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Asking PI I barely interacted with for letter of rec?
I'm a rising senior and will be applying to PhD programs this fall. I'm wrapping up a research project I was doing this summer at another school (basically an REU-like program) and the school is at the top of my field. I learned so much this summer and was able to accomplish a lot with my project. I was mentored by staff scientists and basically worked with them the entire summer. The PI of the lab is very hands off and hard to pin down. I met with him once in the beginning of the summer and have a meeting with him this week as I finish up. I was planning on asking him to write me a letter of rec then. The staff scientists said that what will probably end up happening is they write it and he'll sign it/co-sign it, but I need to ask him myself. I'm just a bit nervous/paranoid he'll say no so if anyone has any advice/words of encouragement, I'd appreciate it.
I understand that letters should come from people who know you well and I plan on my other two to be from professors that I am close with at my school. Given that I attend a school where there are limited research opportunities, I consider it to be integral that I get a letter out of this experience that speaks to my capabilities as a researcher. Based on the advice from the career office at this visiting school and other lab members, the letter should be coming from the PI/professor. The scientists I work with will contribute to a strong recommendation - they themselves acknowledge that it just wouldn't be as valuable coming from them. I guess my nervousness has to do more with the fact that here with big labs and big name PI's everyone says this situation/procedure is the norm and coming from a smaller school I'm not as used to it.

I've said it before, I'll say it again: writing a letter of recommendation for a student you know well is easy, it's a treat, and the letter you write can be GOOD. Writing a letter for a student you barely know is difficult, time consuming, and ends up sounding generic and forced. As someone who reads recommendation letters, it is very clear when the writer doesn't know the student.
I don't think them saying "no" is your problem here. See, even if they say yes, if you have this person who doesn't know you write your letter of recommendation you risk it sounding like a form letter which, in turn, won't distinguish you from the pile of other applicants. Unless the underling that they have write the letter really knows you and your potential, the letter is unlikely to be great. The box will be ticked but it won't be a meaningful tick.

I think this is a good answer, but I'm curious as to what you would recommend the OP to do in their situation?

It sounds like the "underling" does know the OP well. "I was mentored by staff scientists and basically worked with them the entire summer... The staff scientists said that what will probably end up happening is they write it and he'll sign it/co-sign it."

I'd recommend getting a recommendation from someone who knows them well, the staff scientist perhaps. The "underling", with the co-sign if absolutely needed.

I'll contribute an answer from the point of view of the person who works with the undergrad summer research students. I write letters in a similar way (I write the letter, since I am the one who worked with the student and can write a good, detailed, letter, and the professor who heads the lab co-signs it, putting his reputation and experience behind it.) I will try to demystify this process for you:
When a student asks the professor for a letter of recommendation (usually by email), he forwards the email to me with something like:

Remind me about this student, what did he/she do?

Then I'll write back, reminding him who the student was, what the student's project was, and if the student was a strong student, and he will write back,

OK, write the letter and I will sign it too.

This is a totally routine interaction and it would never occur to him to say "no" (unless I said I couldn't recommend the student, having worked with them. And if I couldn't recommend a student, I wouldn't tell them to ask the professor for a letter of recommendation!)
I think you are worrying for nothing. If the staff scientists said to you, "Ask the PI for a letter, what will end up happening is that we will write it and he will sign it", you can expect an interaction like the one above will take place, and you have no reason to think the PI will say no.


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Can I allow my personal life to influence where I do my PhD?
I am about to become a Ph.D student in mathematics. I am having some doubts about where I should do my Ph.D and I would appreciate some advice, or anything really.

I could do research with a very competent professor that is internationally well-known and is also very interested in me succeeding, having helped me with much already. He is also a really kind person. The area he is working in is one of the most fascinating areas in all of mathematics to me. However, it is in a different city from where I live now. As I live now, I have a really good apartment and a girlfriend too who lives here. She would be OK if I moved, although a bit sad. I am afraid of moving to a new city, and more than that, also somewhat scared that if I am not as good as my advisor belives me to be, it will all go terribly wrong.
I could do research where I live. However, the advisors are not as competent as he is, nor as interested in me (so far, I am not their student yet). Further, the areas are not as fascinating (although very fascinating!). I could continue with living my life as of now.

So, what should I think about regarding these choices when it comes to making a future career? I am a bit vague here, since I want general advice to think about.

You've mentioned a number of considerations about what to look for when choosing a Ph.D program, but I'm not sure that any of us can help you make your decision. For some people, going to a prestigious institution is worth it and helps them. For others, that sacrifice of friends and family is too much for them to bear. You know yourself better than the rest of us!

If your girlfriend is willing to move with you, then you've already conquered the biggest barrier to a more challenging and rewarding situation.

So I'm just some random stranger on the internet, but you asked for advice, so here it is.  Given only the information in your post, I think you have a difficult choice ahead of you:
Move or propose.
From a strictly professional standpoint, you make a very strong argument for moving.  Having a more competent and more supportive advisor, and working in a field that excites you more, will have a tremendous impact on your several-decades-long mathematics career.    As Dan C writes elsewhere, if you want to do math for a living, you should enroll in the strongest PhD program you can.  (I'm assuming here that you actually want a career in mathematics; otherwise, getting a PhD in mathematics is kind of stupid.)
From a personal standpoint, you make a much weaker case for staying put.  It's just another city; you'll be fine.  You can always find another apartment.  Do not listen to the Impostor Syndrome; everyone is afraid that they're not good enough.  Your girlfriend is OK with your moving.  There's some possibility that your current relationship won't survive the move, but the fact that you call her your girlfriend, and not your wife or even fiancée, suggests that you don't really think of the relationship as permanent anyway.
Yeah, I know, that's harsh.  And maybe I'm totally off-base.  Maybe your current relationship really is more important to you than the rest of your professional life.  If that's true, tell her so.
Who knows?  Maybe you can do both!
But whatever you decide, don't base your decision on fear.  Instead, ask yourself: What do you really want?  What really matters to you?  Fear of change and Impostor Syndrome are completely natural, and far more common than most people think, but they're just voices in your head.  Letting them control your decisions is not healthy.  You have people in your life who believe in you, who support you, who want you to succeed and be happy, and who know you far better than Some Random Stranger on the Internet—listen to them!

+1 for not letting fear dominate your decision. And when it comes to academic topics, the people on academia are far from random, they are strangers to the OP though.

To be fair, the OP doesn't make clear whether the move is so far away that the choice does become "move or propose". After all, people do maintain long-distance relationships (especially if it's not that long)

@Suresh  Yep, my wife and I did that for five years.  I do not recommend it.

I did for three :)

It's hard for anyone to tell you what to do. Ultimately your decision comes from within your own blend of views, feelings, and priorities.
But there are common patterns of thought that we've all encountered, and it helps to understand how others have dealt with them.
Fear of change.
This is a very natural feeling to have. Whenever you're thinking of moving out of a comfort zone into a new situation, it's easy to focus on the fear of the unknown, because there's nothing else to focus on. In  your case, there's fear of the move to a new city, and fear of how this will affect your relationships.
One way of addressing this is to try and find out more about the new situation and how the change will affect you.

where will you live ?
what will your work schedule be like ?
what will your office look like ?
how will you and your girlfriend manage the distance in the relationship ?

and so on. Right now, your ability to make a decision is clouded by uncertainty. Thinking concretely about these questions will help make the new scenario more real, and you'll be in a better position to evaluate whether the move is worth it or not.
Imposter syndrome
The other fear you've expressed is that "your advisor will discover that you're not as smart as you/they thought". This feeling is called the Imposter Syndrome and is typically associated with academics or those preparing for advanced study. Ironically, your feelings of inadequacy might qualify you already !
But the imposter syndrome is just that: it's a psychological filter that's caused by a focus on negatives and a dismissal of positives. It sounds like your advisor-to-be is very supportive and wants you to succeed. While it's possible that you might find a Ph.D is not for you, it's also entirely possible that you'll do very well for yourself. What will make the difference is not some fate stamped on your head the day you were born, but the work you do, the effort you put in, lots of luck, and many things that are beyond your control.
Here again, getting more information can help - if you haven't already done this, maybe you can talk with the prospective advisor and map out what the first year or so of your Ph.D might look like.
Ultimately whether or not you choose to move depends on many factors, and there's no wrong answer here. But it's helpful to recognize where some of the thoughts you express might be coming from.

