science courses that deal with Bayesian analysis are a good idea. But, is a machine learning course going to be useful? I would like to take if it's possible just because it's interesting.

@Chandrahas yes, machine learning would be a bonus if you can take a good course on it! I also forgot to mention that you should learn version control with git. That's quite simple and you can probably learn it on your own in a day or two (the basics, anyway).

It will depend strongly on the specific tasks you are involved in. In most labs there will be the local guru who can get you started if you are nice to him. And on most large projects there will be several such gurus.
HEP experimental is going to, naturally, have a big hardware component. If you can repair, diagnose, build, or install some kind of electronic or computer hardware, then you may get to go to the lab. But consider how much time that will use that could have been used doing your thesis. If you can code the controller circuits for the hardware, that may be useful, with the same caveat. And in all such cases, you may be competing with laboratory tech staff.
But a PhD thesis in which you invented some new thing that helped out at some big lab would probably have a lot of appeal.
There will be tons of numerical analysis. Signal processing to understand and "decode" the output of a detector. For example, some experiments involve recording a huge volume of candidate events, then filtering it to find the specific category of events you are looking for.  Database, AI filtering, and just plain-old number crunching. Say from a book such as Numerical Recipes. Note that there are versions of this book for several different computer languages, including C, C++, FORTRAN, maybe others. And you should treat this book as a "first intro" to the topics in it, looking for more advanced and powerful methods if you start working in the field. But it gives you lots of things in a form you can "get up the curve" on.
Another entire topic is Monte Carlo methods. This is a method of doing numerical experiments to try to predict the frequency of various events by throwing a bunch of random numbers at it. This would come at the data from the other end by attempting to predict what the detector would see in the case of a particular event. Maybe you can work out the "fingerprint" for a given event. Look for this combo and you know you have found the elusive anti-schmadron.
Another area is data visualization. When you are doing some horrendous large dataset coming out of some experiment, you want some way to present the information so people can comprehend it. Often you first. (Grin.)  Maybe you want to learn apps that deal with such things such as MATLAB and related. Or maybe you want to learn to do 3-D visualization. There are several popular apps that deal with that, but I have not been involved in them.
If you are designing a detector (or some such hardware) you may want to learn 3-D CAD/CAM software. Again, there are several popular ones but I don't know them.

"... if your are nice to him or her"

"HEP experimental is going to, naturally, have a big hardware component."  This is wrong.  Many particle experimentalists work exclusively on data analysis.

The Numerical Recipes book is obsolete.

@AnonymousPhysicist  So sentimentalists don;t do hardware?  OK.

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Institution refuses reimbursement for grant awarded?
After managing a project at a research institution in the US, I was awarded a grant (did it for free, so this is the remuneration). The grant covers travel, books, research equipment ("that does not contain a hard drive") and some other things. They strongly recommended confirming with their representatives if certain expenses are covered by the grant. I decided to purchase PC components and just build it myself. Last August I contacted them to check if they would cover the components cost (2 reps said it should be fine, both were in 1 email thread). Over Black Friday I purchased all parts and sent them all receipts for reimbursement. Now, middle of January, they claim they did not realise I was building a PC (although I explained everything in detail in our email communication back in August) and would not reimburse me as the institution tracks parts "as part of their on campus computing inventory". It is past return period time now for the components I purchased. What should I do now? All communication was over email, so I have everything in writing.

What do you mean by: "... explained everything in detail". Did you specifically say the equivalent of: I will use the grant to purchase the listed supplies in order to build a PC without a hard drive?

I have repeatedly seen grants forbidding the use of their money to buy PCs. A headless number crunching server would theoretically have been OK, but how do you tell the difference if you look at the hardware? The problem is that whatever you buy becomes a property of the granting institution. Keeping track of special scientific hardware pieces is simple, but a PC, consisting of numerous, easily exchangeable parts?

Is it possible that the institution tried to get it approved by the funding agency and were told that it can't be done? Or something else caused a change of perspective in the interval?

I'm a little confused who "they" are.  Are these officials at the funding agency, or the research institution where you did the work, or somewhere else?  Which organization actually awarded the grant?  Are there formal written rules on purchasing?

Is the rule in place perhaps to prohibit improper storage of PHI? And, just to be clear, was your goal to put your own hard drive in this PC? Or did you have some scientific need for a PC without a hard drive?

Yes, I mentioned some of the costlier components that would be purchased. Honestly, even if they covered just these I would be ok with that. "They" are department representatives. I have no idea who funds them and it's probably none of my business.

What you need to do is work it out locally. If necessary, the grant funder may need to make a judgement. But it seems like you were trying to get around a restriction by somewhat questionable means. Not necessarily ethically dubious means, but questionable. A pedantic interpretation of the statement in the grant, and ignoring its likely intent is what got you into the current situation. You need to argue that your interpretation is correct and you need to get others, who have some authority here, to agree with you.
I can't guess whether you will win this or not, but the situation is between you, the institution and the funding authority. Make your best argument there. And note that you can't impose your own will on this.
If this is PC level equipment, I doubt that it is going to be a serious setback to your finances. Maybe it is best to just absorb the cost and spend the funds on things that aren't so close to the margin of acceptability.

thank you for your answer! I am a PhD student and we are talking about thousands of dollars here (not a serious, but a noticeable financial setback). But why would PC components be not considered research equipment? What is research equipment then? On top of that, I asked them 5 months ago if parts would be covered and they said yes. I further made my financial decisions based on their assurance.

I sympathize, but can't affect how they think or judge. They need to be convinced, though it may not be possible.

@JoshuaCalvin by your own admission the grant restricts reimbursement to research equipment "that does not contain a hard drive". You very obviously tried to creatively (and I'd argue, in bad faith) get around this by basically buying a PC without a hard drive. This was clearly not the intent of said rule.

@JoshuaCalvin Why are PC components not considered as research materials, supplies, or equipment? For reflection, I would ask this: Will the computer parts be used exclusively to perform a specific type of computational analysis that can not be done by any other type of computer that is currently available at your institution in order to generate analytical or empirical results as part of a publication-directed (research) project? When the answer is not an emphatic YES, the computer parts are categorized as (non-research related) general (administrative) supplies.

@JoshuaCalvin funding agencies have Byzantine rules about what can and cannot be covered using their funds. Nobody really understands “why” each rule is in place, so that’s a pointless question to ask. I suggest focusing on whether you were given inaccurate information as a basis for arguing that you should get reimbursed, not on whether the rules make sense.

@DanRomik, while I don't disagree, the people with the money often get to make the rules. Also see: https://dilbert.com/strip/2020-01-07

Joshua: I refer to Karl's comment to your question for a possible reason why. But I suggest you accept the consensus (saying your actions tried to subvert rules/intent) as how people in charge are likely to judge things, even if you don't like it. The "no hard drive" rule was probably not made to allow HD-like things like SSDs on a technicality, but rather to prohibit things like Xerox copiers that may have an internal hard drive (so, to be more restrictive, not to enable a loophole). It isn't clear to us how much authority your advisers are treated with, or how much their word will be honored

There are definitely many people who understand why certain rules for use of funds are in place that may seem arbitrary to the uninitiated.

@MichaelHoffman that’s true for some rules, but I suspect that not for all of them.

@Maeher “creatively” perhaps, but what is your basis for the bad faith claim? It seems quite reasonable for a PhD student to not understand the intricacies of funding agency spending rules (which frankly are not easy even for senior faculty to understand), and consequently to interpret a rule such as “does not contain a hard drive” more literally than a more experienced person might. The fact that OP sought, and obtained, reassurance from staff members that the purchase was permitted suggests the opposite of bad faith to me, or at the very least a lack of evidence of bad faith.

