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Add Everything to my Annotated Bibliography
A book I have been reading1, has two (complimentary) recommendations for PhD students:

Add everything you read/encounter to your reference management system
Keep a annoteded bibliography of everything you read.

They argue that (as I read it):

If you looked at a resource and found it was bad, then having a note about how useless (and why) it was will save you looking at it again, if you encount it later.
If you look at something and find it is good, then you will want it later, and want to know why it is good.
If you look at something and find it off-topic, then later you might realise a highly novel crossover between the topics.
The pain/effort of ever trying to find something you've lost because you though you didn't note its full reference down apparently haunts the authors to this day. Indeed the authors describe a article they've been looking for for decades and suggest that if a reader finds it, they would appreciate the contact.

Right now my Annotaed bibliography contrained 16 references (I've been keeping it for a week.)

13 to various papers in my topic area, or for the foundations that lead to it
1 PhD thesis in my topic area, which as well as being good work is also a example of a thesis, that i could use for considering structure
1 Article from another area that is explaining the need for manythings, including my topic, for their area
1 blog post that while I might never cite, explains a concept from my area that I was having difficulties with better than anything else I have read.

My Anotations vary from:

1 sentence summary of the papers topic
1 sentence comparason to another paper
several paragraphs explaining the content
notes saying that I don't quiet get what the paper is saying.
note saying that "This paper looks like it would explain paper X's technique but does not. Don't look here for answers on X."
A see also note
Or a combination of the above.

Is this how Annotated Bibliography's work?
It seems for several papers putting more detail would be a waste of time (Particularly the ones I am annotating with "Don't read this for X"

1 Petre, M., & Rugg, G. (2010). The unwritten rules of PhD research. McGraw-Hill International.

Yes, as far as I'm aware. I'm not really sure why you're concerned, though. It's your personal note-taking system. If it helps you, then that's all that matters. To me, this question seems a little strange. There's not some normatively correct way to write notes for yourself.

I think it is somewhat misrepresenting the concept to call it an "annotated bibliography". That term suggests something formal, organized according to a specific, prescribed structure, but really all you're doing is organizing the resources you've encountered along with any thoughts you may have on them. The resulting compilation of information is for your use only, and so you should organize it in whatever way you find most effective. I do suggest using a reference manager, since it takes a lot of the tedious work out of organizing your information, but if you honestly find a Bibtex file or note cards or stacks of paper on your desk to be better for you, by all means, go for it.
Whatever organization you use, it should have a few key features:

Starting from your notes on a paper (or other source), you should be able to easily retrieve the information needed to cite that paper.
And the other way around: starting from a paper's citation, you should be able to easily retrieve any notes you may have for that paper.
Notes should be searchable, meaning that if you remember making a note about some topic or idea, but you don't remember which reference it was attached to, you should be able to find it (the reference) without too much trouble. This probably limits you to some sort of digital database, unless you have a pretty good memory.
You should be able to access the full text of a paper that you've read, given the citation information. If your citation information is complete, this is satisfied by the ability to go on the internet and download the paper.

A bonus feature, not really essential, is the ability to share your notes on a paper with others. Some social reference managers enable doing this over the internet, or try to (assuming your collaborators also use the service), but it's more frequently accomplished by conversations in the hallway.

I am managing the BibTex file with JabRef, for reference. But JabRef is a (wonderfully) thin shell around BibTex.

It is unclear whether you have satisfied requirements of an Annotated Bibliography just yet. Combining LaTeX with BibTeX should suffice to deliver upon anything that's missing. E.g., you can use command \bibentry of package bibentry to produce a citation, after which you can include your annotation. More concretely:
\section{\bibentry{paper}}

A & B ...

\section{\bibentry{paperTwo}}

C ...

As it grows you might like to start categorising, e.g., pushing the above sections to subsections and wrapping inside \section{Cat A}. To make this more efficient from the offset, you could use macros.
Including the raw BibTeX entry is perhaps useful, which can probably be achieved with package listings.
You may end up with a rather valuable document, so design it to be public, even you may never make it so.


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Interested in doing Master's in ETH, how hard is it?
I have been researching universities and I'm really interested in pursuing Master's at ETH Zurich in Bioengineering. I noticed a plethora of information in their website and it differed from the information found in the websites of U.S. and Canadian universities (e.g. they didn't mention obtaining a supervisor before applying to the program).
I have a bachelor's degree in Biology from Canada (with a somehow low GPA). My question is, how is it hard to get into ETH? I realize it's competitive, but what is the general portfolio of attractive candidates?
I noticed they required GRE, is it absolutely necessary for students who studied in North America?

My advice would be to look up the international rankings of the specific course at ETH. Look at the universities above and below it in the rankings. This will give you an idea of how competitive the admissions process might be. FWIW, speaking as a physicist from the UK, ETH has a reputation as one of the best and certainly one of the most well-known universities in (continental) Europe.

When checking bioengineering you might also want to check ETH's sister university, the EPFL, which is doing really exciting research in bioengineering (personal opinion). More formally: EPFL's school of bioengineering recently ranked 3rd in a world-wide survey. (1st: MIT, 2nd: UCSD, 3rd: EPFL, 4th: ETH;  http://sti.epfl.ch/page-73287-en.html )

@tsttst EPFL is not a ETH' sister, but a ETH itself. https://en.wikipedia.org/wiki/ETH_Domain

While OP asked for ETHZ, @qsp is of course correct that EPFL also is an ETH. Though a former student of one of the ETHs (such as myself) would know the definitions, not only the ETHZ (from OP's question), but also the EPFL could be a good choice (which may or may not have been part of the original question).

How hard is it to get into ETH?

The Times Higher Education World University rankings lists ETH Zurich as 14th in the world for life sciences. This is below universities such as Yale (7th) and Johns Hopkins (11th) but above universities such as UCLA (18th) and University of Toronto (22nd). This ranking implies that the admissions process will be very competitive, as such a well-regarded university will only attract the best candidates.

What is the general portfolio of attractive candidates?

An ideal candidate will likely have experience of performing undergraduate research, a good degree classification or GPA and very strong reference letters. Additionally, they will have clear motivations for wanting to pursue the degree, as well as some idea of their own particular research interests. These would be included in a statement of purpose, personal statement or covering letter.

I noticed they required GRE, is it absolutely necessary for students who studied in North America?

If they state on their website that they require the GRE, then this suggests to me that this is definitely a necessary requirement. If you're still unsure, contact the admissions office of the department you'll be applying to.

(...) they didn't mention obtaining a supervisor before applying to the program.

This is not uncommon, particularly for a partially taught Master's course, where in the first semester or year you will have lecturers and coursework, allowing you to develop your interests and get to know potential supervisors, before choosing a research project and supervisor for the second semester or year.
This question asks about maximising one's chances of admission to US PhD programs and I think much of what is suggested in this answer is applicable to your situation too.
Lastly, what have you got to lose by applying? If you don't try, you'll never know.

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Open access publication fee
I am a young resercher from bangladesh. I have submitted a muniscript to SPGbiomed and the articale has been accepted. Now I have to pay the APC (article processing charge). Is there any grant who can provide the charge on behalf of the author?

Did you search for a sponsor or grant before submitting? Did you check with your supervisor? Did you check if there are other places to publish without fees?

I strongly suggest that you check out this, this, and finally this question.

Check with your professor or university librarian. They are the ones most likely to know. If they don't, assume the answer is "no".
You could conceivably ask for a waiver or discount based on your status as an author from a developing country, as well.

Some universities may be willing to pay such fees. And some journals will waive them when they fall to the author. Or at least they did in the past, though publishing has changed somewhat.

That's why - ask your university librarian.

The department head might also be good. Funding, if available, might not come via the library.

Libraries do fund APCs at least in Germany and the rest of Europe but not for predatory journals.

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How to regain lost focus?
I seem to have lost the focus that I once used to have. Few years back I was able to study for 4 hours straight but now its hardly possible for me to focus for 15 minutes. Any advice on how to regain lost focus in studying?

First, talk to a doctor, perhaps a neurologist, to be sure there is no medical reason for the change. But just aging can be a factor.

what interrupts your focus every 15min? SE mobile app...?

Get rid of your smart phone, and close all your social media accounts.

There are many possible causes, but if you think a "phone detox" is in order, this might help: https://www.nytimes.com/2019/02/23/business/cell-phone-addiction.html

I double down on Alex's advice: quit social media and any other things that can lead to lots of interruptions, and that don't require focus. It is important to drop these things even when you don't want to work: you can't expect you're brain to resist distraction when it is so prone to it on time off. This needs to be a lifestyle, not a switch.