I can't make a definitive recommendation one way or the other here. What I can tell you is that you need to consider the following:

Don't change jobs to get away from your present situation. Running and hiding somewhere else is neither productive nor psychologically healthy. (In other words, make sure you are going to another opportunity, not walking away from a situation—although it doesn't sound like that this is an issue here.)
Is the cost of what you're leaving behind worth what you're gaining? You seem to like living where you are. Is the opportunity for you to work with the big-name advisor important enough for you to give that up?
Before beginning a PhD, make sure that it's something you really want to do. Is the project you will be working on something that fascinates you enough that, even if your work doesn't go well for a long time, you'd still want to go in day after day to get things back on track?

Let me turn the first two points on their heads.  Don't stay put out of fear. Is the cost of what you'd give up by staying worth what you'd gain by moving?

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How are British PhDs looked upon in the United States?
Assuming I got a PhD in Computer Science from Oxford or Cambridge University, how would that affect my chances at becoming a professor at a top US university versus getting a PhD from a top US institution? Assuming also that I had US citizenship?

Career development all the way to tenure is not a given fact, just because you got a PhD. Let alone a professorship at a "top" uni. If I were in your shoes I'd be more worried with put the hours in, doing the hard work... then when you have a solid profile, don't let people use where you come from or where you got your PhD as an excuse to come in between you and your career goals.

In what (sub)field?

This is a bit orthogonal to the OP's real question, but going from the US to the UK for a Ph.D. is a often a terrible idea unless you get a masters first.  The US and UK systems are not set up to be compatible; typically British schools expect students to get Ph.D.s much faster than in the US in a way that US BA's don't prepare students for (and from anecdotal evidence, British BA's often don't either).

Sound advice from @BenWebster, I concur. I also think it's a terrible idea to go from the UK to the US for postgraduate study, in general. Not only are the two systems virtually incompatible, but there's a lot of mutual ignorance between the two. (Sadly, even more ignorance of the British system in the US, I would say.)

I am an American who earned a Ph.D. at Cambridge University. A degree from Cambridge or Oxford is well-respected in the US - I was warned to avoid other UK universities as they are not as well known in the States.  The one caveat is that all of your network for post-docs and jobs will be in the UK, not in the US. It was an amazing experience though so I would not want to discourage you!

I would like to add that the two specific universities mentioned are largely regarded in the US as on par with the Ivy League.

Upper Ivy league, that is (Harvard, Yale, Princeton). The converse is more or less true as well.

In mathematics, I would say that British Ph.D.s are very well respected in the U.S.A.  Probably more so than many US universities.  The US citizenship is a plus, because it means that the university can avoid the hassle of H1 visas and Green Cards.  But a major research university will probably not reject you if you don't have US Citizenship.

Just wanted to point out since no one else has yet. US PhDs are about 5 years, and UK ones are 3-3.5. Given this factor alone, US PhD holders are slightly more likely to have more publications and more teaching experience, which can make them competitive in the UK market. Inversely, a UK PhD holder may (depending on their work) have less papers/less teaching experience than the [presumably American] competitors for US postdocs. Again it depends on the person and the university, but it is a factor.

My guess is that it the effect on academic employment would be relatively small compared to other factors, as pedigree is typically neither necessary nor sufficient for obtaining employment. Arguably, department reputation will matter more, but what you do while you are there will matter far more than that.
It might be helpful to your decision to note that several UK universities are very well respected in the US and elsewhere: Imperial, UCL, KCL, Edinburgh, Manchester, Sheffield, to name a few. Are Oxford and Cambridge the only UK institutions with respected CS departments?

I think this depends a lot on your field; in math, I think Imperial would be seen as comparable to Oxford and Cambridge, but obviously, that's quite different in the humanities where Imperial doesn't even have programs.  The others you listed I wouldn't put up with the top US schools, but would look better on the CV than plenty of respectable US schools.

For CS, Imperial tends to be seen as somewhat better than Oxford. But generally the name Oxford and Cambridge will sound better than any other UK University irrespective of the actual course.

In 2001, when I was applying to do a post-career PhD in the US, one of the professors who read my CV commented on my 1970 bachelor's degree in mathematics from Imperial as a point in my favor.

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Common file-formats for writing research papers
This is a rewrite of a question that was perhaps-naively posed. I rephrase...
What file formats are ok/good/ideal/common/long-term-viable/archivable/useful for research papers?
And, also, there's the history-question:
What is the story of viable file-formats in the last 20+ years?

File formats for what? Data? Papers? Lab notebooks? This question to me sounds akin to asking, "I need to buy a storage container for my... stuff. Can you recommend me a common, archivable, useful one?" It completely depends on the purpose.

Formats for writing, or for reading?

"This question is ambiguous, vague, incomplete, overly broad, or rhetorical and cannot be reasonably answered in its current form." - voting to close

I work in a medical research department and its all .pdf

plain text/markup language
For mathematics, I think TeX/LaTeX is the way to go.  This is the standard way to write papers in nearly all areas of math (perhaps not biomath, where collaborators necessitate Word), so there's little extra cost.  One advantage of this approach is that it's easy to automate outputting in almost any format you want.  Furthermore, as new formats develop, we will almost certainly develop tools to convert TeX source to these new formats.  The arXiv is a great example of this model.

Many people know what I'll say here, but I thought the re-format of the situation was appropriate...
For mathematics and "hard" sciences, PDF (portable document format) is absolutely standard now. Until a few years ago, PS (postscript) and DVI (device independent) formats were typical, but no more.
In mathematics, "Word" format was never common.
Currently, traditional (meaning various things) mathematics journals want a PDF file to send to referees. Everyone has software that can convert PostScript files to PDF, and so on. In fact, "OpenOffice", for example, can convert/export "Word" files to PDF.
So, in sciences, PDF, though "Word" may be forgivable.
The question of future readability of these or any other file formats is hugely non-trivial. (Similarly, kids-these-days, such as my almost-20 daughter, have great difficulty reading "cursive writing" of "old" people. :)
So: modulo issues that the original questioner can't afford to worry about, the current answer is "PDF, and tolerance for Word files, esp. from the humanities...".
The long-term answer about survivable file-formats... is troubling. :)

binary/plain text
Other things to consider (for the future) is the movement towards standard meta-data items contained with the research articles (e.g. structured abstracts, specific research repositories, meta-analyses), and supplemental material for reproducible analysis. These suggest to me the conversation should likely include more than one data file.
IMO we can be more imaginative than word or pdf files. For instance open access journals frequently have everything right there in html on the page. I even think this idea for a fast journal by Yihui Xie using markdown for revisions and compiling to html is a good idea.
This is forward thinking though. Realistic constraints force collaborations to work with WYSIWYG file formats and PDF for writing because such behavior has not permeated enough in many fields (although for exceptions in some fields that extensively write in Latex see Jeffe's comment below). That may change in the future though, especially if journals adapt submission standards that encourage such actions.

Obviously realistic constraints force collaborations to work with WYSIWYG file formats — Unless you're a mathematician, physicist, computer scientist, or somebody else who uses latex.

@JeffE, sure and I didn't really intend that statement to be taken as deterministic about everyone in academia. I have updated to make this clear. That being said though, outside of those few fields which use latex extensively for writing documents that is certainly the exception. Also when you review a paper are you given the tex source?

It's worth mentioning that you can do a lot with pdfs; check out some of the demos at the TeX showcase, including this interactive, randomly generated math quiz, this interactive periodic table, and this animated Lorenz Attractor.

@AndyW: No, typically authors only submit PDFs for review (so referees necessarily only get PDFs).  Many journals use the author's TeX source to prepare the camera-ready copy after the paper is accepted, but a few ask the author to do that, too.  Also, I don't know anyone in my field who doesn't write LaTeX source directly, without using a wizzywig editor.