If they wanted to say you couldn't buy a computer or buy computer parts, they should have said so. What's the point of them stating a precise and strange rule if they don't want people to obey the strange and precise rule they chose?

"You need to argue that your interpretation is correct and".. why? If I get written confirmation from someone that I'll be refunded for X, it's ridiculous to argue afterwards that I should've second guessed the person responsible in the first place.

@Voo, probably if you don't argue the case then you lose by default. Don't assume this situation is normal or logical.

@Buffy Sure I have to argue it. But it should stop right at "Here I have written confirmation that I'll be compensated for buying those things". Isn't that the whole point of asking in advance?

I strongly recommend that you talk to your department chair and ask for their help.
The situation as I understand it is that you obtained confirmation in writing from university employees that the equipment you wanted to purchase would be covered by the grant and you would get reimbursed. Now the institution is refusing to reimburse you. This is pretty unconscionable and sounds like a screwup on the side of the relevant officials.
It is the job of the department chair to try to help you resolve the situation and get the people involved to either find some way to be flexible about the stupid inventory issue (I am reasonably optimistic that if somebody beat them over the head with a hammer they would suddenly find some magical way to make it happen), or own up to the mistake and find some other way to cover your financial loss. The chair may also end up deciding that the department should absorb the cost if the reimbursement issue is truly unfixable.
Finally, before you talk to the chair I suggest carefully examining your own role in the events that took place and thinking about whether your own behavior might be seen to have played a part in this misunderstanding. Did you communicate your question clearly in the emails you sent? Did you miss some ambiguity in the email thread about whether it was okay to go ahead with the purchase? Did you make any assumption about the meaning of what the employees wrote that wasn’t explicitly written in their email (say, interpreting “research equipment” to mean “whatever I think research equipment means”)? If there was some negligence of this sort on your part, the chances of getting the purchase reimbursed would be much smaller. In that case the best thing to do may be to suck up the loss and use the experience as a lesson for the future. Anyway, good luck!

I think this is the only legally correct answer. If written confirmation was explicitly given there is no way they can refuse reimbursement. If the grant cannot be used to reimburse then the employees/dept that gave incorrect advice will be forced to reimburse personally.

In my experience in the US, computers and their parts are considered part of overhead, as are things like desks, office chairs, etc.
When you get a grant, part of it goes to "you", and part of it goes to the university as overhead - they use this to keep the lights on and for other various expenses that you don't directly see, but they also often make some of that money available to the researchers to buy capital equipment including computers.
It's unfortunate that you got incorrect information due to a miscommunication, but it's likely nothing can be done about those funds directly. It's possible there is overhead money that can help you out retroactively, but I don't have experience with that circumstance.
From my perspective, this looks bad for you - it seems like you tried to skip around the "has a hard drive" rule.

It's not uncommon for NSF budgets to include funds for the purchase of workstation computers that will be used in the research for computing the goes beyond standard office equipment.   That doesn't seem to be the case here.

Don't they give you precise rules so you know precisely what not to do? I'm puzzled by this "skip around" thing. They could have given more vague rules and communicated intent but they chose instead to give a precise rule. If they gave a precise rule when what they wanted was for you to respect a vaguer intention, they're the ones acting in bad faith.


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How to proceed with copyright permission if you can't contact the author?
I found a 2016 presentation by an author in my niche field and want to get permission to reuse and modify a few of his figures for my master's thesis. But, the presentation doesn't has any copyright notice.
I can't find a way to contact him. I tried:

Contact information on any support or paper he participated in; there is nothing.
The website of his academia doesn't allow contact from un-authenticated users.
I can't find him through the contact list in the email system of my academia.
His LinkedIn account has a lock to not send messages to him.

He is still in academia, participates in juries of theses, and advises students. I am running out of options. Do I need to forget about using his figures?

You could perhaps try contacting one of the people he works with(e.g. co-authors, grad students) , and ask them how to contact this person

@whoisit I contacted a co-author and he gave me the current email address of him, thanks.

What will you do if you manage to contact him and he denies the permission? Save time, produce your own figures. Moreover, you mentioned you want to modify his figures. It is better to prepare your own in the form you desire.

This clearly looks like fair use, no different than quoting a paragraph or whatever. Particularly because the use is academic in nature and there's no profit involved but even if there were you see famous content creators on YouTube or wherever use these sorts of things in there videos with only attribution.

Yes, you need to avoid copyright infringement and you need positive permission from the copyright holder to go beyond "fair use" however it is defined (which varies).
You can't make assumptions. Even if the author has died, the copyright is still held by someone and you need to contact the holder. Assume that their refusal to reply is denial of permission.
You can, of course, rely on fair use (where available) for some things.
Active academics and often even those retired can be contacted indirectly through their departments. They can pass on a message with information about your request and how to contact you.

You don't specifically mention email (what is "my/his academia?"), but email is the default method for contacting academics whom you personally don't know. It is common to get requests out of the blue from prospective students, people who have read your work and have questions, journal editors who want you to review something, etc.
If he is a faculty member somewhere, then he very likely has a public-facing email address listed on his website (if he has one) or his department's website. In most cases, some Googling will turn it up quickly.
I'd recommend emailing him your question: keep it brief, polite, and to the point. In my opinion etiquette doesn't oblige him to respond, but he very well might.

I used "my/his academia" in the sense of different universities. My mail domain end with universityA and his with academiaB.

@molik I'm afraid that I still don't quite understand. If his email is configured so as to reject email from any unauthenticated user, then that would be very unusual in my experience. At this point, I think my advice is to ask a trusted mentor for advice in person, so you can discuss in more detail what you've tried and resolve any potential misunderstandings. Good luck.

department websites are my go to for this sort of thing - it's almost certain that academics will have some form of contact address listed there

If, for some strange and inexplicable reason, you cannot find an email address by which to contact him, there's always the old-fashioned approach: snail-mail.
Write a hard-copy letter to the person, and mail it using your local postal service. You'll need a physical postal address to do so, but it need not be an address specific to him. You should be able to send a letter "in care of" the department or the university in general, and be reasonably confident they'll redirect the letter to his personal mailbox. Though keep in mind a physical letter can be ignored just as easily as a email can.
That said, I find it highly unlikely that you'll be unable to find a publicly accessible email address for an academic in this day and age. If there's nothing posted on the university website or in previous articles by this person, you might be able to email the general contact point for the department or university and politely ask for the author's email address.


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Asking professor about extending word limit for term paper
I'm currently in my 3rd semester of my Bachelors program and have to write a term paper with a word range of 4000 words ± 5-10%.
I'll be writing about Zero‑Trust Network Architectures and the way they reduce data loss and cyber attack in companies.
This is the second paper I'll be writing during my program but I'm not sure if I'll be able to fit my work in this word range.
would you say, that it's appropriate to ask my professor if I may extend that word range or should I cut some, possible helpful/ important information from the text?
I have already enlisted for the paper with that topic and can't cancel it without it counting as a failed exam.

I remember we had a similar assignment in university, and when some students asked about an extension of the word limit, our professor told us that the word limit was there for a reason, so we learn to concisely say what needs to be said about a specific topic. And this really is an important skill to have. If you can say what you need in as short and to the point manner as possible, it will greatly increase the understandability, the reach and the impact and make your writing more accesible. So I would strongly suggest to try to stay within that word limit and really think about what is important to get your point across and what isn't. If there is such a strict word limit, don't aim for completeness, but rather for distilling the topic down to the key isssues.

First make sure whether the word count limit is a proper rule or rather given just for orientation. I have seen word count indications in some departments about which nobody cares. In other places word count limits are strongly enforced. For sure you can ask your professor whether the limit is a sharp rule or not. If it isn't, you're fine. If it is, chances are you need to learn to write things down in a focused way, leaving out stuff that is less important (that's a good skill to learn in any case).
Keep in mind by the way that reading and assessing such theses is hard work, and word counts are in place to make the markers' work easier. So there are good reasons for them, and normally they work out in the interest of your professor.