This situation is not that uncommon and there are several approaches you might try. Few month ago I couldn't barely manage to sit down and start to read or write for my master thesis. Therefore, I also tried several of the possible approaches until one worked. The short answer is: Change something.

Plan to only study for 15 minutes straight, make a 5 minutes break and go back again to work for another 15 minutes and so on. If this works out, try to stretch the working time to 20 minutes and see how it goes.
Turn on or off distractions, e.g. I usually need distraction and noise around me to study, so I gave the opossite a try. Turn background music on or off.
Change the place where you study. Relocate yourself into a coffee shop or a park. Look for a shared workspace and try coworking.
Play games or challange yourself by setting small achievable goals and honor yourself for achieving them with whatever you like, e.g. some time off or treats. I know that this one sounds kind of weird but give it a try.
Take a longer break for several days, if you can afford this in terms of time.
Turn the internet off, i.e. no smartphone, no browser.
Try other working hours like in the morning or in the night.
Mix the material you have to study or the methods you use, like watching videos, reading, writing, summarizing, structuring, collecting.
Add physical exercises to your routine, e.g. short exercises of only a few minutes every hour (stand up, stretch, walk) and/or more challenging exercises once a day or every few days.

I'm pretty sure that there are much more options. These are only the ones I personally tried. Good luck.

The good old "change something"...

This answer has some very bad advice, and it's particularly surprising to me that it got this many up votes for both the bad advice and the lack of sources to back them up. Are there no psychologists on here? It is well known that shared workplaces are detrimental to attention. Do not reward yourself with time off, if you're in a state of flow (look it up) this is not going to help. It might be good to start off with small amounts of time (I don't know about this) but you need to really thrive for long stretches of focused work. Listening to music is double-edged look up attention residue.

Make sure you are having good sleep and rest periods, along with good nutrition, consult your phisician some times the mind could be reflecting some underlying medical condition. I also give big importance to exercise.

Compile a to-do list. You may already use such a list, but you can try to make such a list more detailed and also include some limited allowance for activities that are now taking the place of doing the work you should be doing. Simply writing down such a to-do list will force you to think about what you should be doing and why that isn't happening, which will go some way toward fixing the problem. This will then lead to a schedule for studying that will work for you.
Writing down notes at the end of the day about what you want to do the next day is also a good practice. This will make it more likely that the next day you'll stay on course working on the things you should be working on.

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Is it recommended to have a free-standing background chapter to avoid cluttering the main text with different topics?
Some general recommendations on master theses are:

a master thesis should be readable without looking up external references
a master thesis should present the topic in a way a someone with a bachelor can understand it

Based on these, I want to have a background chapter which explains particular concepts individually, out of context of the thesis problem. The reader would skip any topic they feel knowledgeable about in this chapter with the confidence that parts of the thesis problem was not skipped when they did so, because the chapter was free-standing.
I feel operating-system internals and malware analysis are not common knowledge, but I don't want to talk about them more than necessary, only the relevant parts. I could weave this into the main text, but I feel it would make it harder to read for both the inexperienced reader and also the experienced reader if at every turn I have to explain other concepts.
My advisor has allowed me to make such a chapter, but I haven’t seen any free-standing background chapters like this in any other papers. What is the consensus?

......Appendix?

I don't know if there is a broad consensus but I have seen background chapters in several papers I read recently in my field (computer engineering). If you have the space to spare (I guess a master thesis will not have a strict page limit?), this seems perfectly reasonable. Make sure to only describe things that are relevant to your research, and highlight/foreshadow how they will matter to the rest of the paper. This will also help clearly demarcate your own contribution from prior work.

I want the chapter to be free-standing, that's why I'm asking. If I removed it completely it should have exactly 0% effect on the paper. The reader would instead be forced to look up all the concepts they don't already know, which would probably be frustrating. The chapter is meant to be skipped over for the experienced reader, so I don't want anything to do with the research question in there. What I'm suggesting is different from the typical literature background chapter.

I don't see how these two goals are contradictory. For the background chapter to be removable, the other chapters can't rely on it - but that doesn't mean that in return you have to pretend within that chapter that the rest of the paper doesn't exist. Usually you can give readers a general idea of why you are bothering to teach them this subject. Something like "this resource is managed by this function in this way so if we manage to interfere with this it would present an attack surface" and then in a later chapter you talk about how you actually managed to interfere.

I think it's fine and normal (and can be done in a Ph.D. thesis as well).

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Can I present an article at a conference, if it has previously been put on arxiv and sent to a journal?
I have written a research article in the field of mathematics. This article has been put by me at https://arxiv.org/, which means now it is accessible by anyone, and also this article has been communicated to an SCIE journal (Science Citation Index Expanded journal). I want to present this article at an international conference. Will there be any ethical issues or conflicts, if I present it at a conference?

Does the conference call for papers ask for original works?  Will there be a conference proceedings volume published, and do papers in the conference proceedings volume have to be original works?  Does the journal expect exclusive publishing rights?  There are situations where it would be completely unacceptable to submit this to a conference, and others where it's normal to have conference presentations based on already published papers.

Question: what does "communicated to a journal" mean? I am not familiar with that

@Pronte Submitted for possible publication

Ok I put in my answer, short story is ask the editor because it's a coin flip

This is totally fine, don't worry about it.
In mathematics, many journals have very long reviewing cycles. It can take a few years before a submitted journal is accepted or rejected. Thus, it is common practice for mathematicians to "informally publish" papers on the arXiv.
For most purposes, in mathematics, preprints are almost as good as published papers. People cite them, present them (even at venues like the ICM!), and even use them for job applications. Many of the biggest recent advances in mathematics remain unpublished (e.g., Scholze and Clausen's condensed mathematics), even though they have drawn global attention.
In fact, giving a talk about it will generally decrease the chance that someone else scoops it, as your work will be known to at least a group of people and they will be aware that the ideas are yours.
As for ethical concerns and review conflicts, there are none. Double-blind reviewing is not really a thing in mathematics (or really, not possible at all). In principle, there are journals that are double blind, but de facto they are really just single-blind in all practicality (no reference anonymization and no reviewer opt-out for seen work, in general, as that could make it nearly impossible to find reviewers in some cases). So don't worry.

Indeed I have presented my work before even making it to the posting-a-finished-manuscript-online stage. (The time I'm working on the paper is the time I'm most excited about the topic!) I wouldn't specifically aim for this, and I've had the final version differ from what I presented in the past, but it hasn't been a big deal in the end.

@GregMartin Indeed, and some mathematicians prefer their own website over arXiv anyways.

You absolutely need to refer to the journal's guidelines!
It may change from journal to journal, e.g., in computer science it would typically not be allowed, but CS tents to give conferences a lot more relevance compared to other fields
If you're in doubt, why not asking the journal editor?

Any journal that would object can as well declare themselves closed for business.

That's simply wrong. Would, for example be ok to communicate the paper to another journal simultaneously? Of course not. - in some fields (like computer science) conference proceedings are considered on the same level as journals, so that could be considered a double submission

Presenting an article at a conference is not the same as submitting it to the proceedings of a conference.

Nope, the main concern would be your paper is rejected, and then before you can get it accepted, someone "scoops" your message without plagiarizing, thus devaluing your original contribution. If you're not worried about that, then I see no issues.
Depending on the field, it might be seen as bad taste to only present work that is currently under peer review (I would hope that you at least get past desk reject). But, if you can also point to previous work that is formally published (with non-arxiv doi), then that will give you credibility.

None of this is of concern in the field of mathematics, as far as I'm concerned.

I should add I'm an engineer and not a mathematician


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Is it Worth it to Pursue a Degree with a Criminal Record?
Recently I went to a job agency that assists people with finding jobs. My career coach encouraged pursuing higher education. The agency is government funded and they basically help people with barriers find employment. One of those barriers are criminal records. He tried explaining to me it's a great idea.
I went with the intentions of getting a job in the trades, like carpentry, but I truly don't want to do that at all. My answer to him on why I wasn't planning to receive a higher education was because I was afraid of the judgement I would get from people. And in the long run it would be a waste of time because there so many people without criminal records competing for the same positions.
I'd like some real world perspective on this. Is he wrong? Or am I the only who needs a reality check?
Here is more backstory.

I was 19 when I got arrested.
I was an alcoholic/weed user (only for a few months)
Tried to rob a bank and subway store with a demand note. I was so blackout drunk that I went to the subway. When they didn't want to give any money I went to the bank a minute walk away and tried there and they gave me money. (like $500 bucks)
Now I'm 24, finished probation last year.
Haven't reoffended or got in trouble ever since. (I spent around 10 months in prison and I'm genuinely afraid to ever go back.)