@eykanal Thanks for sharing (I had never seen truly interactive in PDF before). Although I suspect the potential for interactivity in html is greater though. For one example, see some Elsevier journals related to spatial analysis now provide the ability to embed google maps in supplementary data. Wouldn't it be nice to have live applications in which you could pan and zoom graphics with tool tips for observations, or dynamic tables with publicly available data? I'm skeptical these things can be done in pdf (or only one file).

@JeffE, I can say the exact opposite for my field, in fact several of the journals in my field make you submit papers in WYSIWYG editor file formats! I use latex and wish others did as well, but to move the conversation forward I would say reliance on PDF's for archiving research is not a great solution.

@JeffE If my first paragraph after the binary/plain text note isn't clear I'm not quite sure what else I can say. PDF's aren't suitable for archives of data or research unless they are supplemented with material outside of the PDF, hence multiple file formats like I suggested. Reading the stuff who cares whether it is pdf or html webpage or printed paper or whatever, an archive of research and interactive collaboration takes more than just reading though.


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Can I apply for a post-doc in global studies in North America?
I am doing my doctorate in global studies in Germany, and would like to apply for a post-doc position in North America, especially in Canada. The topic I work on has considerable policy relevance, and I see that some North American professors are working in those areas. I am a non-EU citizen. Is there any chance that I will be accepted?

It's fairly routine to hire foreign postdocs in the US. The main issue to worry about is the work visa - the faculty mentor might not have much of an idea so if you did get an offer you'd have to discuss it with them and probably some admin folks at the university.

How is PostDoc admission procedure in North America? Should one apply to the research group or to the university centralized system? Thanks

The mentor hires, but the ad might be posted by the university. But in my (limited) experience all communication is directly with the hiring PI. The ad posting would probably have instructions on how to apply.

Actually, the postdoc hiring (not "admission") process varies significantly depending on the field and the university.  Most postdocs are hired directly by PIs.  But others are hired by departments (for example, most math postdocs) or sub-departments (for example, the Simons postdoc in theoretical CS).  Still others are "hired" by funding agencies (for example, NSF mathematical sciences postdocs, or the former Computing Innovations postdocs).

I can only speak for the US.
Yes!  US universities routinely hire postdocs from all over the world.  A few positions may be reserved for US citizens, due to funding requirements, but those will be indicated in the postings.
As one way to check, go to the web site of a department that interests you, find the web pages of some of the postdocs, and read their CVs.

How is PostDoc admission procedure in North America? Should one apply to the research group or to the university centralized system? Thanks


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Well-regarded institutions offering distance education (PG) in applied Math
Which are the well-regarded institutions in Europe (apart from the Open University in the UK) and America offering distance learning postgraduate degrees? I'm especially interested in Applied Mathematics.

@CharlesMorisset Yes.

It would help if you clarify what kind of degree you are looking for (masters or doctorate, the latter is unlikely to exist) and what you plan to do with it (industry, teaching, ?)

There are a number of schools that have distance-learning programs, including for applied mathematics. For instance, the University of Washington offers an online master's of science program in Applied Mathematics.

I had to edit this comment to help avoid vandalism. Answers under about 300 characters can be easily vandalized.

@aeismail, indeed, someone just tried to vandalize it again just now.


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Entering into PhD program after having dropped out of bachelor's
When I was 23, I quit my computer science undergraduate studies at USC with only one semester worth of units left and a low (less than 3.0) GPA due to personal reasons.  I just turned 30 and have rekindled a desire to pursue research in computational neuroscience.  Is there any realistic hope of eventually getting into a PhD program and pursuing a career in academia, or is it too much of a long shot given my personal circumstances and the job market?
Basically, what I want to know is, if I were to finish my BS, kick ass in a master's program (applied mathematics), and have great GRE scores, would that overcome my abysmal undergraduate record and gap in years away from school?
The biggest obstacle in my view is getting into a terminal master's program with my undergraduate record.  If I were to get into a 1-year terminal master's program in mathematics at a sub-par university and do great, would I have a chance at a higher ranked university for my PhD?

i would like to tell you you can do. but if you made good scientific project then you will defiantly got selected

See this earlier question and this blog post describing my experience.

The odds of a career in academia are long in general, and certainly your situation is going to make the odds even longer.
That said, people tend to only look at your most recent degree.  It seems pretty likely that if you got into a masters program and did very well there, you'd have a good shot at getting into a solid Ph.D. program.  But you'd actually have to do very well in the masters program (probably "best in several years" level).  Furthermore, even once you get into a solid Ph.D. program the odds are against your getting a job in academia.

...even once you get into a solid Ph.D. program the odds are against your getting a job in academia — This is true, but not because of your undergraduate grades.  It's true for everyone.

Yes, it is the most recent, and the most advanced, coursework that you've done that matters. Especially if this current work really shines, people can comprehend that you (and many others, often very capable) weren't very conformist or even focused when younger. Don't even spend time talking about that, but, rather, if given an opportunity, show what you can do now.

I flunked out twice as a undergrad engineering student at a major mid-western university. The second time it was a  "go away and don't bother to reapply" situation.
I was determined to be a graduate engineer, my dream since age 10. I went to work as an adult  technician at the university to save a few $$. Six months later I started night school as an "adult special", determined to learn everything I had missed during the first two years. For the next year, I basically did every example and every problem over in a special set of notebooks I kept, using the open tutoring office in the old department whenever I had a question. I bought or checked out similar math textbooks to get extra problems to work where I was not perfectly confidant of my ability.
I never got less that an A or A+ (95+) in any class, repeating all the classes that I had received C's or worse in, and met informally with each member of the admissions committee to let them know of my progress. They were encouraging but non-committal. I then re-petitioned for admission to a bachelors upper division degree program and requested that my night school grades by substituted for failing ones. I was readmitted on probation but with the old grades.
I continued on that same track for my junior year - all high A's, all homework triple checked before submission, lots of all-nights, no parties, few weekends.
At the end of that year I was taken off of academic probation. A few months later the department head and the chair of the graduate admissions committee/vice department head separately approached me with an invite visit their labs and discuss their research. I had previously made the acquaintance of some of their other grad students to get an idea of what was happening.  Both visits resulted in offers of an RA in a PhD program. So no teaching, just $$ support for my Masters research (optical physics/lasers).
After the Masters thesis I was recruited by a local startup - I made a choice not to go the academic route for a number of reasons. the chance to be in on the ground floor in a new technology, money, a new wife, and a desire to start a family among them.
I was lucky to get a third chance. Good luck to you.

My expectation would be yes. Of course, you will have to explain in your application letter that your undergraduate grades do not really represent you any more, etc.

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Can one acquire "tenure" through teaching or being something like a Research Associate at a university lab?
This question is specific to the United States.
Can one acquire something like "tenure" if either
(1) their primary / only responsibility is teaching undergraduate courses
and / or
(2) they work as a Research Scientist for a university lab but are not professors.
I am wondering about job security, basically.

Professor of the practice at Duke is a permanent position without tenure. It has levels: assistant, associate, and full. Contracts start at 3-4 years and get longer as you move up with 10 year contracts for full.

That's not a lot different than a lecturer position at Michigan except for the title.  A FT lecturer appointment is also a permanent position but without tenure.  I'm entering year 3 of my initial 3-yr appointment as a Lecturer III; when it renews, it will be as a Lecturer IV for another 3-yr term but with a "presumption of renewal".  Successive renewals will be for 5-year terms.

For comparison, Teaching Assistant Professors at Illinois have renewable one-year contracts; after lots of lobbying, Teaching Associate Professors and Teaching Professors in my department now have renewable three-year contracts.  (These positions are only a few years old; the campus is still getting used to the idea.)  The closest we have to "[adjective] professor of the practice" are "clinical [adjective] professors", who (I think) all have one-year contracts.

Rethinking my comment above, I want to clarify (for those not in academia)  that the "except for the title" is a truly big deal in academia.  Universities do not hand out PoP titles except rarely.  To get a PoP is a huge achievement.  Realistically, it's not easy to get any title that says "professor" in it as teaching faculty at most universities.  Lecturer is a title they give to most teaching faculty and it's title everyone who has it hates. (I'm always slightly uncomfortable when students call me "professor" knowing that's not my actual title.)