Your professor or advisor should be able to give you clarity about the assignment and how strictly word counts are enforced (or the penalty for exceeding them) if you ask, so there is no problem with asking.
As another answer mentioned the word count is there to make the assessors life easier  but it also ensures fairness in the assessments across your cohort. That is if you send in 8000 words you are effectively demanding twice as much Professor time as everybody else, which isn't fair.
Writing a piece to a given word length is a skill, and that is a part of what is being assessed.  If the assignment is 4000 words on a broad topic then it is a part of the assignment to decide what to say and in how much detail.  For future reference you are likely to encounter a lot of situations in professional life where you will have to make a strong argument or deliver a report to a fixed length, and getting your point across within that space can be a challenge.
On the other hand I've seen journals with a 3000 word limit consider 6000 word papers because the author knew the editor.
For what it's worth in my previous school we allowed students to exceed the word limits on our assignments, but we only gave credit for material that was inside the word count.

Not only does a word count encourage more succinct writing and limit marking load, there are further reasons for why they exist and are enforced. First of all it is hard to mark consistently when papers have widely divergent lengths (the amount of depth you can go in to differs). Second, it influences assessment load, yes universities do try to limit that. Third there may very well be institutional rules about this. I your case ask the professor for advise.


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How do I respond to a review report provided as an annotated PDF?
Often, one gets a notification email with, typically 2 to 5, review reports compiled together and one would respond to each of these reviews with a list of "quote/response" items (if needed, referring to the revised manuscript) in form of a response letter. Now, facing the case of both an email with review reports and a commented PDF basically replacing/extending one of the reports, how would I pragmatically write the response letter? Should I respond to the PDF-based review ...

by copying each of the PDF comments into the main response letter, add a reference to the commented PDF, and add my response item?
with another commented PDF (i.e. my comments would be next to the reviewer's comments and, if needed, refer to the revised manuscript) and refer to this PDF in the corresponding section of the main response letter?

The first solution sounds more coherent to me while the second solution may be more easily usable by editors or reviewers. Apart from that more general guidance, I haven't found anything. This might be a bit of a trivial question but I appreciate any suggestions about best practices.

As one of the people who writes reviews in the form of annotated PDF files + a summary review, I think I'm in a good position to answer this question :-)
At least in my case, annotations in the PDF are often of relatively small points. I expect you to address all points raised in annotations, but you don't have to prove it to me by mentioning them individually in your response. Many will be typos/grammar annotations, some about missing axis labels, etc. In your written response, just mention somewhere that all of the points raised in annotations in the PDF that are not specifically addressed in your response have been taken care of -- that's enough for me, and likely the editor.
That leaves maybe ten longer comments in the margins of the PDF. If you think that they are worth addressing individually, copy the text into your response and add your reply. That should be easy enough to do.

Just curious: how do you ensure that your annotated PDF review is anonymous? In my experience, PDF-producing software tries to put your name everywhere, which is a pain when you need to stay anonymous.

Most of the time I just don't care if someone finds out about my name if they must because I'm confident in my review. But I have checked whether my tablet puts my name into the PDF and it doesn't seem to.

Either approach is fine.
The quality and clarity of the responses is more important than the format.

I wouldn't jeopardise the response. I would neatly adress all the points raised by the referee as usual in a single letter addressed to the editor, clearly indicating when you respond to criticisms or suggestions only stated in the pdf report by quoting or grouping them (depending on their importance, as usual).


text:
should I go for a Ph.D.in electronic/electromagnetism engineering?
Hello Academicians and everyone,
As you noticed from my question. I am willing to do a Ph.D. in electronic/electromagnetism engineering. I am very interested in the topic of electromagnetism and its application. I love everything that has to do with Maxwell equations.
Nevertheless, I have a big concern, My Health(burn out, gastritis, stress, migraine). as I am at the beginning of my thirties and had a lot of health issues during my master degree. I had to take many short breaks to get back to the track in the meantime.
I had some professors (who think I am healthy as Batman and don't know what I am facing) who suggested me to do a Ph.D. with them but I am scared to death because of my situation and I don't want to end up in Hospital because I  usually push until I get sick.
I need your advice and suggestion from your sides. How do you manage your stress? how did you manage to successfully finish your Ph.D. without ending in Hospital? or it would be better not going for this Ph.D. in my case?
Thanks

Voting to close -- we are not medical doctors, and we don't know your situation well enough to advise you do/don't get a PhD. You might consider editing the question (or making a new one) so that it focuses on stress management (strangely, I don't see a general "how to manage stress in grad school" question in our archive), or on accommodations that can/should be made for those with chronic conditions.

There is no question that stress can kill you. But there are ways to reduce it. One of the big stress factors among students - especially high achieving students - is pushing too hard and never taking a break.
One advantage you have over many others is that you now recognize the issue and can learn to take action before the level becomes unbearable.
One problem with learning is that you are trying to change your brain - physically. To learn requires rewiring the synapses that connect the neurons. But the brain doesn't work as well as it might if you force it to work too hard all the time. You need to give it periods of rest. If you try to force it to learn it will work less efficiently. But that may just induce some people to try harder, increasing the problem and adding stress, but not learning.
To give your brain a break you just need to do something different. It may include physical rest or not. In fact it may include intense physical activity. In grad school I used bicycling as an outlet. 50-100 mile rides. Maybe 35 if time was tight. I rode in a group, fairly fast, but not so fast that we couldn't chat as we rode. As an undergraduate I practiced judo on a college team. I was terrible at it, but it provided a break from studies. Nowadays, I use Tai Chi which is a mind-body fusion exercise. An hour several times a week will make a change in your outlook. Some academic departments actually have groups that regularly do some activity. Tennis. Racketball. Swimming. A computer scientist I know (very high level person) once joined a theatre group.
Moreover, when you are trying to solve a difficult problem, pushing the brain harder may be counterproductive, but giving it a rest lets it work differently. Many researchers have gone to bed with a nasty problem unsolved, only to awake with the solution. It might even come in the middle of a bike ride. Your brain doesn't turn off in these situations, but the overall body structure (including the brain) will work differently.
My advice, then, is to find a way to deal with stress. If you are at a university or similar institution, there may be some "counseling" office that has short courses on such things or people skilled in teaching stress reduction. If you can find ways to manage and reduce stress (you probably can't avoid it altogether) you can function at a higher level whatever you do.

Thank you so much Buffy . It is really what happening to me, I take a break only once I am sick. You are absolutely right about what you said. Actually, I used to practice Karate ( with black built) but all my problems started after I got spine disc from pushing too much as well in karate. During my the time I was practicing karate, my academic performance and problem solving are quite higher than Now l, even though with less time and effort. I LL have to rework on my lifestyle which goes against me as you said!

The answer probably depends on what you want the degree for. Although grad school can be fun and rewarding, the point of a PhD is ultimately to learn how to conduct original research in your field and (just as importantly) to find a future job doing that original research. Unfortunately, it's extremely difficult to have a research-oriented career outside of academia (although this varies with the field in question), and getting an academic career involves--- regardless of your talent and skill and determination--- being extraordinarily lucky; it's not something you can get just by working hard enough or wanting it enough. Fortunately, if you're mainly interested in working with and studying electromagnetism, there are avenues for doing so outside of getting a PhD that won't tax your health.