Given this backstory, there's not much leeway when it comes to justification. It shows I was irresponsible and dumb. This is also in Canada, where we have a record suspension system. From what I've looked up, people with backgrounds worse than mine (like sexual assault) have received record suspensions.
In Canada, if you commit a summary offence it takes 5 years for a record suspension but an indictable one is 10 years. You can think of summary offence as misdemeanors and indictable ones as felonies.
Given this backstory, would you think its a bad idea to pursue a degree? My plan is definitely in a STEM field. However, all of what I've seen online seemed to show none of them are friendly to past convicts.

The intention to pursue a degree is itself a rebuttal of prejudice. I do not know whose judgement you are afraid of, but as a teacher, I can assure you I neither know nor care about past criminal records of my students

I don't think that the premise that you will face more prejudice at a university than you would learning a craft is accurate. But if it were, I suppose the answer to your question would depend entirely on what you want from life. Do you want to have a shot at a career you find fulfilling, at the cost of having to overcome your fear of being judged for your past – or do you want to avoid dealing with your fear of being judged, at the cost of pursuing a career path that you do not like?

In any case, if you are worried about facing prejudice based on your criminal record, I would imagine you would get the most accurate and honest answers by directly reaching out to someone who has already faced the same problem. Most people here can only speculate about the experience of students with a criminal record.

Is your agency coach able to put you with anybody who has already taken this path? This seems like a situation where peer mentorship might be helpful.

Yes. If murderers and other people who committed crimes can publish research and make breakthroughs, no reason you can't. I indirectly know someone who has a criminal history (had way rougher of a life than mine), and now they're a PHD candidate in crim. So, if it is what you want, pursue it. Who you were is not who you must be going forward.
So long as you can do STEM work at a professional academic level, then most people won't care and won't ask, in fact.

Typically, college educated people tend a bit more to socially progressive views, which a priori includes the belief that rehabilitation should be the centerpoint of the criminal justice system. I'm not claiming that you won't be judged in academia, but I'd expect there to be less judgement, not more, compared to society overall.
In your particular case it should help that on the "stupid vs evil"-scale your crime is quite far to the "stupid"-side. If you complete a university degree, then the claim that you have substantially changed since you were 19 seems very, very convincing to me.
If I understand you correctly, then you can get a clean record in 5 years from now. Getting a university degree would take up most of that time, and if need be, you could continue for a Master's afterwards and then approach the job search with good qualifications and a clean slate.

Comments have been moved to chat; please do not continue the discussion here. Before posting a comment below this one, please review the purposes of comments. Comments that do not request clarification or suggest improvements usually belong as an answer, on [meta], or in [chat]. Further comments continuing discussion, offering opinions, or inciting debate will be removed.

To offer a different perspective: if you don't get a degree, what are you going to do?
Ultimately everyone needs to earn money to put food on the table. You having a criminal record doesn't change this. You still need to find a job somewhere, and a criminal record is almost surely going to make it harder. It's probable the employer will wonder if you can contribute positively, since the criminal record indicates you can't.
A degree helps because (especially if you do well) it demonstrates that you've left your criminal past behind. It indicates you've learned new skills. It gives you opportunities to demonstrate you can contribute positively to your university (e.g. via extracurricular activities). It also gives you the opportunity to get references from your professors. All these things will be very helpful to getting a job.
Accordingly, in a vacuum, the answer is 'yes'. The real question when it comes to pursuing a degree is: can you financially afford it?

Absolutely yes.  Many colleges welcome such students, and in my experience they are usually highly motivated. Since you are done with probation you wouldn't even need to negotiate attending night classes with your PO (something I've had to help a student with). Some colleges even have a designated person or office for dealing with any special issues. One such student even created a web page to help others.
One of the interesting things about a college degree is that people care a lot less about what happened before your degree.  So if you get good grades and good references from faculty that will help with a good job and grad school options.
One thing that I would say, is that you don't have to lead with this information when you start meeting people on campus, just like you might not reveal other personal information to people you have just met.  But also find your support system.  For example, on my campus there are some faculty members who also teach in prison or who have other relevant experiences. I always try to let people know that they are the ones to go to if you need support.


text:
Mistakenly passing a student
I miscalculated the mark of one of my students and mistakenly notified him that he passed the class. However, I noticed my mistake after some hours and fixed it, thereby resulting in him failing the class. Obviously, the student is very upset now. Should I have left the mistake and pretend I hadn't noticed it?

On the few occasions where I've accidentally mis-reported a grade, mercifully the computational error was not great, and it was within my authority to change the pass-fail line (or other relevant line) by a small-but-sufficient amount to make my initial report "become correct". Of course, I correspondingly "improved" other peoples' grades to match. That is, if we are talking about a small adjustment, I feel that the initial grade announcement should be "made true" by changing the grade line.
My rationale for this is that precise gradelines are pretty meaningless, so a small change (in favor of students) is completely harmless, and thus avoids the very-bad fallout from recanting on a grade.
If some bizarre, large computational mistake occurs, so that one has reported an "A" instead of "F", it's probably not feasible to make the better grade "true". Whatever your local policies allow/require, do be sure to manifest the same "adjustment" (and only upward, by my thinking...) for every student in the course. Large errors, and/or large changes, should probably be discussed with other people in your department so that they'll  not be "surprised" at any further fallout.

In my opinion, mistakenly passing a student is no different from mistakenly failing a student. Both are mistakes.
As humans, we all make mistakes. What should we do after we find out we made a mistake? We admit we made a mistake. we report it if necessary. We correct it if we can. We apologize to the person who was hurt by the mistake. We accept the consequences due to the mistake.
You should have a syllabus at the beginning of the semester which contains how the students will be graded. Both of your students and you as the lecturer should follow it as the game rule.
You made a calculation error which changed the student's grade by mistake. You found it out and you changed it back. I see nothing wrong here.
What you have not done is to communicate to the student to explain to him why his grade was changed from pass to fail. And you should report it to your department that you made a mistake by making a calculation error.
Yes, the student will be upset because he now learns that he failed the class. He probably would go to your department to complain. How the department would handle it is up to them. They should have an established process. You follow that process.
If the department says it’s up to the lecturer for the final decision. I would give the student the grade he deserves, that is, I would fail the student in your particular case. This is because of correctness, fairness and consistency.
For the sake of correctness, I must give the student the correct grade he should receive. For the sake of fairness, I should grade every student the same way, the way in the syllabus.
For the sake of consistency, I must consider the case: what if I mistakenly fail a student next time? Do I not change his grade from fail to pass after I find out I made a mistake?
Having said all these, I would like to tell you what I would do if I were in your shoes. I would fail the student and then send him an email to apologize and offer him help, such as giving him private sessions so that it would be easier for him to re-take the class next semester, etc. After all, you messed it up and you need to do something to clean it up.

"who was hurt by the mistake" - for that, shouldn't it first be established in the case at hand in what way, or whether at all, anyone was hurt? (Personally, I would not consider a student's disappointment about a bad grade as "being hurt".) "you messed it up" - as I stated as a comment on another answer, the student messed it up. The student did not fail because of the mistake, so I would consider it extremely unfair to provide them with any extra teaching (such as private sessions) that all the other students, who did exactly the same as the student in question, are not entitled to.

@O.R.Mapper By "hurt" I mean the student's feelings in this particular case, not his grade. Students are humans, too. You tell him he did fine, then you tell him he failed the next minute. I would feel terrible if I were the student. This is what the OP messed it up, not the student's real grade. I would give the stduent's real correct grade, but make it up for him because I hurt his feelings.

Hmm, ok. I consider it very risky, as it is hard to measure in a reliable way at what degree the student's feelings were hurt (plus, of course, nothing in the university rules usually makes any guarantees about not hurting someone's feelings), whereas providing extra lessons could easily open up the route for disciplinary action against the instructor (if they are verifiably increasing that student's chances to pass with the intention of not doing the same for any other student who asks). Depending on the circumstances, this could also call into question the validity of the student's ...

... degree. I see your reasoning and why you feel the instructor has to make up for something, though.

"both are mistakes" this statement shows a lack of ability to discern differences

I think that the best way to go is to talk with other professors/lecturers in your department to know what they would do in that case because the best thing to do may depends on the policy at your department about how to handle grades. Personnally, I would not let the student pass if he don't deserve it.