No, generally speaking, tenure is not offered to teaching faculty, usually called lecturers, or research scientists at American universities.  The AAUP has long argued that teaching faculty should also be eligible for tenure and they report that a small number of universities have created tenure tracks for teaching faculty.  But it's rare.
That said, if you can get hired full-time as a lecturer, your job security is pretty good, mainly because (speaking from experience serving on the lecturer search committee here at Michigan) it's so hard to find qualified individuals who want the job, given that it's so dramatically less attractive to academics than a tenure track appointment.

But note that Michigan is an R1 university and so not typical of all universities (and colleges) in the US. The standards are very high for tenure.

There are many “regional comprehensive” institutions in the US where faculty can get tenureas professors llargely on their teaching record with very little research required.

@BrianBorchers I think we're splitting hairs.  Those institutions often still make a distinction between tenure track and lecturer positions, which do not lead to tenure.  It just doesn't take the same research achievements to achieve tenure.

There are also some universities that technically don't offer "tenure" to teaching faculty, but do have a very similar system called by a different name.  For example, the University of California has Lecturer with Security of Employment.

@NateEldredge Yes, and there are some universities that have created Teaching Professor titles, which is the other big pain point in lecturer appointments.  (We've been pushing for that at Michigan, pointing out that the title is a big reason why people don't want the job but to no avail so far.)

@Lisa I'm not a professor (though the students call me that), I'm a lecturer (who's been pestering for a PoP title. :)  There's a LOT of age and gender discrimination in industry (don't get me started on Microsoft!) but as a 68-yo woman, I've encountered basically none as faculty at Michigan in CS.  If I'd realized how much nicer it is being faculty at a university than slaving in industry, I'd have gotten a PhD (I only have an MS) and been here decades ago.

At CUNY both Lecturers (essentially teaching faculty) and lab technicians can earn the equivalent of tenure.  For lecturers this is called a Certificate of Continuous Employment.

@Elin CUNY is one of the schools mentioned in that AAUP link I gave.

@NateEldredge Should have pointed out that UC is another of the schools mentioned in that AAUP link.

Your first case is possible at some but not all US universities. There are many whose primary mission is teaching with only minor research responsibilities. The usual way it is put is that you "need to keep up with the field". But at many other universities, research is a major part of any tenure decision.
Your second scenario is probably much less likely. The titles you give often don't come with tenure, though in some top level places, Research Scientist would be more likely to be tenurable. But even then, some guidance of graduate students (i.e. "teaching") might be part of the job and evaluated in any tenure decision.
I'll note that at some very fine institutions (CMU, Duke, Stanford, ...) there is a special track for teaching faculty (Professor of the Practice is a common title) and these positions, while not tenurable, come with, say, renewable ten year contracts. But they also have high standards both for teaching and for "keeping up". In this case, keeping up usually means that you also publish, though publishing pedagogical work rather than strictly scientific work is probably mostly the norm. People that I know in these positions either have doctorates or some other outstanding qualifications as educators. The positions are very secure, even if not tenure, strictly speaking. (Information here supplied by a Duke PoP).

Professor of Practice is rarely tenurable.  (Offhand, I can't think of any US university that grants tenure for PoPs.)  Stanford, Duke and CMU do not offer tenure to teaching faculty.

@NicoleHamilton, maybe I got it wrong. I'll ask a few folks. The "moral equivalent of tenure" is there. Long term employment - certainly beyond any seven year limits.

Well, yes, that was my point in my answer:  If you're good enough to get hired as a FT lecturer, your job security is pretty good, precisely because it's so hard to find good people who want that job.

@NicoleHamilton Huh. I really thought Susan Rodger and Owen Astrachan had actual formal tenure at Duke, not just de-facto tenure.

@JeffE I'm not familiar with their specific situations but I see they're both PoPs.  Duke's policy re: titles is that a PoP is a non-tenure track position.  But my guess is their jobs are very secure, same as mine is as a full-time lecturer at Michigan, even without tenure.  At many (most?) universities, the only faculty who are really at risk of losing their jobs are non-tenured assistant professors and adjunct or affiliate faculty.

@JeffE, I've corrected my statement on PoP. Long, renewable contracts, but not tenure.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Is declining an undergraduate award which causes me discomfort appropriate?
I have been offered an award to be presented to me at my graduation this summer at an English university. The award is not for academic achievement per se. It's for gaining my science degree despite having suffered significant illness at a crucial point in my degree. The award is for a student who has overcome a significant obstacle (which could be anything) and successfully completed.
Specifically because the cause of my problem was illness, this nomination has made me feel acutely self-conscious (even before I've received it). I've spoken to student friends and family about it. They all give predictable advice - "we understand, but accept the award, it's good for your CV!". Any possible benefit to my "CV" doesn't begin to enter the calculus for me.
This was a significant illness, and I struggled hard to be "normal" again. This award would make it hard to feel that way. I would find an allusion to this episode, particularly on a day such as graduation, rather difficult to handle. I doubt very much that the specific motivation for the award would be stated at the ceremony, but even so...
I realise my academic department are trying to be generous towards me and recognise my efforts with this award. It is a good university and they care about their students. I am going on to postgraduate study at the same university. The award is sponsored by an alumnus who themselves had a significant problem during their studies. Can I decline politely or is this a no-no? Could it be seen as self-indulgent to decline?
Update: I wanted to thank all of the posters here for empathic, thoughtful and surprisingly non-judgemental answers. This is clearly a well-regulated and insightful community.
Many of these answers conflict, and some posters have admonished others, but I wanted you to know that I have read everything carefully, that I am open to seeing this from all perspectives, and that I have found almost all answers and replies helpful.

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

I suggest a third way:
Write a concise e-mail to whoever is handing out the award that you would prefer to receive it silently for the reasons you cited (not wanting to be reminded of your disease), i.e., without being mentioned at the ceremony, but via mail or similar.
This has several advantages:

You spend at most as much energy on this as declining the award, probably less since you do not have to worry about how to politely decline it, etc.
You avoid what you want to avoid.
You will never face regret for not taking the award and in the future you are completely free to use it or not (for your CV and similar).

The main reason to consider accepting this award (the likes of which often carry a smell of rather a self-serving act of the institution) is to consider its effects on others in the future - you may act as a motivation for people to come after you to overcome difficulties. In my opinion that is the main consideration for OP to take - so, not to consider their own perspective in which such an award clearly does not seem to send the right message, but if they want to help sending a message to others in a similar situation in the future.

It is a bit disingenuous to say "you are free to use it or not." If a university makes an award, the fact that it exists is in the public domain, just like the rest of one's academic record. Any person or organization has a reason to check the OP's academic record will therefore discover its existence.

@alephzero Wouldn't an organization checking up on a CV mostly just be confirming completion of a degree? I would be surprised if anyone found out about the award by themselves. Perhaps this is a location difference (I'm in the USA)?

This may be a good solution, but it's also possible that this conflicts with the intent of the donor (i.e., raising awareness) and could create issues. In particular, the statement that even mentioning the incident is "difficult to handle" might create the impression that OP is overly fragile or dramatic (justified or not).

@cag51 Raising awareness of significant obstacles? What?

@alephzero there's public domain and public domain, or to put it another way, there's a big gap between broadcasting and secrecy, with plenty of room to acknowledge but not declare such an award

@sgf raising awareness that significant obstacles can be overcome.

@CaptainEmacs You likely meant merely that this is something to take into consideration, and didn't intend to make the OP feel obligated by this line of reasoning, but I think that it deserves emphasis that while it would be admirable for the OP to motivate others, they shouldn't feel that they have to disregard their own concerns in favor of others.

@Acccumulation Yes. I specifically said "main reason to consider" - rather than to dismiss. Still, it is obviously OP's decision and fully so, no obligation intended. I thought the whole formulation was in that spirit.

I would find any allusion to this episode, particularly on a day such as graduation, rather difficult to handle.