Actually, I loved electromagnitism since I started studying it. This topic I am interested in is concerning the medical care device where electromagnitism is used for scanning and so on. Furthermore,as you said, I want a career in industry where I can see the applications and contribute. So you think it would be better to find a PhD in company where I can combine research and industry?


text:
Is there a noticeable trend for PhD graduates from elite universities ending up as assistant professors in top universities?
I am currently pursuing my PhD at a highly reputable university and am deeply engaged in academic activities, such as publishing quality research papers, serving as a reviewer for top-tier journals in my field, and have had the pleasure of seeing my work recognized by the academic community through numerous citations.
Despite my belief that success in a PhD program largely depends on personal effort and development, I've noticed a trend that seems hard to deny: PhD graduates from elite, top-tier universities often go on to become assistant professors at similarly prestigious institutions. On the other hand, it appears to be less common for graduates, regardless of their talent and accomplishments, from universities that are not within the top tier to secure assistant professor roles at these elite universities.
I am wondering if this is a well-recognized trend within academia, and if so, if it is something we as academics need to accept as the norm. I am interested in hearing the thoughts and experiences of others in the academic community on this matter.
Thank you in advance for your insights!
related but not the same question:
Is it possible for someone with a PhD from a top-200 university to find a faculty position at a top-20 university?
Is there a bias in top tier PhD admissions at top tier universities to favor those with undergraduate degrees from other top tier universities?

What is is described (for the US situation) by Anyone's answer. What should be depends on your political beliefs, so that is not a topic for this site.

Could you please specify the country?

It is well-established that there are such hierarchies of institutions. Last year there was a very interesting study of US academia showing this effect across fields: K. Hunter Wapman, Sam Zhang, Aaron Clauset & Daniel B. Larremore, Quantifying hierarchy and dynamics in US faculty hiring and retention, Nature 610, 120-127 (2022) link. The authors "analyse the academic employment and doctoral education of tenure-track faculty at all PhD-granting US universities over the decade 2011–2020". Among the relevant findings are

Faculty hiring networks in the United States exhibit a steep hierarchy in academia and across all domains and fields, with only 5–23% of faculty employed at universities more prestigious than their doctoral university (Fig. 6a,b and Extended Data Table 4). Measured by the extent to which they restrict such upward mobility, these prestige hierarchies are most steep in the Humanities (12% upward mobility) and Mathematics and Computing (13%) and least steep in Medicine and Health (21%; Fig. 6b).

As a whole, by domain and by field, US tenure-track faculty hiring is dominated by a small minority of US universities that train a large majority of all faculty and sit atop steep hierarchies of prestige. Just five US universities train more US faculty than all non-US universities combined. As we expand our view from fields to entire domains, inequalities in faculty production further increase, reflecting elite universities’ positions at or near the top of multiple correlated prestige hierarchies across fields. In principle, universities are on equal footing as both producers and consumers in the faculty hiring market. However, the observed patterns of faculty hiring indicate that the system is better described as having a universal core–periphery structure, with modest faculty exchange among core universities, substantial faculty export from core to periphery and little importation in the reverse direction or from outside the United States.

Extended Table 4 is well worth a look if you're interested in how this plays out across "the 100 most prestigious universities, as inferred from patterns in faculty hiring".

At least in experimental fields, a department that has been historically successful in getting grants will likely (1) have an excellent set of equipment readily available, (2) have a variety of professors working in similar topics so there is synergy, and (3) have a number of collaborations with other universities so their students get broad exposure. Moving into the 'core' takes effort. One example that worked is UC Santa Barbara back in the 1980s, where they hired a bunch of folks from Bell Labs to jumpstart their semiconductor research (and invested a lot of UC money).

A similar thing happens with undergraduate institutions: you can get an excellent education almost anywhere. Some places will make it much easier to do.


text:
Drop from co-authorship of manuscript
I was on a internship abroad. We started a topic that is also carried out by their other student. The new research was repetitive, so I decided to take my time and automate the process. I spent some really long days and evenings preparing a proper script, which greatly improved the workflow.
But what happened - well, it turned out that the other guy copied the script from my home directory to himself without even asking for permission. I immediately informed the supervisor about this, but the guy not only did not react, but from that moment on he completely changed his attitude towards me, he started ignoring me and stopped talking at all, as if he was offended that I dared to inform them about such reprehensible behavior of the  student.
I returned home. After some time, I received a general email, addressed to me and, surprisingly, that PhD student, that a draft of the manuscript is prepared and attached to the email. It turned out that the authors of the paper would be three: me, the doctoral student and the host.
I was very hurt by the behavior of the supervisor, that is, his lack of comment on the theft of the code and his change of attitude towards me to completely negative, as if I had done something to them.... This is the first time something like this has happened and it is another practice in a row.
If I'm honest, I wouldn't want to be associated with them in any way.  Preferably, I would completely erase this internship from my resume and forget about it...
What do you think about the whole situation? Do you think it is wise to resign from the authorship of such a publication? Or to leave it as it is, because it is, however, a job that I put all my time into?

Your description sounds like a classical example of how to not handle the issue of who will co-author a paper. Anyway, it appears strange to me that you were not involved in writing of the draft, or were you? Writing is a substantial contribution obviously. So something like shared first authorship might be fair, don't you think?

Oh, and do you like the manuscript, do you agree with the results and conclusions, do you think it will make a relevant paper?

"Theft of code" ? I've been involved with various bits of coding at a (UK) University for 20+ years and all code goes in shared repositories and can be used by all members of a particular group. As long as the student didn't claim to have written your code, he did nothing wrong and your attitude comes across as refusing to work in a team, which will prove a major hindrance for your future career. There is a chance that you completely misunderstood the assignment.

@Snijderfrey  The work was split so I did all the studies, while the hosting professor wrote the paper and only after send me and the other guy the draft to see and make eventual corrections. I truly don't give a hoot about it.

@Marianne013 Reaching my home directory (not shared repo) and copying the intellectual property, which the defined program is, isn't a thievery? After all, it was not my assignment but my own solution to improve the workflow.

Can you think of a better title than "drop from co-authorship of manuscript" to describe your problem to potentially help people who have similar troubles to you in the future?

@farmaceut: Stuff you write at work (university) belongs to your work, not to you. Code that only you can run is useless to the project and you might as well not bother. What I see is a bright summer student who refuses to cooperate with anyone and then throws a hissy fit when people try to work around his non-cooperation. I realize this sounds harsh, but I urge you to try to see the other side if you want to stay in the field.

@Marianne013 Stuff you write at work belongs to your work --- This is a sweeping over-generalisation. The issue of IP in academia is much more complex than that. For instance, academic researchers keep authorship of papers they write --- the papers do not belong to University in any legal way.  The rules on software are even more diverse.

@Marianne013 I am totally bewildered that there’s people here who think it’s ok to go into someone’s home directory without permission and use the code without asking. Where I work this is a huge no no and would likely make you very unpopular with your colleagues. Sharing code is important and good, but going into people’s private directories  and taking things without permission is absolutely unacceptable.

Publications, particularly first-authored publications in certain fields, including Chemistry, is the main currency of academia. You worked hard to develop research for this paper, and you deserve to have it on your CV as an author.
It is a shame that your internship was affected by a conflict with another student, and that the promoter was not able to manage the conflict appropriately. Academics are often excellent in research but not always perfect in managing people, particularly when it comes to managing conflicts.  It is common for a PI or promoter to not know how to behave in a situation like this. Combined with stress and sometimes fear of exposure, it can result in shutting down the communication, similarly to what you observed. This is of course a poor experience for you — I am sorry that you had to go through this.
However, this episode is now behind you. It does not seem that you need to significantly interact with your former collaborators in order to complete the paper and get it published. I appreciate that work on this paper may bring back unpleasant memories and contribute to stress. You may need to discuss it with a professional or a mentor you trust. However, I think, the benefit of publishing the paper and having yourself recognised as a first author is also significant.
If you plan to develop your career in academia or a research-related industry, please consider completing this work to publication. You can then cease any further relationship with this group.