Since you didn't communicate directly with the student: You need to talk to the professor in charge of the course. Being an authority figure in the eye's of the student, more experienced with the university's policies, and in the position to make the necessary decisions to smooth things over (i.e. extra credit, or making it a take it or leave it situation), the most appropriate course of action is to just pass by your professor's office and discuss it with her/him tete-a-tete.
You sound very remorseful; empathy is good, but take it easy, these things happen, and it's a beneficial experience for all parties involved since some day you or the student may be put in similar situations.
Good luck.
EDIT: In response to O.R. Mapper (Due to comment length restrictions):
You're right, the student did have the chance and failed.
I'm only giving advice based on OP's general direction.
I've seen young professors dismissed because of a collective number of small mistakes, but also because they were consistently tough/harsh.
Hence, why I'm giving advice based on what I can infer is what the OP wants to do, but does not know how to do.
This is a course of action I've seen put to use in a variety of occasions by several professors that have the same empathetic regard towards all of their students; regardless of their academic standing.
In regards to the larger decision of being tough or lenient; that is a much larger question that only the OP can decide. I'm only working with what is apparent to us.

Um, I assumed the OP is the professor in charge of the course. Maybe the OP will clarify.

Actually yes, I am the only one in charge and unfortunately this is also my first year working as a lecturer.

Honestly, in that case, I'd go with extra-credit across the entire class. It's not fair that you modify the grades of one student without giving the rest of the class the same chance. That way, the student has the chance to prove him/herself and not skate through because of your mistake.

@HBSKan: Could you expand your answer to provide a rationale for why you deem extra-credit as a reasonable course of action? You write like that, "the student has the chance to prove him/herself", but in fact, the student already had that chance - and failed. The fact that for a few hours, the student got the incorrect notification that they had been successful does not change anything about that failure. To reiterate: The OP's mistake did not diminish the student's chances in any way, the student did not fail due to the OP's mistake. But maybe I'm missing something here?


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How to Ask a Professor to be thesis referee
I finished my thesis writing and my supervisor ask me to send it to another professor who he want to referee my thesis, I don't know this professor either he don't know me, The problem my supervisor refuse to talk with him first, just to tell him that he want him as a thesis referee.
I don't know what to say to him in the email when I send him my thesis.
Could you help me, please?

Hello Dr. Foo,
My advisor, Dr. Bar, recommended that I should contact you to referee my thesis, "Underwater Basket Weaving." I was wondering if I could meet with you to provide you the thesis and answer any questions you may about it beforehand. Please let me know if you'd be interested and, if you are, the best time and location for me to meet you. Thank you for your time.
Sincerely,
Spongebob

Be polite, be clear, be accommodating. Your professor is unlikely to introduce you two because he probably doesn't want to appear as if he's using the potential referee as a resource rather than as a colleague. Furthermore, interacting with people you don't know through e-mail and real life is commonplace in academia, so it stands to reason your supervisor would want you to try it out.

he is in another city far from me so a meeting is impossible, here's what I want to send: My name is .., I m a student
At the recommendation of my supervisor, Professor ..., I am writing to humbly request your service and expertise to serve as an ``External thesis referee’’
I attach below my thesis report.
I am grateful for your time and consideration and I have very much hope that you will be able to fulfill my request.
Yours sincerely,

Mention that your supervisor recommended that you should contact him/her to referee your theses.

Yes, cite your supervisor's recommendation as the reason.

ok I will cite the reason, thank you for your help

In addition to the suggestion provided by "Compass", one idea might be to also motivate why his professional accomplishments make him suitable as a referee for your particular thesis. For instance: "Given your experience with A, B and C... ", "I believe that your knowledge about [super specific topic D] makes you the most suited ... of my thesis regarding E"


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Difficulty being admitted to good PhD programs in the UK
Since last September I have been working hard on my applications, applied to multiple good CS departments yet none of them even wait-listed me, all rejected me, I have also got rejected informally by supervisors I approached.
Now I know I am not an established researcher in this field, I did not publish anything yet nor I have a concise experience with a certain topic but I know that I am not far off and I can pull my weight to reach the desired level by a number of the departments I applied to. The issue is that I almost all the time get unfriendly, cold treatment from professors, none of them is willing to take 5 minutes to discuss anything.
I am told that professors will always accept me even if I had average or below average marks because I am bringing my own fund for this degree yet this whole notion seems false.
My master's transcript does not look good, I have failed 2 courses and recovered but that 'F' will always look like a stain on my transcript. My bachelor's transcript is average (upper-second in UK scale).
How can I improve my chances to get into a PhD field that is not far off what I did in my master's?

@RoboKaren it looks like the OP is applying to programs in the UK, so although it's a useful link I'm not sure it's a duplicate. A few comments of my own: if you're applying to well-funded departments and professors who do not find it difficult to find finding for students, entry is indeed likely to still be competitive. If a professor wants more students, but currently has no funding for them, you have a much better shot.

@UpTight I think the question is best re-framed to focus on how to optimize admissions and things to do given that you're bringing your own funding. As far as I know, the linked question doesn't address that at all, and it's a not-too-specific question that has a broader impact. Note that questions that only apply to a specific case are much more likely to be closed, it's actually one of the custom close reasons.

I agree with @Alexandros that your reply was unnecessarily rude.  UpTight, if your communications with potential supervisors have not been 100% polite, perhaps this is one reason for their unwillingness to talk.

@UpTight: Nobody gets points for flagging questions to be closed. Right now, I would advise that you follow Roger Fan's suggestion and refocus your question.

If enough members vote to close the question as a duplicate, that usually means that (as far as we understand your question) a suitable answer can already be found on StackExchange. You can help us to help you by clearly explaining why the linked duplicate does not satisfactorily answer your problem.

Are you cold-calling professors, or working through networking? For example, it might help to contact a professor who saw your work improve during the master's degree program, and see if they can give you any advice or introductions.

You say "I know that I am not far off and I can pull my weight to reach the desired level by a number of the departments I applied to." Perhaps, but it depends on what the professors who interview you think, not what you think. Like, explaining the masters courses you got an F in will be important. How would you handle the situation differently now?  Why did you get an F (lack of effort/ability/personal/financial/other)? Does your reference back you up on that? Did you try to retake them (even if it doesn't alter your final grade)? Are they important prerequisites for the PhD?

"I am told that professors will always accept me...because I bring my own funding". This seems wrong and may come across as  presumptuous. Who on earth told you that and why do you believe them?

"I did not publish anything yet nor I have a concise experience with a certain topic" Really makes us wonder what the point of your master was. Was there a thesis? Was it entirely taught courses and no research? If it was a research masters, at least prepare a one-page printed presentation on your masters and explain what you did do and learn, instead of what you didn't learn.

You have not published anything, your masters is bad, you have two failed courses and you are still surprising that people do not consider your application? Have you thought that may be professors are looking for different kind of students?

@smci not all masters are the same in all countries. My undergrad was 3 years and my masters another extra 3, however,  publishing anything was absolutely unrealistic,  due to the nature of the course (I have 5 theoretical lessons a day + extra hours for lab work). That didn't stop me to get into a good PhD in a good British university.

@Ander Biguri: I'm very well aware that masters are not the same in all countries - I did mine in one country then had to sell my expertise in interviews in another. My point to the OP was he has to actually sell the package to interviewers in a way they might find persuasive, not just keep insisting he thinks he can do a good job despite his track record. As I said, even on a taught masters with no formal research, (and/or little relevance to the target opportunity) be able to succinctly explain what you did learn. I said lack of publications is not a showstopper, but needs explaining.

@smci Totally agree with that. In the end, a job (or PhD interview) is you selling yourself. You need to prove that you are worth.

You seem to be operating on the assumption that "I have my own funding, therefore, I can go wherever I want". That is simply not true. Taking on a graduate student is not only a matter of money, it is also a significant investment of time on the part of the advisor and believe me, at top departments, time is a more scarce and precious resource than money. If the professor does not see a reasonably good chance that this investment is going to result in a comparably good outcome (i.e., a student with high-profile publications and a strong thesis), then very likely they won't take you, even if you bring your own funding.

I am told that professors will always accept me even if I had average
  or below average marks because I am bringing my own fund for this
  degree yet this whole notion seems false.