It's up to you  what decision to make about the award, but it sounds like you might really benefit from talking to a counselor about your feelings about your illness and recovery.  Your school may have free or discounted counselors available, or your insurance might cover it.  It's completely understandable that going through such a difficult experience has left you with very strong feelings about that experience, but you might want to work to get to a place where remembering that this happened and that you survived it with great resilience is something that you can handle hearing sometimes and even be proud of.  The award itself, either accepting or declining, isn't the important thing here.  The important thing is your feelings about your experience and your mental health going forward.

Downvoted because the answer seems to make unsubstantiated assumptions about OP's mental health. OP may wish to or already be seeking support, but not wanting to have a personal trauma spun into a public spectacle is not a sign that it is necessary.

@Kami - I can't downvote your comment, but it seems to make an unsubstantiated assumption that talking to a counselor somehow implies mental health problems. Not true.

Usually the advice is indeed to accept awards offered to you, but in this case I can understand you wishing to decline it - and you are perfectly in the right to do so.
My advice would be to talk to your academic advisor, ombudsman, student counsellor, or whatever this role would be called in your institution, and tell them the same thing you posted here - that you are honored that they want to present the award to you and that you are grateful for that, but that you cannot accept the award. Just do it in time so that they can still nominate somebody else, and I cannot imagine that your department will have hard feelings about this.
As for the "CV value" of an award - yes, in principle every award helps your CV, but I suspect the value is often overstated (and, mind you, it will only really help for your next career step - for instance, applying to grad school - later in life basically nobody will care about awards you won during your undergrad). I personally don't think it's worth it if it makes you feel less good about yourself.

"Later in life basically nobody will care about awards you won during your undergrad" - not just that but by putting it on a resume/CV, you're inviting prospective employers to ask about it and clearly, that's not a discussion OP wishes to have.

@aleppke "you're inviting prospective employers to ask about it" that's quite of a drama the way you put it. Most people will just notice it en passant, to which you can laugh it off and take the praise. No need to make a big deal out of it.

@gented OP has clearly stated that the topic makes them uncomfortable and they do not wish to draw attention to it, let alone have a discussion on it. If this was something they could laugh off and ignore, they wouldn't have posted this question. Employers can and do ask about things listed on a resume so if you're not prepared to fully discuss something, don't put it on there.

@aleppke I don't know what type of employers you have experience with but I have been both in Academia and industry and never have I been asked - except en passant - anything that wasn't a project or my education.

@gented I'm not guaranteeing that everything on a resume will be asked about. I'm simply stating that anything listed on a resume is considered fair game to be asked about. Whether it actually comes up is up to the individual interviewer but if OP doesn't want to take that chance, it's better to not include the award in the first place. Remember, this is an extremely sensitive and personal topic for them and they don't want to draw attention to it. They're not looking for advice on how to get out of conversations about it, they're looking to avoid the conversations altogether.

I'll add my two cents.  Universities are constantly having awards and honors turned down.  I have more inside information than most academics would, so I have to be careful about what I say here.  But if I could be open, I could site several examples at every level, where a university thought they were pleasing someone and they weren't.  Billionaire donors who didn't really want a statue of themselves in front of the building which they funded.  Special recognition for being the first black/woman/gay professor who got a Nobel/best-seller/whatever.   Corporations and funds who didn't think that that sort of publicity was exactly in line with the public image they wanted.  And a number of students turning down awards and even money because they didn't want to accept anything from a entity that was for/against the Palestinian state/gay rights/abortion/puppies.
What I'm saying is that universities are used to being turned down.  They are adept at back-pedaling and adjusting for such things.  The admins exist solely for the purpose of keeping good relations with alumni and donors, so whatever you do is what they want to help you with.
You can turn down the award with thanks and have no worries about repercussions.   My opinion is that the extra line on your CV isn't worth much.

@BryanKrause  Odd perception you have there.  I'm not complaining about anything.  He wants to know if it's OK to turn down the award and I answered "yes" and explained why "yes" was the right answer.  I don't know where you get "rant" from.  Maybe you're projecting.

This seems like a good and relevant answer to me, especially compared to a number of other answers which merely suggest that OP should accept something he considers a violation (albeit a well-meaning one) because apparently his illness and recovery are no longer about him. This answer lists (taking on faith they are true) examples of people who have been similarly uncomfortable with unwanted accolades, and have turned them down with no problems. That does seem to answer the question.

This seems like a good answer to me because, on top of all the things detailed in the comment above, the answer does not make any assumption about the OP's feelings, reaction, experience .... it is just a very detailed and generic answer, that can be transposed to many situations, explaining that turning down an award might not be the issue one think it could.

recognition is what it's all about (for others to see; not for you to look at). That's what keeps people from worrying about a statue they don't think they deserve (like @Pharap's comment on Mari's answer. See also my comment about how to do it gracefully even if you feel undeserving). - If you cure cancer; we're building a statue, and you can file all your complaints in the 'suggestion box' (the garbage). - Don't be humble to the point of being conceited.

@Mazura The OP's problem (or virtue) isn't humility but embarrassment. What if you got selected for an award for being the first hemorrhoid sufferer to earn physics degree?  Such awards are meant kindly, but they are condescending, and condescension hurts.  The OP strove to do just as well as "normal" people, succeeded, and they STILL look down on him and pat him on the head.

Fair point, I'd feel embarrassed. But why would the Uni know if I had hemorrhoids? If they know I did (which they obviously knew something), then I couldn't discount the fact that I may or may not have received special treatment. If it was e.g., ADHD, keeping medical history between us is the OP's prerogative. But them 'striving' is the important part, and if they are willing to further disclose to everyone else, then other people with ADHD can take heart. Embarrassment shouldn't be the deciding factor; worrying about landing future jobs or health insurance should be.

Actually, it's not embarrassment, as stated by the OP, the award and the ceremony itself will cause the OP undue emotional and therefore physical duress. Since we're being frank; OP needs to grow up and learn how to say no and not need affirmation from other people to know when to say it. Ironically, I say that because it's easier to do once someone tells you that saying no is a thing you can do.

@Mazura  It sounds like embarrassment to me.  And he knows how to say no.  His worry is what the repercussions might be.

They, the university, should have first consulted with you, not everyone feels comfortable about receiving awards, especially one connected to a personal serious illness.
But... you should feel proud nonetheless, and someone in the audience that day might be going through a similar situation, seeing you accept the award could give that extra incentive they need to persevere through the difficulties.
I would, in your shoes, seriously consider accepting the award, not for the CV but for that one person in the audience who might be battling their own demons and be on the point of despair. You are the living proof that it is possible to overcome an illness and still succeed with in one's studies.

The university did consult with him.  That's how the situation got to be where it is.

@Buzz it seems that the OP was only notified of this award. Was it face to face or via an email? I don't know about theses things but a consultation conjures the image of  a conversation between the benefactor and the recipient of the award.  In that case, the OP would have had the opportunity to express their reluctance and/or discomfort, and the representative could explain the motivation behind the award.

This award is not for the OP, +1.  "consider its effects on others in the future" ... "the message that it sends to the broader university: It is OK to help people."

It could equally cause a person to think "this person can do it, but I can't, that makes me even more of a failure". Or there could be someone else who was equally deserving (or perhaps even more deserving) of the award thinking "how come this person got the award? do my problems not mean anything?".

@Pharap - that's why when you revive an award like this, in recognition of something, you're supposed to mention how you wouldn't be here if not for the help and support of xyz. And if you really want to shine them on, you accept it on behalf of them in the light of knowing only that you couldn't have done it w/o them, and in the hope that in the future no one will ever think 'this' person could but you can't. Fear of a more deserving person is throwing out the baby w/ bathwater; you begin your speech w/ someone prob deserves this more than me, but I accept on behalf...