Let me summarize the facts as I understand them:

As a visiting researcher, you wrote some Python code that
substantially improved the process of collecting and/or processing
the research data.  Another student then used this code without your
permission, and the supervisor did not take action when informed of
this.

After you returned home, the student and supervisor wrote a draft
paper based on the collected data, with the intent of publishing it
with you as the first author.  They sent you a draft by email.

Throughout the process, you feel aggrieved because (1) the student
used your code without permission, (2) the supervisor was
uncommunicative, and (3) you provided the majority of the
contribution to the paper.  Consequently, you are considering
withdrawing yourself from authorship of the paper.

I'm going to answer on the assumption that the above is accurate.
Someone used my code without my permission
To me, this is a surprising thing to be upset about.  In my experience
doing research in Computer Science in the U.S. and collaborating with
others in Europe and Japan, it is standard practice to freely share code
among the team, and when ready, to release it publicly under an open
source license.
Code sharing is not just a matter of convenience or social culture, it
is important to the scientific process.  Quoting
A survey of researchers’ code sharing and code reuse practices, and assessment of interactive notebook prototypes
by Cadwallader and Hrynaszkiewicz (PeerJ, 2022):

Sharing code improves reproducibility, especially when made available
before publication (Fernández-Juricic, 2021). Lack of source
code—along with raw data, and protocols—has been described as the
main barrier to computational reproducibility of published research
(Seibold et al., 2021).

Sharing and publication of code is not required, but it is expected, and
a different arrangement requires explicit discussion and negotiation
(both among the team and with the employing institutions), ideally in
advance of doing the work.  Furthermore, when sharing is not the
intention, the code should carry some sort of notice to that effect.
If I were the collaborating student in your scenario, I would be
somewhat irritated that you had simply left the code in your private
home directory, rather than putting it into a shared repository and
proactively telling the rest of the team about it.  (That
said, I still would not have looked into another user's directory
nor used what I found there without prior authorization;
that part is questionable.)
If I were the supervisor in your scenario, I would be confused about why
you were complaining about the student using your code.  I think the
supervisor probably should have done a better job at working with you to
understand the issue, explain the local research culture, and come to
a mutually acceptable resolution.
They wrote a paper without me
First, let's review the criteria for authorship on scientific papers.
I'll quote
Guidance on Authorship in Scholarly or Scientific Publications
from the Yale Office of the Provost:

All co-authors should have been directly involved in all three of the
following:

planning and contribution to some component (conception, design,
conduct, analysis, or interpretation) of the work which led to the
paper or interpreting at least a portion of the results;

writing a draft of the article or revising it for intellectual content; and

final approval of the version to be published.  All authors should
review and approve the manuscript before it is submitted for
publication, at least as it pertains to their roles in the project.

Some diversity exists across academic disciplines regarding acceptable
standards for substantive contributions that would lead to attribution
of authorship.

You already contributed data for point 1.  You've now been sent a draft
to review, satisfying points 2 and 3.  So you should be an author,
assuming you follow through by contributing to the draft.
You might feel that the paper is already "done"--it is not!  You still
have plenty of opportunity to make major changes if you feel they are
appropriate and valuable.  Personally, what I would do in this situation
is read the draft, give it a day, then imagine I was going to present
the work at a conference.  What is the most valuable contribution?  How
was this achieved?  What might be good next steps?  Having come up with
your own answers to these and other important questions, now go back to
the draft and ensure it conveys what you feel is important.  Change as
much or as little as is required.  Then be prepared to work with the
other authors to arrive at a paper you all are satisfied with.
I did all the work
To be blunt: no, you didn't.
At a minimum, the student and supervisor wrote the first draft.  The
student also did data analysis; they did so, at least in part, by using
your code, but they still did that work.  Data analysis is far more
than just running a script and blindly accepting the output.  Whether
that student's contribution is precisely "equal" is unimportant, and
you're not in a position to accurately judge that anyway.
It seems to me that your collaborators are fairly acknowledging your
contributions by making you first author.
They didn't communicate enough
This part seems like a valid complaint.  But remember that there are
likely significant cultural differences, and they are probably unsure of
exactly how to collaborate with a foreign researcher.  None of the facts
I'm aware of in this situation suggest malice or disrespect.
Furthermore, improving communication can be done by either party.  If
you think there's a problem in that regard, start by expressing that (in
a constructive way).  Instead of addressing the problem, it seems like
you chose to work really hard on learning and coding, which of course
has its benefits, but in this case led to a build up of resentment.
Conclusions
For this publication, remain as first author, but be sure to earn it by
actively engaging during the writing process (points 2 and 3 of the
authorship criteria).  Try to put the science ahead of your personal
misgivings regarding your collaborators.
Going forward, regarding code sharing, either adopt a different attitude
toward sharing, or make it clear to your collaborators and employers
ahead of time that you consider your code to be personal intellectual
property--but that will likely limit your opportunities.  And when you
find yourself in a difficult work situation, don't just work harder
while ignoring the problem.

Two things: maybe you do something like this in US, though in my culture this is stealing. Secondly, I asked about dropping from the co-authorship  as a consequence of the unpleasant situation. Not whether I should be the coauthor, or first, or last, or corresponding or not.

I agree that code sharing is a good thing, but it should have been done via a polite discussion and commits to shared repository. Personal directories are personal for a reason, and should be treated with respect. You should not expect people to pro-actively embrace your work culture, if you never told them what this culture is.

@farmaceut You went to a foreign country to explicitly be in the lab of foreign researchers, and interact with them in their home environment. Your culture isn't the relevant one here. You have to expect that everyone involved is playing by the rules and norms of the country you did the internship in.

@R.M. A visitor can not expect their host to change the rules for them, but it is very normal to expect the host to communicate the lab rules in a welcoming, inviting and clear way. Ultimately, hosts are responsible for the environment they offer to their guests, and clear communication, particularly regarding mutual expectations, is a key part of a productive work environment,

@R.M. I've never come across a culture where it's acceptable to root around in someones private home directory and use the code you find in there.

Like user438383 and @DmitrySavostyanov, I've never encountered this sort of "sharing" in the US or Canada. Code in a shared repo is up for grabs and it's certainly common to ask about other work ("May I have a copy of the model you presented at lab meeting?"). However a) there's at least a pro forma request and b) the credit is shared too.

@farmaceut you're thinking as an individual. Think as part of a team. The team wrote the code. The team used the code. The team will publish the results of that work. Where is the theft?

@thelem The team did not write the code. A single individual did. If the code had been put in a shared repo or otherwise released to the group as a communal thing, then it would have been team code. Ideally, this is what should have happened, but it didn’t. The fact that the code was even related to what the team was working on is actually kind of irrelevant here: it was written by one person and put in their own, private, personal folder. Someone else gained access to this person’s private folder and took material without permission. That is theft.

Since others have already given very good responses, I wanted to try to add another view that might be helpful: From what I can gather, I believe this is an example of questionable behaviour from all parties involved.
Starting with the obvious:

Using somebody else's work without at least acknowledging it, is questionable at best. The other student should have asked if they can use your script or they should have at least acknowledged it directly to you.
When bringing it up with your supervisor, they might have had multiple reasons to be unsure about the situation or think that it is best for them not to get involved. But at the very least they should have responded and given you pointers about the appropriate behaviour and not "leave you hanging".