I think you've hit the nail on the head right there. I have no personal knowledge of any PhD program in the world, outside of zero-reputation programs begging for students/diploma mills, where having mere funding will get you in. Now, maybe if you have the funding to have a new building built in your honor you could get the President/Chancellor to put in a good word for you, but I don't think that's the kind of funding we are talking about. Even then, though...
Maybe I'm reading this wrong, but when I read over your question and responses I feel a sense of feeling entitled to other people's time and resources. I have funding, admit me; I have a question, answer me; I want to be admitted, work with me; I want to meet with you, make time for me.
While we are all entitled to basic human dignity and respect, and I feel that's a very broad line, that's really it. Any good professor has many things they wish they had more time to do - work with existing students, do research, improve their program, improve their courses, reach out to the community, write a book, maybe spend more time with their kids and family or indulge in a hobby, consult, serve the University in another capacity, etc.
If a professor you approach gets the sense that you think they are obligated to work with you for any reason, that you are entitled to their time and energy, the vast majority will shut you down cold with little hesitation; for them it will be a reminder that there are indeed people who deserve their time and they wish they had more time for those people, but you aren't one of those people so go kick rocks.
So it might be time you seriously considered how you present yourself, and alter your strategy for how to approach a prospective degree program. While you feel that you can perform at the levels the department demands, they don't know that - so you need to consider how they might see you and feel, and how you can best present yourself as someone worth taking a risk on. There are a number of questions and answers on this site on how to approach prospective advisers, as well as general "open letters" from faculty around the world giving their advice on how to handle such interactions as well. I'd strongly recommend you make use of them, and I think you will have a lot more 'luck' if you take good advice to heart.

+1 for "it will be a reminder that there are indeed people who deserve their time and they wish they had more time for those people, but you aren't one of those people so go kick rocks"

OK, it's elephant-in-the-room time.
The problem is your grades. A 2.1 isn't a problem, especially if you were close to the grade boundary for a first, especially if it was from a high-ranked university. But it is the minimum level required for most UK PhD programmes. Given that, any admissions committee is going to want to see evidence of improvement through your master's but you seem to have gone backwards. That's a huge worry and makes your claim that you can "pull your weight to reach the desired level" sound hollow. Your master's was your second chance to actually reach that level; applying for a PhD is not a good way to ask for a third.
You're competing against people whose grades are well above average and you don't mention anything in your post that compensates for that. If you have really good grades for courses in the area of your prospective PhD, it would help to emphasize that in your applications. Even then, there's the worry that the "fascinated by subject X but bored and unmotivated by everything else" candidate will find that research in subject X actually requires techniques from boring subject Y to make progress, so will lose motivation and quit. And you're still competing against candidates who found the other courses boring but got good grades in them anyway.
Being able to self-fund shouldn't make a difference unless the department already wants to accept you on academic grounds.  If the department wants you and it's a choice between you and a candidate who is roughly equal but can't get funding, you win. (Or, more likely, you both get offers but only you can take yours up.)

What kind of field within computer science are you aiming at?
I have no experience with UK universities but in the Netherlands supervisors are more concerned with your ability to do independent research than grades, although without publications this would be hard to prove.
In any case, what really gets you kudos with supervisors is if you come up with research topics yourself. Look up the publications of your targeted faculty to find their interest, do some literature research in that direction to find open question and come up with an approach on how you going to make a contribution to that. Write that down in a convincing manner before you approach them. For me this has really helped to stand out after a disappointing bachelor that took me 5 instead of 3 years and a grade average that would imply an immediate rejection even for any type of honours or research master let alone PhD.
I think this would be especially useful to you having already found funding, as coming up with research topics of appropriate level is really time consuming and somewhat of a scarce resource, professors will be reluctant to provide it to you if they don't think you worth it. Although you may get paid externally you still 'occupy' a topic that may have gone to a more promising student. The topic you come up with does not have to be something you will actually be studying eventually, but it provides some proof that you supervisors will not be constanty busy pampering you in the coming years.
Also, if you got the coding skills and it is applicable to your field: one of the easiest ways to get publishable results is to implement an existing algorithm that has only been described theoretically, and get some experimental results. Just browse arxiv to get some recent papers which are more likely not to have been experimentally verified.

I'm in the same position: two fails in my MSc transcript, which makes things difficult.
I chose the path of becoming a researcher before I apply for PhDs. I am now on a research internship that will hopefully lead to a publication; I am looking for more research experience; get introduced to people in the field so that they can formally and informally give you nice references.
So basically:
- get research experience. At the beginning it's hard to get into, but the more stuff you have on your CV, the easier it is to get new positions;
- do networking;
- be VERY proactive, make yourself known;
- try to get published, obviously.
Hope it helps, good luck to both of us ;)


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Are there still journals who only publish their papers in the paper form?
As far as I can say, for the papers published nowadays, there is usually a possibility to get an electronic version of the paper. (Often it requires payment or institutional subscription, but many publishers offer the papers free of charge for older issues.)
Are there still journals, which do not offer possibility to get electronic version of the paper online and use paper version as the only way of distribution of their journal? If yes, is it the case only for small publishers? Are there differences between various disciplines? (I have experience mostly with mathematics.)

Only if there are sufficiently many answers to the main question (Are there still journals who only publish in paper form?).

We could answer better if you tell why print-only journal are important to you. Is it because you want to publish in one? or is it about how much you are missing in a literature review? About in which format you need to write an article?

@Lydia I am not sure it is any help in answering the question, but I become interested in existence of such journals because of this: I was asked to write an opinion on a paper for some journal as a referee. I did not know the journal before. I wanted to have a look on some previous papers, to see what the standards of the journal are. But I did not find any possibility to get to the articles online. (On the website, only papers in each volume were listed without any links.)

You might get better answers by asking in a mathematics-specific exchange.  Maybe pose it as a hypothetical--if you have a high speed internet connection, but are not attached to, or near, a university with a physical library, which (important) journals would you be losing access to?  ALthough even that might be too broad--the question of which journals are "important" is surely highly discipline-specific even within mathematics.  I agree that it would be interesting to know--kind of a hard one to research online since you're looking for things that aren't online....

Yes. But they are more or less irrelevant at this point. Very, very few people will bother to read them.
One journal in my own field was strictly print until a couple of years ago. They are finally included in one database, but with a five year embargo (meaning only very old articles are available electronically). Another newer journal with a similar target audience is completely open access. Obviously, the open-access journal is getting cited more, the established paper-only one less and less.
In my opinion, the aversion to making a journal available electronically is based on old-fashioned technophobia. There is no serious rationale for it. Yes, they could get more money from actual subscriptions if libraries and/or individuals were willing to pay for them, but that's simply no longer a viable model.


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Is there something I need to do on arxiv if I lose academic affiliation
When publishing on arxiv, users with recognized academic affiliations may be exempt from the endorsement process, as mentioned in arXiv primer.
Suppose that I have already published preprints on arxiv. Later, for some reason, I lose my academic affiliation. (For example, I might be between the jobs, I might leave academia.)

Do I need to inform arxiv that I no longer have an academic affiliation and should I be endorsed again before publising another preprint on arxiv?
If I change to other university/academic institution, is there something I should do on arxiv other than updating my user information?

According to http://arxiv.org/help/endorsement :

Existing submitters will not require endorsement to submit papers on topics that they've been active in.

Once you've submitted successfully, you're in for life. If you change fields (e.g. from physics to biology or something) you might have to be endorsed.
As I understand it, the endorsement system is mainly to keep cranks from uploading crankery. Leaving academia or changing affiliations won't turn a serious researcher into a crank, so I can't see any reason why arXiv would want to revoke your endorsement.


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Ref. request : book or survey about conducting experimental studies
I am currently conducting researches that are almost mainly theoretical (I am a TCS researcher gone rogue = I also work on applying theory stuff to real life problems). In the future I plan to conduct several large experimental studies involving technical experiments AND human validation of the results.
I am a neophyte in conducting this kind of very large studies involving technicalities and "humanities". I ask around and search on the web for a textbook about this matter and do not find any comprehensive resource.
So the question : do you have any pointer to a book/survey/other explaining the whole process of a large scale experimental study? It can be from any domain.

Related: a question I had asked on stats.SE: http://stats.stackexchange.com/questions/29332/a-course-in-experimental-design-for-data-miners - you might also consider looking there for answers.

Don't rely on (a) book(s) alone. Yes, there are some very good books, but it's a craft and you need expertise and general rules often have to be adapted to specific domains. You can develop that expertise, but that takes time (and resources, and trials). So I would strongly recommend to find someone who has a strong background in empirical studies in that area (publication record in peer-reviewed journals!) and try to work with that person. Second best strategy is to use the university service department (if you have it for empirical work).

I would say that the classic in experimental social science methodology is Shadish & Cook's "Experimental and Quasi-Experimental Designs for Generalized Causal Inference".
It covers various forms of experimental research design and also go into considerable detail in explaining the logic and practical steps of each.