You have every right to object to any mention of or allusion to medical problems, whether current or historic. In the UK, medical data are subject to very robust confidentiality provisions (this applies even in respect of internal NHS systems -- I have opted out of NHS Digital, the computer system that facilitates sharing medical data between GP practices and hospitals... and Google... and the UK Border Agency), and nobody should be disseminating them without your explicit consent (this applies even if you are writing a confidential reference for someone's job application and even when answering questions such as "How is X?" in a social context), unless it were on an urgent basis to protect your "vital interests" (e.g.: if someone had a reasonable and good-faith belief that you are in imminent danger, it would be legal to share concerns for the sole purpose of preventing such danger).
You also have every right to object to being singled-out as having overcome adversity (even if no medical data are disclosed) in a public ceremony. If accepting the award in the ceremony is a condition of receiving the award, that would entail declining the award or graduating in absentia.
As others have said, it may be possible to receive the award without any disclosure of medical data and without being singled-out in the ceremony. If you opt for this course of action, you should be aware that a record of the award will probably still exist somewhere, so it may still be possible for somebody to discover that you "have overcome a significant obstacle" or whatever. You should check the wording of the award and how it is described in reports (presumably, when the donor made financial provision for award, there would have been some sort of document articulating the conditions).
I would suggest structuring your reply to the university as follows:

start by saying that you have not yet decided whether to accept the award, and require clarification of a few matters to help you decide;
ask for full disclosure of all documentation relating the award, including the official rules for how it is awarded;
say that you object to the award being presented in a public ceremony, because it would be "triggering" and make you feel uncomfortable;
say that you object to any medical data being kept on file in any archive or documentation relating to the award;
insist on the right to review (and veto) the exact wording of any official report on the reasons why you were selected for the award (as a minimum, the university will probably be required to write such a report for the donor); and
explain that if your aforementioned conditions are incompatible with receiving the award, you will have to decline.

Why do you assume the mentioning would trigger a traumatic response rather than just feel awkward? And wouldn't the latter suffice as a reason for not wanting to be mentioned publicly?

If the UK laws and practical application are anything like USA’s, you may need to remind them in advance that it would be illegal for them to mention certain things.  Our HIPAA is routinely violated due to carelessness or ignorance.

Let's just settle down with the assertions about HIPAA and medical privacy. HIPAA covers a specific set of organizations and educational institutions are most definitely not bound by HIPAA by virtue of being educational institutions. Similarly, I'd be surprised to find that you would find that you are "protected" in the UK, especially as it sounds like the OP's illness was broadly known. As ever with legal advice on the internet: you get what you pay for.

In situations like this I often find the best solution is to ask yourself which alternative you would regret the most, and which alternative you would regret the least.
Imagine yourself 5-10 years down the line.
Do you think you would regret accepting the award more than you would regret not accepting it?
Do you think you would feel 'dirty' somehow for having accepted it?
When it comes down to it what matters the most is how you feel about each alternative, not how strangers on the internet feel about each alternative. Forget everyone else (the award committee, the alumnus, your family, the potential attendees and everybody here on this website) and ask yourself how you see this award.
Is it a badge of honour earned for having made it through a particularly perilous trial,
or is it an albatross that will forever remind you of a dark part of your life?
We cannot make that decision for you,
only you know how you feel about it and how you think you may feel in the future.

You have to look as yourself as a brand and to your reputation.
I was once offered a performance award in an academia setting, and I equally did not had the slightest wish to attend the ceremony, for several reasons not pertinent to these answer.
I decided to go just for my reputation, for the sake of good relations, and not annoying anybody. Nonetheless, the ceremony itself went ok, people had a good impression for me being there, my family was proud of me, and I got to put it on my CV.
Do not forget in the academia world forging alliances and reputation counts a lot. IMO, your family is offering good advice, go for it!

This award does not help me to feel normal

Declining the award will not make you feel any more normal either, if that is your underlying problem. Take the award and make whatever you want of it in the future: there will be plenty of occasions where you will indeed deserve something and will not get it, so do not overthink it too much, see this chance as to balance it out.
I have myself suffered a significant illness during my Academic time and was on and off praised for having overcome it. Just take the good things whenever people do not mean bad - then time will heal up your emotional suffering.

If you don't want this award, just let them know. I'm sure they will understand. I can't see it affecting your future career either way, to be honest, so if it makes you uncomfortable, just politely decline the award. I don't see this as being at all self-indulgent; you didn't ask for it, you don't want it, and you have absolutely no obligation to accept it.

I can see two points of view to address. When you accept the reward for overcoming the dificulty you are publicly marked as "the one who had the dificulty".
One point is, that very few people want to be recognised as they-who-suffered-that. People tend not to display anything they are not comfortable with. From that point of view, declining the award is acceptable.
The other point is why does the university want to award you?

They acknowledge your higher-than-usual effort to get the degree. Maybe there is a cash to compensate part of your extra expenses.
They want to show, that your dificulty can be overcome; that the difficulty is a challenge to beat, not a terminal.
They want to show themselves as a supportive institution.

Your comment on the sponsor shows to me that second point is significant there. They want to motivate other people to embrace and fight their difficulties and not give up. The more people overcoming something the more willingful you are to trying it as well.
The choice is yours; noone can force you to pick one way or anither. Think of you as an example for youngsters, if you like that.
If you don't want to attract further attention to the difficulty, you can not-mention it in your CV, LI profile, etc. You can let your photo be only in the Hall-of-Fame at the university surrounded with other awardees.

I see that many before me have come with very good comments, but I feel that I have one thing to add (if I didn't miss it).
If you don't feel good about accepting it but consider accepting it to further your career, think about how you will feel every time you apply for a job and the interviewer asks "oh, I see you got this award, tell me about it".
That means that you'll re-live the pain you're feeling now every time you apply for a job.
And the reasoning "but I don't have to include it on my CV" kinda ruins your argument about it furthering your career.
This is just a thought from me.
But basically I agree with stuff mentioned above

you didn't ask for it, you can decline.
you're not rude to decline such a sensitive award.
we cannot decide for you, it has be your own decision and you'll have to own that decision.

I feel your pain and I really hope that you have found comfort in these comments and that you feel better.

I realise my academic department are trying to be generous

Do not fall for that (common) mistake!
Try and accept that the university people are probably right in seeing your great accomplishment, which to you may not (yet) feel like one.
The award will be good for your CV, but remember that you really did earn it. They don't give it to you despite your struggle, which may or may not continue, but because your graduation was objectively a great accomplishment attributed not only to your learning skills but in addition much to your personal strength and endurance.
They wouldn't even consider you for the award if they did not know that you succeeded with your graduation despite having a much greater burden to handle than is expected from the 'average' student.

I doubt very much that the specific motivation for the award would be
  stated at the ceremony

Like above, trust in them that they know what they're doing! They are very well aware about the sensitive nature of the issue, as they are about their decision to award you.


text:
My MRes will be unclassified - will this make applications outside academia less competitive?
I have just graduated 2.1 in a bioscience subject and have been offered an MRes / MSc(Res) (masters by way of research). I really want to do the MRes because I want to test my aptitude for research, publishing and continuing to a Ph.D.
It's a well-worn trope, but I had also hoped to build upon my 2.1 by earning a distinction to make potential applications (in/outside academia) more competitive. I believe I would be capable of that given my performance on a final year lab research module.
However, during my application I learned that the MRes as offered in my department is “unclassified” - it is only pass/fail. It does not attract the classic masters classifications of pass/merit/distinction.
I am in my mid-thirties. I am split 50/50 between my heart (using the MRes to continue to a Ph.D) and the pragmatic (exiting academia and applying for a bioscience-based postgraduate scheme or job so I can start earning while I learn). My aptitude for staying in academia is something I intend to get a feel for while doing the MRes.
Will the fact the MRes is unclassified mean that I am not appreciably increasing competitiveness of my application for positions outside of academia?
To take one example, the NHS Scientist Training Programme has a minimum entry standard of 2.1. However, someone on the admissions committee tells me that 2.1’s are screened out in favour of 1st class degrees. In that scenario, a masters with distinction could patch that up.

2.1 what does this mean?

If you has a 2.2 or for some other reason did not meet the requirements for a position you are interested in, then having a classified MSc would be very helpful. Vary rarely do positions require a 1st. Automated culling of applications based on a 1st or 2.1 generally doesn't happen. Someone will still look at your application if you have a 2.1 and an unclassified MSc. If they see good research, the 2.1 will not matter anymore.
That said, a student with a 1st is looked at differently then someone with a 2.1. If at the start of the course, you were given the option for a classified or unclassified degree it would make sense for you to choose the classified degree. If you are choosing between equally ranked courses that will both offer you identical learning and research opportunies and one is classified and the other is not, the classified one has the potential to help you more. The benefit, however, is tiny and differences in opportunities, subjects, and/or personal preferences, will offset any benefit between a 2.1 and a 1st.