But I am also unsure about your behaviour in this situation:

First, did you not contact the other student about the situation? It sounds to me that you immediately went to your supervisor without trying to resolve the issue directly. That might also be a reason why your supervisor reacted distanced to the problem since it is not their job to resolve your issues for you (only to mediate and - as a last resort - intervene).
Second, I find it a bit odd, that you were working on a shared project, with a task that was shared between others and chose to keep a tool that is useful in finishing this (shared!) project just for yourself and are even offended when others deem your work useful. Again, the way they used your work is questionable but at the same time it is also questionable to treat your contribution as a disconnected task that everybody needs to reinvent on their own.
Third, I understand that you are offended that others went through your personal folder (though how personal are they if others have access to them?), I would be too. But I keep wondering how you found out that the other student copied your script to their personal folder? I am not pointing that out to fault you, but to highlight how easy it is to end up "sniffing" in other peoples folders without any bad intent. Are you sure that the other student is aware that you wrote the script yourself? Maybe they think you copied it as well or it was even supplied by your supervisor. The way most OS link previously used files at several places, the other student might not even be aware that the script originated from your personal folder.

Nevertheless I agree with the already given responses that you should not pass on a chance of a first authorship so early on in your career. If you ever choose to work in academics you will regret not being able to put that in your CV.
Maybe it helps to contact the other student and tell them about your grievances. They might not even be aware that this was an issue for you.

As someone who has spent a lot of years studying human behavior, I can tell that you are either quite young or you lack social exposure, or both.
There is nothing so wrong with what the other student did, sure he or she lacks a decent level of courtesy, but the real problem is your ego, it's why you feel entitled to the permission to use your code in a team project.
Your grievance was baseless and so was your escalation of the matter, you could have processed the matter from a positive light which means your code was worth using and be proud of yourself for distinctively contributing to the project. The student probably already told the supervisor where the code came from.
The probable reason why your supervisor did not react is because he may have had reservations about your behavior before this came up, maybe your unwillingness to share, your sense of entitlement, or your self centered approach to team work.
Don't get me wrong, I did not write this to make you feel bad, but if it does, then it's because the truth sometimes sting. And seeing how you easily get "very hurt" you need to take a chill pill and learn to take criticism.
You wrote this story here to make yourself look like the good guy, but experience has taught some of us that there are always three sides to a story, in this case, four, yours, the student's,  the supervisor's, and the truth.
Finish that project and if possible request a meeting between the 3 of you to iron out the misunderstanding. And make sure you leave your ego at home when you go for that meeting. All the best.


text:
How to ask a potential supervisor for a (challenge) project?
I intend to apply for master's positions in Computer Science and I have done some projects, especially in ML/AI/RL. I would like to ask for some guidance and even a challenge project, from a professor (or professors) who might be potential supervisors. I would like this challenge to showcase my abilities to them. I have done some projects but I think I can do better, if I have some guidance. the challenging aspect means that the professor could be more certain of my abilities in this area of expertise, and that it would be highly relevant to them, since there are many projects that are challenging, but the supervisor would not find them relevant enough.
How should I phrase such an Email? Should I include my CV and credentials? I am at a loss to find the right words to write, since this has never been done before. I would appreciate any suggestions or guidance. Thanks in advance.
Note: I am mostly targeting the US and Canada.

In which countries are you applying? An answer for Germany would be quite different from the US. And I'm not sure why you think any MS project wouldn't be a "challenge".

I edited my message to address your valid questions.

Does this answer your question? How should I phrase an important question that I need to ask a professor?

My question is more about how to phrase my question, rather than etiquette. this is not a commom request.

I wouldn't recommend making such a request at all, for the following reasons.

PhD admissions in the US (and I believe also Canada) is a departmental matter.  Attracting the interest of a particular potential supervisor, while it does still carry some weight, is not decisive in the same way that it is in the European system.

Related to the previous point, departments need to make sure that the admissions process is fair to all applicants.  If the decision to admit you were to be based on your performance on a project that was offered to you, while other applicants were not given such an opportunity, that would be a problem.

Coming up with projects for students that are challenging yet feasible is hard work.  Speaking as a professor, I might be willing to put in the effort to create such a project for a current student, but not for someone who is merely a prospective student.

While there may be some difference of opinion on this, a student's ability to succeed on short-term, artificially-posed "challenge" projects may not be a good indication of their potential for success at research.  Real research problems are much slower, messier, and less well-defined.  They often don't have such clear goals or endpoints, and those endpoints can shift as the project goes on.  It can happen that students who are great at "challenge"-type problems find themselves more frustrated by problems that are less neat and tidy.

Also, real research will involve interaction between the student, the advisor, and possibly other collaborators or members of the lab.  A purely individual project like you propose will not provide any measure of how you work in more collaborative settings.

I think that if you write such an email, no matter how carefully you phrase it, there is at least a 99% chance that the recipient will decline, and will just ask you to apply to the program through the normal process.
If you really want the ability to demonstrate your abilities in project form, I would instead suggest finding a professor at your current institution to work with.  That person can then write a letter of recommendation that will tell the committee about the quality of your work and skills.  I think that is a better way to go, even if it the topic is not 100% "relevant" to what another potential supervisor works on.


text:
As a post doc, is it OK to ask your PhD or PostDoc supervisor for advice on solo publishing?
I have a result from my Phd that I've been trying to get published somewhere. I don't know if I should ask either my Phd or PostDoc supervisor for advice (In theoretical computer science / math).
I am a bit reluctant because I'm not sure to what extent your PI is an advisor as a postdoc especially for self publication  and about the breakdown of group projects versus personal projects during a post doc  (although I did all the research during my phd).

By self-publishing you presumably mean publishing as a solo author? If so, self-publishing is not the right term to use: https://en.wikipedia.org/wiki/Self-publishing

Welcome to Academia.SE. Please ask only one question per post. I'll remove the second question for now -- you can ask it separately, but I suspect it's a duplicate of this. I'll also edit the title to reflect Adam's correct comment.

If you mean publishing as a sole author, yes, you can ask and it might be good to get their advice on whether your work is ready for "prime time". You aren't required to get that advice, however, if the work is yours alone. If you submit your work then you will get feedback from editors and reviewers. But, advice is good when it comes from people you trust.
If you mean publishing on a personal website or otherwise not involving a journal or conference, again, you don't need their advice, and you can do as you please with your own work. But, self-publishing in this sense won't advance your career much in the early stages. It will be difficult for the right people to find your work. Once you are established it isn't such a big issue if the people who want to read what you write already know how to find you.

I mean the former I initially submitted it to a conference a few months into my post doc without getting their advice got rejected now two months later I'm trying to think about what to do.  The work is mine alone that I did during my PhD which is why I initially didn't ask their advice.
Anyways how should I word such an email?

Part of your supervisor’s job is to prepare you for your future career, so you shouldn’t be afraid to have this conversation. But I’d definitely approach it in person not by email- it’s hard to mentor someone over email!

@Aant  I personally like to write conversations in email I   often have trouble speaking in person.  In this case especially because we collaborate a lot I do want to politely emphasize that this is finished work that I completed during my PhD that I'm wanting to solo publish.


text:
Does the editorial board of a journal have the ethical right to refuse publication for insulting the reviewer?
In their response to a review, the authors insult the reviewer, question their professional knowledge and the comments made regarding the finalization of the publication.
The reviewer cannot refuse them on the basis that they are insulted and requires revision of the work based on the comments they made.
The reviewer does not agree to withdraw from reviewing the submitted publication, and the authors rudely refuse to correct the comments they made.
Does the editorial board of a journal have the ethical right to refuse publication for insulting the reviewer?
08.24.2023.
Dear colleagues!
I want to inform you how this particular situation was resolved. The authors withdrew the article a few days ago in protest against the reviewer's remarks.
Thank you very much to everyone who took part in the discussion! Your thoughts helped us a lot not to make a hasty rash decision.
Best regards,
Anatolii Smikhula.

I realize that it is too late now, but I think the editor should have insisted that the authors rewrite their response, before sending it on to the referee. Referees are volunteers, they shouldn't have to put up with abuse.