A must-read for those interested in experimental research design. Thank You !

The best book about experimental studies you can read is surely Sidereus Nuncius by Galileo Galilei, the father of modern science.
That book was published first in 1610, but it's still very current. It explains to you how Galileo Galilei built his technologies (the telescope) and how he run up his experiments to discover new stars and planets.
Definetely, a must-read book for every scientist.

I don't question the historical relevance of the book (and I haven't read it), but I'm not sure this cover the requirements for modern-day experiment...would it be really useful for a scientist starting in the experiment domain?


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Are virtual machines good for reproducibility and open science?
Virtual machines (VMs) provide a way for scientists to package not only scientific software, but also data, external dependences, and even entire operating system configurations, facilitating a faithful and exact reproduction of a particular computing environment used to derive a particular result.
Are VMs and other container systems used in this way actually a net positive for open science? If the scientific software used to compute a result can only be replicated in a very particular computing environment, is it useful and reliable?

I like to think of VMs, containers, and the like as allowing repeatable research. I don't consider it reproducible if the results can only be repeated by having exactly the specified VM/container used by the original researcher.
That doesn't mean VMs or containers are not useful for open science; they do provide a means for people to rapidly disseminate the computing environment within which the results were produced. They also provide a point of reference should software used change at a later date which causes repeatability issues. If open source software is used it would be possible to track down what changed and why this affected the particular results.
At the very least, VMs and containers provide a good means with which to document the computing environment used to generate the published results.

Well, Yes, but I would say that wouldn't I, since I wrote the Recomputation Manifesto. about this.
While the recomputation manifesto focussed on reproducibility, I think if anything it's more important for Open Science than for raw reproducibility. Because you can see inside the experiments behind some claim, and see if they are valid experiments or not. Also - and this is a point not emphasised enough - making available experiments and code etc behind a paper in a VM (i.e. in working form) enables people to build on them and stand on the shoulders of giants.
Reproducibility by VM has been criticised as a very limited form of reproducibility, see e.g. Titus Brown's blog post. That is indeed true, but I would also respond: "Sure, but if we can't even bother to reproduce the exact experiment done, what hope is there for richer reproducibility?"
Also I would argue that even this relatively poor form of reproducibility could be critically important. For example, if we could do the physical equivalent of recomputing the exact original Cold Fusion experiments, we might know what happened to cause those results.

CERN have been running such VM-based reproducibility infrastructure for a decade (overview) and found it useful enough that they recently scaled it up in the cloud, so that may be a good place to start digging deeper.
In the biomedical field, systems like Docker have been found useful and reliable enough that they got some traction.
Given the complexity of preserving executability in the long run, I think the focus should be on ensuring that relevant code has been independently run in a somewhat contemporary manner, with results documented in a way that is suitable for long-term preservation. This is the approach chosen at places like Research Compendia, and getting this to work at scale would seem to me like a great net positive for open science.

Virtual machines are good for dissemination, and irrelevant for reproducibility.
What virtual machines facilitate is running the original researcher's software and dataset.
In terms of open science, virtual machines make it easier for others to understand the original result and derive other results. To derive other results, the full methodology used to derive the software package needs to be made available, including software sources and configuartion parameters. Virtual machines are useful in this respect because they provide a reference configuration: often the exact sequences of steps to install the system are not tracked as the system undergoes maintenance, but configuration files can be extracted from the VM image.
For reproducibility, rebuilding the original researcher's software in a different environment is not enough. There is no assurance that the original software implements what the research article claims. Reproducing the result entails writing independent software to verify the claims. Having a virtual machine available doesn't hurt the ability or desirability of writing independent software.

If nothing else I find building a Docker image of your project a good way to track all your dependencies.  Otherwise, it is easy to forget e.g about that little R function that assumes you have a particular unix tool like "imagemagick" installed on your system, or forgetting to include your latex bibliography...  here's an example: https://hub.docker.com/r/sje30/waverepo/

Yes, I'm much less worried that Docker images could be abused for "reproducibility" than VM images.


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Is listener's fees in a conference justified?
In a conference, where I am an author, I noticed that there is a substantial fees for registering as a listener for the conference.(10-30% less than the fees for professionals, students etc  but it is still on higher side).
Is this justified given that as an author I would like my work to be presented in front of as many people as possible and receive comments for the same. Is this common practice in conferences across Computer Science or any other field ?

The main reason for fees is that there is a cost for renting the auditoriums and perhaps other services (refreshments, facilities etc.). Under such circumstances all participants need to pay to support the conference. Exactly how the pricing is done differs widely but in most cases it is based on costs divided by a certain number of projected participants in different categories. There are conferences which I have attended that seem horrendously expensive and are held in luxurious places with organizing services and then there are those run by a smaller society where making a cheap efficient meeting for the members by the members is a priority. In all cases you pay just to get in.
So pricing will vary depending on venue and organiser. Depending on how the conference is organized you may be able to gain some insights into how the costs come about and then make constructive comments to the organisers on how it should change; particularly if the organisers are a membership organisation where you are a member.

Is it justified?  Well, if people pay it, then yes. If they don't, then no.
I don't think it's any more complicated than that.
Conference organisers want to earn a living by doing their job. Just as you do.
Some will seek to make as much profit as possible. The market will decide whether or not they are succesful in this.
It's just the economics of the private sector within a mixed economy. So looking for a moral dimension is like dancing about architecture.

-1 for "Is it justified? Well, if people pay it, then yes. If they don't, then no." You've confused capitalism, which is an economic system, with a moral one.

@Tom, when people make a decision to pay for something from their own resources it is a clear sign that they believe they will be better off having done so. There is a degree to which suggesting that they shouldn't have that choice is itself morally suspect. And certainly suggesting that someone else should be forced to pay their part is full of pitfalls.

@TomChurch No, I haven't. The OP has. That was rather my point. Apologies if my terseness misled you.


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Academic Name Decision
I was just wondering about academic names for publication. Why do some writers use initials then surname (for me it would be A.D.R MacLean), some their names with initials (Aidan D.R. MacLean), and some just their names (Aidan MacLean)?
What are the considerations and what would you pick if you were me?

Part of this is journal styles. Some journals do all initials + last name, and some let you pick. I am always (for example) Azor B.C. Ahai but some journals will make that A.B.C. Ahai. I don't know what fields do what. For me, Azor B.C. Ahai is my name, not Azor Ahai, so why wouldn't I use it?

There is an Azor B. Ahai out there in a different field, but that was only a minor factor for me.

The main thing is that you are consistent in the name you use. I had a colleague who signed with F. Middle Last because he personally didn't like going by his First name, and usually went by his Middle name, so signed his publications accordingly.

When I was just starting out there was nobody with the same initials and last name as me to be found in recent decades. Still the case. On the other hand, my advisor used his full first name because there was a 'namespace' collision with somebody else in a related field. Do a few searches, pick what you like, and use Orchid...

Some concerns are:

Separating academic and private life. A "John Richard Doe" who publishes academic work as "J. R. Doe" might not want other academics to find their private Instagram account "John Doe" where they mostly post drunk party pictures.
Avoiding confusion. When there are already a "J. R. Doe", a "John Doe" and a "John R. Doe" doing related work, then this person might decide to publish under the name "Richard Doe" to avoid getting mistaken for one of their peers.
Personal preference regarding what "sounds better"

Some of my female colleagues prefer to publish as J.R. Doe rather than Jane Doe, to avoid their gender being immediately obvious to readers.

A male colleague of mine uses his initials out of solidarity with female colleagues. He doesn't want to take advantage of readers or reviewers knowing he's male from his name

I would not worry about it too much.
It is largely personal preference about how you want to be professional known.
Also, I have had co-authors use nicknames and not include my middle initial.
None of these have impacted my career.
Simply setup an ORCID and use that number to identify your publications.
Other answers highlight the benefit of ORCIDs (e.g., https://academia.stackexchange.com/a/100500/33210).
Other answers such as this one were more important prior ORCID and other tools like it that allow you to "claim" your publications (other tools include Google Scholar, Scopus, and Research Gate). Personally, if you only use one tool to link your publications, I suggest ORCID because it's a non-profit.

After you start publishing papers and books, they will appear in databases (like NASA/ADS). Your colleagues will, from time to time, look up your publication profile in these databases. (E.g., when a journal editor gets a manuscript, (s)he starts checking who is acknowledged in this field and can be approached with a request to referee this work.) If your name is, say, J.Smith, it will be difficult to single out your publications, because there are many J.Smith`s. So, you better publish under your full name, Jane Beverly Smith.