This may be discipline and location specific, but it might be useful to someone: in Scotland at least, it is nearly impossible to get ESRC or AHRC PhD funding if one doesn't have a first/distinction on something. If you don't have it on your undergrad, you need it on your master's. There's literally a set of boxes to tick on the candidate evaluation and you can't tick the top box if the applicant doesn't have a 1st/distinction. An uncategorised MRes would mean no box ticking.
Granted the last time I did ESRC PhD proposal review was about 3 years ago, but the situation hasn't improved. We basically tell students that if they don't have a 1st it almost certainly isn't going to happen.

It will be entirely a matter for the potential employer. If you really do want to apply for the NHS Scientist Training Programme you need to have a frank discussion with the people who run that programme. They will have their rules, but, I hope, ought to be open to reason that takes them beyond box-ticking.
Early in my career I had the opposite problem: I was theoretically qualified to apply for a UK Government job with the Master's degree that I held, but was told that it would be better, in my own interests, to apply after getting a PhD.
Bureaucrats might be faceless, but sometimes can respond helpfully to questions.


text:
Project organization: files, docs, organization + icloud storage
I have separated my question into sub-questions as suggested in the comment by user “padovapadova“ ( see my original post)

I started my PhD 3 weeks ago. I already read a lot of information,
research papers, publication and so on regarding my topic, but I still
don’t have a complete final idea about my topic. Before applying I was
quite sure about my PhD topic idea, but after discussion with other
members of research group, my supervisor and attending meetings… I
think I have to work on my first idea. You probably had such
experiences and can share your advices, tips, hints which were helpful
for your first year in PhD

How do you organize your work on your project? Do you save your files on cloud (Dropbox, Mega, OneDrive, iCloud, Google drive…) or just on your PC?

If you have been around computers enough, you should know you need to keep things in at least two places, preferably geographically separate.

Here is my foolproof aspiration for organizing my academic data. Take what you will and find what works for you!
Step -1: No Software
A few years ago my university shifted from physical lab books to a fancy digital note-taking software. I thought it was going to save my life! I have always been, and still am, incredibly disorganized. I thought having all my note-taking happen in a simple browser window would turn my research life around.
It did not.
Now, if you find a piece of software that works for you, by all means, use it and never let go! But if you have trouble adopting one, you may be suffering from digital cognitive friction. After all, in theory, you just need a stack of notebooks to stay organized. In theory that's all it should take me. And yet I am not even physically notebook-organized, which means that any successful organizational system must be even simpler than opening up a notebook and writing.
No logins. No menus. No side-by-side panes. We need to go all the way back to basics.
Step 0: Open a new folder
And pat yourself on the back. Organizing a project from the beginning is much better than trying to organize a sprawling disorganized year-old festering mess.
Step 1: Simple folders, simple files, simple filenames
Simple folders mean things are stored by kind. Here's a sample directory structure:
flux-capacitor_1985
|
|--papers
|  |--Einstein_relativity_1915.pdf
|  |--Brown_gigawatt-energy-requirements_1955.pdf
|
|--notes
|  |--DeLoreans-are-cool_1980.md
|  |--possible-teenage-collaborators.md
|
|--invoices
|  |--Libyan-Glowies_1984-06-21.docx
[...]

If you can organize things more deeply into subfolders, good for you -- if you find yourself agonizing between "physics" and "mathematics" for Poincare's papers then don't bother. It is better to have a folder full of thousands of well-named simple files than to have an folder empty of files you couldn't organize because you couldn't pin down a sub-organization system to your liking. Remember that if they are well-named simple files then your computer can search through their contents for you. (This is an adaptation of the YODA principles for data organization.)
Simple files are, as far as possible, plain text. Store written documents as Markdown plain text files, which are both very readable in Notepad and very pretty when formatted. Store tables as column-separated plain text files for easy AWK-ing. Store plots as plain images (and generate them from scripts which have the filenames coded in, so you can search your scripts directory for a plot's filename and have the relevant plot's name come up). Of course, you will have PDFs of journal articles, PPTXs of presentation slides, and binary output from instruments or programs you can't control -- but that should be just about it.
Simple filenames make it easy for either you or your computer to decide what's in a file based on its name. Here is an excellent presentation on how to name files -- read and apply it.
Step 2: Frequently backup
There are all the usual cloud solutions like Google Drive, Dropbox, OneDrive ... But if you have an external storage server, you can use SyncThing, and if you want to backup to a thumbdrive you can use FreeFileSync.
Notice that since you have organized your files using folder structures and filenames, the organization automatically travels with any backup.
Step 3: Version control
Are you not organized? Then here's the next level: turn your project folder into a version-controlled repository. Version control means you'll be able to track and revert changes across everything you do. No accidental deletions, no uncertainty about when a script suddenly stopped giving the "correct" results, and no more worrying that you won't be able to backtrack your steps.
If you can learn Git, you can even host your repository on GitHub! And guess what -- it automatically formats your Markdown files for you!
One Step At A Time
Notice how each step is worthwhile in itself. This way, no matter where you stop, even if you don't get all the way to creating a fancy-as research compendium, you can pat yourself on the back for being more organized than me than you would otherwise have been!
Also notice how the steps synergize with each other. Simple folders and files mean you can automatically apply version control, and mean that a GitHub repo will be as perfectly navigable as your desktop folder. They also make it easy to back up your work.
Also notice that this is a bare framework on which you can add things. You can absolutely run Mendeley or Zotero off your papers subfolder (and thus make sure, by the way, that it can't corrupt anything else). You can experiment with Jupyter Notebooks or the DataLad system or anything else you please -- again, having a simple folder of simple, well-named subfolders and files can only help. You can almost certainly do better! But these suggestions, I think, are a good starting point.
All the best!

I routinely work with dozens and hundreds of gigabytes of data and have to perform quite a bit of housekeeping after each experiment session to ensure we have enough backups. If you can offload at least a bit of that to the infrastructure at your lab/university or not handling it in the first place, great!
Overall, my organizational rules would be:

A lab should have a centralized data storage and a backup system. Students come and go, you sometimes need to revisit old data and results. I have found that by-year->by-project folder structure works better than the other way around; it feels easier to navigate (YMMV!).
Raw data should be stored separately from the rest of the artifacts you produce and no one should ever write over it, including in the same folders.
Split work into stages and keep a document describing what goes where alongside the processed data - you do not want to revisit it three months after and spend a week figuring out if you should take files from "preprocessing" or "stage 2a" folder - it may make perfect sense in the process, but you will forget this structure in a heartbeat. Write it down.
You may (and should) have a working copy of your data locally, unless there is a binding agreement like NDA prohibiting it. Better safe than sorry. That said, this is more of a backup solution in case EVERYTHING goes wrong with the existing lab storage, do not spend a ton of time and effort trying to keep it as neat as the "main" storage.
Notes you are taking will be mostly temporary, I find it impossible to keep them loaded into my brain at all times. Go through them periodically: weekly is a good periodicity for meetings and for writing down what seems the most important at the time. If you do not produce an article in a few months, write down your findings in a similar, more detailed fashion to keep things orderly. Keeping one "master document" describing what you know about the current project up-to-date can help.
As others have already pointed out, text files are the most valuable. Thankfully, they are extremely lightweight and between code, .md (which is fantastic indeed!), and text documents you should be using cloud and, possibly, version control for storage.
Keeping your knowledge base healthy is what I struggle with the most personally. Reference managers help a bit, but it seems the bulk of it gets to stay inside your head for you to be able to navigate your field.