The first sentence summarizes three very different types of behaviour: insulting the reviewer, questioning their professional knowledge, and questioning their comments. I think it would be good to distinguish more clearly between them.

@DavidESpeyer At least in my field, all exchange are done via a peer review system automatically, and it's not common (if exist at all) to have a period of time where the review is visible by editor/area chair but not by the reviewers, it's sent directly to the reviewers and editors at the same time.

What is the context for mentioning that the "reviewer does not agree to withdraw from reviewing"? Did the authors request that the reviewer withdraw? Or did the editor raise this possibility? Or is this journal not double-blind and there is some pre-existing conflict between the reviewer and the authors?

Betterthan Kwora. The authors, of course, do not know who the reviewer is, but I think the reviewer can guess who the authors are. Not only that, the reviewer and the authors know each other, and if they had met in an open discussion, I think the problem would have been solved in 5 minutes. The reviewer says that if the work will published in this form without his edits (he will see this work in the published issues) - it will be a shame for the journal, because one of the methods used is outdated 50 years ago.

One of the founding principles of peer review is critique of the work; ad-hominem attacks on the authors themselves are considered unethical, right?=> Feels fair to me to expect the same of authors towards reviewers & editors!  There are of course large grey areas where the criticism is worded toward the work/review but is brash enough to insult the person... but at least for literal insults I don't see ethical obligation to accept.

"the authors rudely refuse to correct the comments they made" — I think several people answered reading this as "authors refused to revise the submission according to reviewer's comments", but are you instead saying "authors refused to retract their insults"?  @Anatolii I recommend editing the question to clarify. (1) did authors make changes reviewer requested, OR argued why those wouldn't improve the paper? That's crucial to accepting/rejecting... (2) were authors informed their responses were out of line and refused to retract them? (3) did reviewer/editor/both flag them as insulting?

"The reviewer cannot refuse them on the basis that they are insulted" — I recommend rewording as "cannot" is ambiguous here. Is that a description of journal's documented policy, an ethical position taken by reviewer/editor/author, or merely a fact that the review software did not offer such an option?

The only ethic really is to abide by their own existing policies. Ideally they'd be transparent about the decision making process, e.g. stating that the tone towards the referee is part of the decision, if that is indeed the case, but I doubt that is a specific policy. I.e. I doubt they have a policy that they are required to give the author their actual internal thought transcript. They just need to officially record a reason justifiable by their policy.

A journal has no obligation to publish anything, actually, so I don't see an ethical issue. If they refuse to publish something of value then there is an opportunity cost but nothing more. The authors are free to go elsewhere.
But the reason for rejection might be much more complex than you present. In particular, a refusal to address the comments of a reviewer can, in itself, be grounds for rejection whether the authors insult the reviewer or not.
Authors demanding that they are correct and the reviewer is an idiot isn't a proper argument in determining the value of a paper.

Edited to add:
I haven't said and don't believe that there are no ethical concerns with publishing. But some commenters seem to be conflating an obligation to treat people fairly with an obligation to publish any particular paper. These things are not the same. No, you can't discriminate. Yes, you must obey the law. But a paper is a paper, not a person.
Some papers are rejected for space considerations alone. Some because the journal has a different focus. And yes, some because the authors ignore advice and insist on their view. It may even be that a few are rejected because the authors act so badly that the editors just want them to go away. It might be different if a journal had a complete monopoly, but they don't.
Even Einstein was humble about Special Relativity and commented on it at the time, in spite of the fact that it countered the "received wisdom" of the leaders in the field at the time.

A journal has no obligation to publish anything, actually, so I don't see an ethical issue. – I strongly disagree. If there were an obligation, it would be more than an ethical issue, namely a legal issue or similar. Of course, publishing decisions are governed by ethics. For example, a journal that publishes everything ignoring peer review or that only publishes articles from authors who are friends with the editors is clearly not acting ethically.

@Wrzlprmft What are you disagreeing with exactly? Buffy is just saying that there is no ethical problem with a journal rejecting any particular paper. He/she is not saying that there are no ethical issues involved in choosing what to publish.

Although I do not see any ethical issue in this instance, it's pretty easy to come up with a counterexample to the argument "A journal has no obligation to publish anything, [therefore there is no ethical issue for rejecting a paper for any reason]". For example, there is an obvious ethical issue if a journal rejects a paper solely because of the race of an author. If I misinterpreted your statement, I doubt I will be the only one to do so, so some rewording may clarify your intended meaning.

But the reason for rejection might be much more complex - Is this a more "complex" reason?  Maybe just different?

@gib: What are you disagreeing with exactly? – The logical step: no obligation ⇒ no ethical issue. Also see Vaelus’ comment. — Buffy is just saying that there is no ethical problem with a journal rejecting any particular paper. He/she is not saying that there are no ethical issues involved in choosing what to publish. – I fail to understand the contrast here. Rejecting any particular paper is a choice on what you publish. I also disagree with the first statement on its own: Any particular rejection can be unethical.

@Wrzlprmft Let me rephrase. Buffy is just saying that there is nothing ethically wrong with a journal rejecting one particular paper, since it is just a question of editorial judgment. He/she is not saying that there are no ethical issues at all involved in choosing whether to accept or reject papers in general.

@gib: So, the point (according to you) is that the act of rejecting a paper is not ethically wrong as such? I agree with that, but it’s totally unsurprising. Also, this interpretation does not explain the follow-up: “if they refuse to publish something of value”. If a journal refuses to publish something that it can recognise as valuable (i.e., meeting its publishing criteria) without good reason (such as the authors not cooperating), it is acting unethically. Also, imagine this answer to the question corresponding to Vaelus’ example (“Is it ethical to reject because of the authors’ race?”).

@gib but that's not what buffy is saying. The answer strongly implies the logical step: no obligation ⇒ no ethical issue.

But some commenters seem to be conflating an obligation to treat people fairly with an obligation to publish any particular paper. – Neither the question nor your answer, nor any of the comments mentioned fairness up to this point. I guess you are implicitly equating fairness with something else, but I cannot even make a good guess what. Also, as written in my previous comment: If you only want to say that journals are not obliged to publish absolutely everything, that’s a no-brainer not worth mentioning in the first place and does not agree with the next sentence.

@Wrzlprmft  I think Buffy's original answer and clarification are very clear and sensible. The part about "something of value" clearly meant "if they refuse to publish something that subsequently turns out to be of value, or is judged by most experts in the field to be of value." (It didn't mean they refuse to publish something despite knowing that it is of value.) I don't think Vaelus' example is relevant, as we were not talking about that kind of reason for rejection. Fairness is one aspects of ethics and I think Buffy's use of that term was clear.

@gib: Well, there clearly is a two-way communication issue here: I misunderstand Buffy and you and Buffy’s description of my criticism does not reflect my intentions. I can only guess that it involves implicit assumptions. — I don't think Vaelus' example is relevant, as we were not talking about that kind of reason for rejection. – If the reason for rejection (rudeness) is relevant to the argument, shouldn’t the paragraph in question at least mention it? — Fairness is one aspects of ethics – All the points so far equally apply if you replace ethics with fairness (and similar).

@Wrzlprmft I think if we all came back to this in six months, we would probably understand what the others were saying.

"A journal has no obligation to publish anything, actually" <- That is false. A journal has an obligation to publish in line with its scope and the process it has declared for screening and reviewing potential publications, and so as to further the knowledge of the (scientific) community it targets.

@einsupportsModeratorStrike, hmmm. The "process", of course, includes editor judgment and discretion. What you describe is a value, and an important one, not a requirement. Suppose, just for example, and somewhat common, that two papers arrive approximately simultaneously and say the same thing. Do both have to be published? Is everything in academia purely objective, measurable to the ultimate degree, with no possibility for disagreement?