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Should I accept offers from universities in two different countries to account for any possible uncertainties in getting visas?
I’ve received an offer letter for B.Sc Computer Science from San Francisco State University (CA, USA) and Wilfrid Laurier University (ON, Canada). After accepting the offer letter from SFSU, I also applied for a US visa. However, in case of uncertainties with the US visa, will it be favourable to also accept Wilfrid Laurier University’s offer letter and apply for a Canadian visa later?
(both the offer letters are for the Fall 2022 semester)

Favorable for whom? Do you expect visa issues? Have you discussed with the institutions?

@JonCuster I do not expect any issues, but there are always some uncertainties.

We cannot predict the outcome of your visa.  If you break your agreement with SFSU you loose your $100 deposit.

Accepting two offers when you can in reality only accept one is a guaranteed way to burn bridges at at least one of the two places. I don't see an upside for you doing this.
I am not an expert on the US visa system so I do not know how likely you are to run into problems, so take my next sentence with a grain of salt. From what I understand talking to people I have worked with, if you have accepted an offer from an American university, you should be able to get the visa. I don't think you would get an offer if the university thought there was a large chance you could not get the visa. There should also be an international office at the university you can contact to get more information about this; you can always ask them how often visa applications from your country are rejected and for what reasons.
There is always an option to apply again next year to universities outside the US if the visa process does not work out.

It's undergraduate admissions.  There are no bridges to burn.

"if you have accepted an offer from an American university, you should be able to get the visa."  That's not plausible.  "I don't think you would get an offer if the university thought there was a large chance you could not get the visa."  The university does not know.

@AnonymousPhysicist can you please add a detailed answer?

@RehmatSinghGill For what it's worth I think the best advice you will get about the visa is by contacting the international office at the university that made you the offer and the department who made you the offer. Explain your situation and any specific details that might be relevant. I don't think anyone here on the internet can do a better job. My answer is just meant to be kind of generic, and assumes you are from a country where students regularly are admitted to this university and that you don't have any special circumstances. But -- do not accept two offers intending to turn down one.


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I want to change PhD programs because the city is unsafe, how do I approach this?
I am an international grad student in a middle-tier mathematics PhD program in the USA. I am still in my first year. Soon after joining the program I realized there is no active faculty who works close to my interest. Also I don't like the city, and one of the reasons is there is repeated incidents of crime nearby
Now I know it does not make a good impression to change PhD programs but I don't want to stay in this place for obvious safety reasons. So I want to apply to other PhD programs in the next cycle. I have good relationships with my professors and I don't want to make the impression that I am taking advantage of the program.
As I need recommendation from my current program to reapply, can anyone suggest what should I do in the meantime to make my profile stronger? Also should I tell my letter writers now that I intend to leave?

I'm sorry to hear that, C.g. I edited your question to give it a more descriptive title and make the English more idiomatic. I think though, that your two questions are a bit unrelated. We prefer to answer one question per post, so I'd suggest you'd focus on the second one, since the answer to the first isn't really affected by your situation (at least from my POV).

Does this answer your question? Is transferring to another university an option for an unhappy PhD student?

Also see linked questions from ^.

It seems very unusual to want to leave grad school in the US because the city is unsafe. To me, this suggests that: (1) you have a very strange decision making process, or (2) you were the victim of a crime and are having some distress as a result, or (3) this is a "convenient" reason to justify leaving, but not the actual reason you want to leave. In cases #2 or #3, you may prefer not to share all the details here, and that's fine; I just mention this because others (in real life) may have similar reactions if you frame your decision as you did here.

@cag51 really? To me it seems unusual to want to be in a graduate program at an unsafe location. I have visited several highly ranked US universities where my local hosts gave me stern warnings not to stray from a small area around the campus due to crime and safety issues. (In one case these warnings were voiced at an official orientation talk at the beginning of a conference, where the organizer stated euphemistically that since we are in an “urban campus” certain precautions are warranted). This was a huge turn-off for me personally. And I’m a person with a fairly high tolerance for risk.

Sure, I can understand taking this into account when making your decision of where to attend. But leaving in the middle, when you like the program and everything else is going well? I would suspect that there are additional undisclosed reasons. For this question, that's fine, the reasons are irrelevant. But I hope OP is making a well-reasoned decision and is able to communicate that reasoning to people they want to maintain good relationships with.

@cag51- Its is entirely possible that OP didn't know/comprehend the magnitude of crime before joining and weren't suitably warned. Have you come across cases where such concerns were misused for convenience?

You may want to do some research before you choose another program. Many US University campuses are in unsafe places, unfortunately (there are several reasons for that). And do not go to the University if there is nobody to work with. Your explanation of the desire to change is quite valid.

I agree with the others about doing your research before applying and being candid with your advisors. If you want to go somewhere else, you have to tell them and hopefully, they will be kind and supportive. The best way to ensure their kindness is by giving them a warning and having open communication. If you are not you will know you have made the right decision.
Personally, my advisor has told me that if I end up hating it at my current institution I could leave after my master's (I am in a masters-PhD combined program) and his kindness is honestly what made me choose him as a professor in the first place.

There is no need to agonise over the strategy to do this --- just be candid with your supervisors and seek a recommendation based on your existing work.  If you are not enjoying yourself in the city, cannot find an appropriate faculty member to supervise your topic of interest, and are anxious over crime problems, these are perfectly good reasons to move to another program in another city.  Your present supervisors (or the graduate program director if you don't yet have supervisors) should be able to give you some kind of basic reference based on your work in the program so far (e.g., have you been doing required things, completing milestones, etc.).


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Is it bad form to cold-email professors to do post-baccalaureate research?
Suppose I am interested in doing more research in a particular area in order to strengthen PhD applications, but I have just finished my undergrad degree.
Is it considered bad form to cold-email professors who say on their websites that they are accepting undergrad researchers in their lab asking to do research this summer/next year, though I’m no longer an undergrad?

What does "cold email" mean?

Its like the email version of 'cold-call' - meaning to initiate contact with someone who does not already know you.

What is bacc? ----------

If you are not an undergrad, you cannot be hired as an undergrad. Most undergrads are unpaid (don't work for free!), and of those that are paid, many are paid using funds that can only go to enrolled students (the percentage varies by field). Besides, most school-year undergrad positions are on the order of 10 hours/week, although some summer positions can be full-time.
According to @J.., sometimes new grads can be hired for full-time summer internships in a transitory capacity. Usually, this would be people continuing to work in labs they have already started with, or professors hiring someone they're familiar with. I find it unlikely a professor would hire someone new for only a few months, and if the opportunities were available, they'd likely to be posted.
Now that you have your degree, apply for jobs.
Cold emailing isn't a good strategy for that (especially not in the current climate), mostly because budgets usually don't allow to hire as many people as you need, much less to have money laying around waiting for someone to ask for it. Apply for posted jobs and work your network.

Great, thanks for this information. Supposing I did get a full time job elsewhere, though, would professors have a problem with me offering to do unpaid work (say 10 hr/wk) just for the experience/to get my name on a paper?

@Chad Some immoral professors would be happy to let you labor for no compensation. Don't do it. You should absolutely not offer to work for free because it devalues the jobs you should be applying for (why pay $45k+benefits for an RA when I can get someone wealthy enough to work for free), and forces out undergraduates who should be taking those positions. In some places, it may be illegal.

This isn't always true.  Lots of professors will pick up undergrads for four month (term) employment over summer months for research project/work-experience type positions.  It's not uncommon for these to be full-time and paid.

@J... The OP has graduated, but it's a fair point about summer programs.

@AzorAhai True, but I've also known new grads to pick up such positions, either while finalizing grad school arangements (or as a prelude-to with same prof), or just for a few months of experience while they are job hunting.

@J... Gotcha, guess I haven't heard of that practice, but I'll note it.

I think that it is fine for OP to offer to volunteer for positions as long as they have made the free, informed, and consensual decision to do so. Unfortunately, the world is competitive in any market place. OP will need to compete against others who might have been in a more privileged position to do undergraduate research. Whether it's "immoral" for a prof to allow someone to get volunteer experience is, I don't believe, relevant to the OP getting the experience they want. Of course, if one does volunteer, they must set their own boundaries to avoid being taken advantage of.

@GrayLiterature I disagree, for the reasons I stated.

@AzorAhai To be fair, in such cases it's also been my experience that the professors in question typically post these positions when they're available, so it's unlikely to be something that comes out of a cold-call.  If the professor has positions like this available they will typically be made public and OP will simply make a bad impression if they've not bothered to discover this for themselves.

I actually think 'cold calling' is not so bad if you do it the right way. Actually, for most researchers it is vital. Let me explain by talking about some right and wrong ways to 'cold call' academics:
The wrong way

Write poorly worded or grammatically incorrect pleas for supervision/experience/paid work. EVERY academic and researcher gets these - and we all hate them;
Get their name/title/role/institution/department/gender wrong. Speaks for itself, doesn't it?;
Being too transactional (i.e. I need work/I need money/I need experience/I need supervision/gimme this/gimme that/ etc). It may sound harsh, but they have their own problems to deal with! They typically don't really care less, particularly if they don't know you from a bar of soap.

The right way
Some of these may sound obvious, but I'm pretty confident that if you manage to do at least more than one of the following you will get a positive response inviting you to follow-up every time:

Focus on your interests. For example: They work in a lab doing X. Hey guess what, you wrote a paper on X in second year and got a distinction and you have maintained an interest in X ever since. You are keen to build on... (etc etc). You'd really like to LEARN MORE about X, Y and Z and are considering working toward a PhD in that area;
Demonstrate your knowledge. For example: 'I see you are working with X proteins [or whatever], I'm really interested in how the Z process works with those...';
Make an effort. Show that you're willing to make an effort to develop 1 and 2 above. This may involve you travelling some distance for a tour of the lab or offering to meet/zoom/skype in a place/time/platform that suits their crazy schedule rather than yours.

[Bonus tips]

Flatter their ego.* Yea I know. You shouldn't have to. But these people have probably dedicated their lives to what they are doing. A little recognition from time to time wouldn't be so bad, right? Trust me - this one works. Young, old, male, female, intersex, etc; EVERY academic will read and respond to your email if you tell them that you have read and enjoyed their paper on Using Z Processes with X Proteins [or whatever].
[* Edit - note sensible comments re going over the top with flattery below]
Use conferences. This is tricky during a pandemic - but if you can get yourself to a conference or seminar of some kind where you know they will be there then strike when they are vulnerable! Time your move during breaks when they are heading for the pastries and NOT in the middle of a conversation where they are securing a deal for more funding for their lab. Give it a try... it works ;-)

Why do these things work?
Here's my take on at least a few reasons why these work:

They were in your situation once too, probably;
These days academics are always on the lookout for good students. More students means they can grow their lab and get more PhD completions over time, which counts as a performance metric for them;
Cheap labour. Let's face it, that's definitely part of the equation. If you look like you can be an asset for their research project and you won't cost a fortune in terms of time, funding, training or stress, then you are basically in.

Anyway, try these out and see how you go.  And good luck!

Some good advice: wrong/ and right way 1-3. Some bad one: 4! Don't flatter their ego. A smart prof can distinguish whether you are genuinely interested in their topic (good!) or just padding vacuous compliments to flatter them (bad!). 5. is so-so. Conferences are good to meet people - again interest in topics matters most. When the prof heads for the pastries, do not stand between them and the food, it's almost as bad as standing between them and their funding; profs do not eat as much as PhD students, so if they want to eat, they are hungry ;-)

Agree with most of this, but - be very careful with the degree of flattery on the first email. No more than would justify your reaching out to them, e.g. "I understand one of your research foci is XYZ" is good, "I understand you are one of the prominent researchers of XYZ" or is acceptable flattery, but don't go beyond this level (e.g. "supreme authority", "world's leading" etc.)

I agree with both of these comments - its actually worse if you overdo #4 above. Handle with care!

Some professors have money available to hire recent grads as research assistants, but this is a bit more difficult than hiring an enrolled undergrad (as other answers mention, hiring students at the university/college is cheaper and requires less administrative work).
Whether cold emailing is bad form is pretty subjective, and I think it is not. Keep your email short (professors are busy), polite, and clear about what your interests/timescales/constraints are (are you interested in working on research full time? are you flexible about being paid?). If they don't have something available for you, thank them for their consideration and move on.

-1 Do not be "flexible about being paid."


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What does "All deadlines are: 11:59 PM UTC-12:00" mean?
For example, what would this be for July 1st, 2020, in New York (Eastern Time)?
Is UTC-12 the same as AoE ("Anywhere on Earth")?

there you go https://www.thetimezoneconverter.com/

I feel this is off-topic as it has nothing to do with academia and everything to do with understanding timezones (i.e. programming on a boat).

@Conrad On the other hand, it's a deadline format that people in academia might encounter more often than others, given the international nature of most conferences/submissions.

Merged answers from What does UTC-12 timezone mean for a submission deadline? to here.

Does this answer your question? What does UTC-12 timezone mean for a submission deadline?

"UTC-12" is a timezone 12 hours behind Coordinated Universal Time, which is (more or less) the time in Greenwich, UK. Nobody actually lives there, though.
A day is 24 hours, and the Earth is divided into 27 major timezones from UTC-12 to UTC+141, with the UK in the middle(ish). Therefore, someone in UTC-12 is the very last person to reach a time. At the time it is 12:01 AM UTC-12, it's 12:01 PM UTC+0, and 11:01 PM UTC+11.
So by setting the submission deadline to 11:59 PM UTC-12 on a given day, it ensures that anyone anywhere in the world who submits on the appropriate day will be on time. Hence, "anywhere on Earth."
New York is UTC-4 during the summer, which means the deadline is 7:59 AM the following day.

1: It would seem like only 24 timezones would be necessary, but a few regions chose to move to UTC+13 and UTC+14 for their own reasons. Someone in UTC+13 is 25 hours ahead of UTC-12 (so 1:01 AM the next day). The details aren't important, but in case you'd like to do your own reading.

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

UTC-12 means that it's 12 hours behind UTC. That's the maximum distance in our 24 hour day clock. So UTC-12 is the timezone where calendars end.
That's probably the motivation behind using it as a deadline. For example, if the deadline is January 31st UTC-12, then as soon as it's not January anymore anywhere, the deadline has passed.

Is UTC-12 the same as AoE ("Anywhere on Earth")?

AoE could be interpreted to apply daylight savings time. UTC never applies daylight savings time.

note that while UTC-12 is the maximum distance in that direction, going the other direction there is an UTC+14 timezone, meaning there's actually a 26 hour difference between the two ends of the timezone map

@SztupY I didn't know that, but reading about it it's pretty interesting.

(+1) For those of us more geographically minded, this time zone is in the central Pacific, and is two hours behind Honolulu Standard Time.

Since UTC-12:00 is the westernmost/'latest' timezone on Earth, this is indeed another way to denote 'Anywhere on Earth'.
Eastern Standard Time (EST) is not used in New York on July 1st; instead, they use Eastern Daylight Time which is UTC-04:00, so July 1st 11:59PM UTC-12:00 is July 2nd 7:59AM EDT.

I learned this in doing my own research: "Latest" may be confusing; as the time in UTC-12 is the earliest within a given day (see how Wiki refers to UTC+14: https://en.wikipedia.org/wiki/UTC%2B14:00).

That's why it is in quotes; 'latest' as in 'the last timezone to reach a certain date/time'.

Note that Wikipedia refers to both UTC+14 and UTC-12 as the earliest and latest timezone: https://en.wikipedia.org/wiki/UTC%E2%88%9212:00 ...


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How to contact someone asking them to be a co-supervisor
I just finished my master's recently and I wish to do a PhD. I chose to continue working with my supervisor during the master's thesis, but I want to work on it with another professor as a co-supervisor who I met during my Erasmus stay in another university.
How can I contact the co-supervisor? Must I send a CV, a letter of motivation and a copy of my master's thesis attached or just an email asking for the co-supervising?

Please explain a bit more clearly what you mean with "I met". Are they aware of who you are? Do they know you enough to have a good impression of you?

Why do you want a co-supervisor in general, and why would this specific co-supervisor be an asset to you and your primary supervisor?

@lighthousekeeper We met in a seminar where we talked a bit about my work and studies in general. That's why I thought to send my CV so that he knows me better.

@JonCuster I want this co-supervisor because it's useful and enriching for my subject and my work.

It would be a mistake to do this without the happy approval of your "current" supervisor. You need to discuss this with them if you haven't already.
And, the best way to bring the other person in to the process is to have the supervisor contact the other person. They can work out between them what they need to see about your history.
Of course, your supervisor might suggest that you make the contact. They will probably suggest how to do it properly.
However, a masters thesis and a cv in a first email isn't going to be helpful. It is too much information. First ask about the possibility and offer to send anything they need to help make a decision. You may also need to introduce the two people together, if they don't already know one another.

Thank you! It's helpful for me.