@Buffy: "Do both have to be published?" <- well, I'd say they both need to be acknowledged somehow, and anyway this is a difficult situation which may even necessitate negotiation with both sets of authors. But I would say that, in your example, not publishing that same thing at all because of the timing collision is not an appropriate outcome. Now, obligations are not 100% absolute: If authors start harrassing you over the phone and with messages, cursing the reviewers and the board, not being responsive to communications etc., - then you might wash your hands of their submission I guess.

Your comment about "discrimination" reminds me of the quib  "being an asshole is not a protected group". It's frequently surprising to me how often people act downright insulting, and are then shocked to learn that the target of their abuse is not inclined to help them in the same way as they help other people. This peer review example also broadly falls under that umbrella.

@gib: I think if we all came back to this in six months, we would probably understand what the others were saying – Nope; I checked.

To dissect the ethics, it helps to first think about what ethical obligations journals have in general. The ones that I can come up with and that may be relevant to this situation are:

Avoid publishing unsound or misleading work. – This is the main point of the peer-review process. To conduct this process, it is necessary that the authors address the comments of the peer reviewers, whether they follow the suggestions or disagree with arguments. Moreover, if authors do not do this, this suggests that they are not interested in delivering sound work, which in turn reduces trust in the manuscript as a whole.

Do not impose disproportionate constraints on the authors. – Behaving in a civil manner and engaging with the arguments of the reviewers (even in disagreement) is certainly not expecting too much.

Treat all submissions equally and fairly. – If the journal rejects all manuscripts of authors behaving in a similar manner, no problem here.

Avoid harm to their volunteers. – Reviewers (and often editors) are volunteering for the journal so they should not suffer from insults. Insults to the reviewers can be avoided by the editors checking the responses, but they can also be deterred by a policy to reject any manuscript when the authors engage in such behaviour. (Mind that such a policy needs not be public in my opinion, since it can be expected by common sense.)

For whatever it’s worth, as a reviewer I have several times successfully recommended the rejection of manuscripts on account of the authors not engaging with my comments. While my educated guess in these situations was that the authors did not understand my comments (on account of not fully understanding what they were doing) and wanted to distract from that, the ethical rationale is similar to your case.

Where do ethics come into this at all?
First, any authors dumb enough to insult the reviewers are probably too dumb to write a good paper.  Sure, you can disagree with a reviewer's comments. I've been on both ends of that, many times. But you disagree politely.
Second, presumably, the authors didn't make the changes the reviewer wanted. That's grounds for refusal. I have, as a reviewer, recommended rejecting a revised MS for failure to make my suggestions.
Third, what about ethical obligations to the reviewer? I do statistical reviews for two journals. For those journals, I do many reviews; I get paid, but many reviewers don't. The journal should also be protecting the reviewers, both from a practical POV (reviewers who are treated badly may leave) and even an ethical one. You shouldn't be insulted at your work place.

Actually, with respect to your first point, brilliance and arrogance are pretty highly correlated. I've met a few such folks.

Fair enough, but the really brilliant people I know and have worked with know how to tone it down.  You tell your colleagues the reviewer is an idiot. You thank the reviewer for their time and make your counter-argument.
(I've worked with a lot of smart people, two of whom were really geniuses. Insulting the reviewers is stupid.).

Yep, I've met them also. Most of my collaborators. Maybe all, but I'd have to think about that for a while.

@PeterFlom My guess is that they got angry with the comments and then sent back a reply which was waspish in tone.  My advice to people in this situation is write whatever you want to say however you want to say it, then review it next morning you will probably realise the tone is wrong once you have calmed down.

@Buffy I have met lots of very smart mathematicians (not going to name drop them), some of them I know them very well, and actually most of them are very humble and not arrogant in the slightest.  It might be subject dependent.

Arrogance does exist, also in academics. This, together with cultural differences and non-native English speakers not hitting the right tone can IMHO lead to someone getting insulted. (When I was a student, there was an old professor who was widely known for insulting speakers - I think they even warned external speakers when he was around)

the authors didn't make the changes the reviewer wanted. That's grounds for refusal. – But that’s not the question here. Of course, it is ethical for an editor to reject a manuscript when the authors refuse to make changes the editor is convinced are important, but that would be unrelated to the insult. For example, if the authors refuse to insert a hyphen suggested by the reviewer, you wouldn’t reject the manuscript on that basis. If they insult the reviewer for suggesting this, you might.

" the authors didn't make the changes the reviewer wanted" ... wait: reviewers can in fact be wrong. That's the editor's job to decide whether the review or the reply is more convincing.

"First, any authors dumb enough to insult the reviewers are probably too dumb to write a good paper. " <- You have obviously not experienced the depths to which review quality can sink to in some journals.

It doesn't really matter how dumb the review is.

IMHO to be really successful requires a difficult balance between the self-confidence to continue with a promising line of research when the evidence so far is not shaping up the way you would like it (and dealing with criticism) AND the self-skepticism to be your own "reviewer #3" so you don't ignore evidence that doesn't support your position and you do ask yourself the difficult questions.  The latter is what stops you from "going emeritus".  However, self-confidence and arrogance are not the same thing - I'm not sure arrogance does anybody any favours, no matter how "brilliant".

@Buffy brilliance and arrogance are pretty highly correlated I suspect that is Berkson’s paradox at play. (People who are mediocre and impossible to work with don’t get tenured positions; people who are insufferable but publish stellar work get a pass.)

I think the editor has a duty to reject the paper for insulting a reviewer as they have intentionally or unintentionally gamed the peer review process by making it difficult for the reviewer to recommend rejection without apparent conflict of interest.  Personally I think there should be a zero tolerance response to insulting a reviewer or any other attempt to subvert peer review.
Anybody that insults a reviewer is shooting themselves in the foot.  The purpose of review is not just to accept or reject the paper, it is to improve the quality of the paper.  The author is getting for free the services of an expert reviewer whos time and effort they could not afford to buy (at academics usual consultancy rates) [I borrowed that from a good paper on peer review, but I can't remember the details].  If the reviewer hasn't understood your paper, it is your fault for not writing it clearly enough and you should go back and rewrite it.    If your paper still doesn't get past review, act on the feedback you have had so far and send it somewhere else.  Insulting them probably means you will continue to write papers that are hard to understand and have little impact - not a good choice!
Note sometimes we will get reviews that are just wrong, where the reviewer is wrong even though you have spelled it out as clearly as can be (in my case I remember an example where the reviewer wouldn't accept an algorithm was O(n^3) rather than O(n^4) even when I wrote out the algorithm as three nested for loops with only scalar quantities in the inner loop).  We are all only human, and the right approach is to remember that you are only human and it is only a matter of time before you submit an equally dumb review (if you haven't already).  Thinking you are incapable of writing a dumb review is the best recipe for writing one.

As an editor, you have the power to ignore reviewers or/and authors.  You can refer the authors to the many resources on the Internet on how to write a proper response.    Request for the paper to be returned to the authors, and ask them to 'fix up' their responses.  Similarly, you can do the same for reviews submitted by reviewers.  In some cases, reviews can be edited to remove unprofessional remarks before being released to authors.

Any reviewer deserves respect as they spend their little free time reading and commenting on your manuscript. The scope of this process is to improve the publication and catch mistakes that the authors have overlooked. The authors have the right to respectfully disagree with a reviewer's comment, and explain their reasons in the rebuttal letter. If the controversy cannot be resolved, the editor comes into play and takes the final decision. When this happens, the editor usually consults several experts including the other anonymous reviewers. There is always a way to appeal if you firmly believe that you have been treated unfairly. Insulting is definitely not the approach you want to pursue as you have much better alternatives to argue in your favor (provided that you have any good argument based on scientific evidences).

This post does not appear to attempt to answer the question asked.