I'm going to suggest what you want is some minimal kind of thing that takes as little time as possible. Don't become a sys-admin to support your studying. The place you should be trying to cram in as much information is your brain rather than some computer disk someplace.
Get something that works without too much trouble. Make sure you can store binary files so that you can zip stuff (or whatever your favorite file compression software) and shove it in the archive. And make sure you can take it with you after your degree.
Depending on how much data you produce, you could probably just carry around a thumb drive or some such. $20 of thumb drive on an attractive lanyard of some kind, and you can probably hold more text than you can type in your life.
Organizing the files then depends on how many and how big and how often they change. What works for me is, at the end of the day, to grab all my files from my working directory and copy them into a named-for-the-date directory on an archive drive. If I am working intently I may shorten that to every 4 hours or even every 1 hour.  Storage is cheaper than my time in most circumstances. A simple named-for-and-saved-every-day file system is usually quite convenient if I need to back up or restore.
I tend to work on the hard drive on my desktop. Then I archive daily to the LAN drive on our office system. It's backed up automatically. Then periodically I will copy the whole thing to something like a thumb drive or a second LAN drive or some such, depending on the project.
Your experience may vary. If you are producing 100 GB files every hour or two then storage may be a challenge.


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First year PhD Student: advices, recommendation, publication and conference
I started my PhD 3 weeks ago. I already read a lot of information, research papers, publication and so on regarding my topic, but I still don’t have a complete final idea about my topic. Before applying I was quite sure about my PhD topic idea, but after discussion with other members of research group, my supervisor and attending meetings… I think I have to work on my first idea.
You probably had such experiences and can share your advices, tips, hints which were helpful for your first year in PhD

I have a problem with materials I am reading now. To make my notes and highlights (organization) the main idea of papers I read I am using Word, but it doesn’t seem the best idea to do that. Maybe do you have your favourites you used, would happy for all your recommendation?

For organizing the tasks I have to do (read, review, send documentation, email…) I am trying to use todolist app, to make my life more “digital”, but I still have a paper notebook to write down my thoughts are coming to my mind during work… and at the end of the day I copy them to app.

Is there a platform where I can find all information about upcoming conferences, workshops and meeting I can attend or publish my paper?

I am thinking I have to start a collection of my publication, and maybe I can start with overview of papers I have read

How do you organize your work on your project? Do you save your files on cloud (Dropbox, Mega, OneDrive, iCloud, Google drive…) or just on your PC?

What was important during your first PhD year?

What was important during your first PhD year? --- This will vary greatly by subject and by country. For example, the primary concern that virtually all graduate students in the departments I was a Ph.D. student in (total of 3; long story . . .) for the first year or two was not messing up too badly in required course work and passing the department's Ph.D. qualifying exam. Reading papers, much less working on research (and even less than this in working on anything for publication), was 2 to 3 years away for nearly all of the first year students.

Too many questions, can you ask them on seperate posts? It would be better to find the answer you want

Is there a platform where I can find all information about upcoming conferences, workshops and meeting I can attend or publish my paper? - make that a separate question and I'll happily answer ...

@WolfgangFahl, thank you for your comment. You will find a new question here


text:
Should I put the whole comment responding to reviewers' comments
My goal is to respond to reviewers' comments. While doing that should I put the whole comments or only the parts I am asked to change. Related: Proper way of responding to reviewers' comments
In a case where I do not have any response to some reviewers' paragraphs, should I put them in to my response as well?
For example:

Overall, the article is good quality... Some positive comments... In section 3, equations 2 and 3 are presented without proper explanation.

My response:

Overall, the article is good quality... Some positive comments... In section 3, equations 2 and 3 are presented without proper explanation.

My response

OR (where I did not put any positive comments):

In section 3, equations 2 and 3 are presented without proper explanation.

My response

In my response, should I take the complete piece of paragraph considering positive comments as well or only the part that wanted me to change?

My coauthors and I have always started from the review in its entirely and interspersed our responses within the review; the combined review response document comprises the entire text of the original review and our responsive comments.
It's not necessary to respond to every specific phrase in the review but I would not delete parts merely because they are not suggesting a change. You can of course thank the reviewer for compliments they provide in the review, if you choose.

Unrelated but can we do something like https://hobsonresearch.com/wp-content/uploads/2018/01/responseletter_hacks.pdf page 5, where boxing reviewers' comments piece by piece, while keeping the entire comment?

@alper Certainly, I think the overall guiding principle here is to just think like a human and remember the purpose of this is for other humans. Can another human easily follow the review response and see 1) how each response relates to the review, and 2) distinguish between the reviewer comment and the response effortlessly? Then it's fine, unless you've been given explicit instructions to format in any specific way.

Not a big deal, go with whatever floats your boat
Really, neither editor nor reviewer is likely to care as long as you address their salient points.
That said, you might want to take the third option if the reviewer's report is exceptionally long (since it's the most compact option).


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What does "tenure" mean?
I often find academics with tenured bracketed beside their position. What is meant by a tenured position? Is this different from a permanent teaching position?

In short, tenure means that you cannot be fired (you have a very permanent position).  For more details, look at this question:
In practice, how secure is a tenured position in the US?  In particular, look at the first link in the first answer to that question, which is an article in Science that talks about the role of tenure.

One should emphasize that, in the U.S. system,  tenured professors can be fired. But they can only be fired "for cause" - e.g. for violating the law or university policies, or if the university is in a position of "financial exingency".  So tenure is vaguely like a unionized position in some other industries: it gives the person quite a bit of job security, but it is not an absolutely guaranteed job.

To have tenure is an acknowledgement from the host institution of the academic's record of published research, teaching and contribution to the administrative life of their department/institute/college.
It is difficult, but not impossible, to fire a tenured academic from their host institution. See e.g. http://www.hr.msu.edu/documents/facacadhandbooks/facultyhandbook/dismissal.htm
An academic with tenure is typically only dismissable on very serious grounds of misconduct. That it is so difficult to dismiss a tenured academic arises, historically, from the idea that university researchers should enjoy academic freedom - the ability to research unfavourable topics, persue and advance unpopular or controversial theories, to challenge the status quo without fear of reprisal in the form of dismissal.
The tenure system is itself, somewhat controversial, see e.g. http://www.mindingthecampus.com/originals/2012/07/how_to_save_tenurecut_it_way_b.html

the ability to research unfavourable topics, persue and advance unpopular or controversial theories, to challenge the status quo without fear of reprisal in the form of dismissal. but without funds you cannot research them anyway.

@StefanoBorini: That really depends on the field.  I don't need grants to do research.  I only need grants to fund PhD students to do their research.

Don't you still need money for computers, travel, paper, pencils, etc.?

Yes. For example, see my answer here: http://cstheory.stackexchange.com/questions/4131/why-would-a-tcs-researcher-need-funding/4139#4139

The implementation is a tenure contract, which specifies a starting salary, starting date, and often a maximum duration (e.g. 30 years). Other possible details include startup funds (e.g. US$1M over 10 years), lab space (dry/wet lab, exclusive use square footage), and access to shared facilities (big experimental equipment). Lab space and shared facilities aren't free, so the cost is often deducted from your startup funds.
There may be requirements in the contract about the maximum number of days you can spend off-campus doing consulting work, the minimum amount of lab activity required to be considered active (papers per year, grants submitted/funded per year, students trained per year), minimum service work (hours spent on committees, hours spent writing policy documents), and minimum teaching commitment.
If you fail to meet the minimums, your department may start to revoke some of your privileges. You may wish to read this other question about enforcement of the policies.
There's a wide variation between different universities and departments about what gets written in the contract and what is actually required due to departmental politics. The political part of the equation can be a lot more important than the text in the contract on a day-to-day basis. Consider what could happen if the department runs out of lab space or if you have trouble getting new grant funding for a couple years.


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Will self-citation be viewed as self-promotion in academia?
As we know, citation counts are important to judge one's research activity. Is it good to cite one's previous works? Will it be viewed as an act of advertisement or self-promotion?

If it's relevant to the present study, yes.

Usually things are structured so that self-citations do not affect citation-counts.

@paul why is that? is it assumes that such citations are not/cannot be objective or truly related?

@Ran ... Yes, I think there is the presumption that self-citations might be motivated simply by increasing citation-counts, rather than intellectual/scientific reasons. "Conflict of interest" potential, once again, even if the conflict does not actually occur.

Some cases of dubious self-citations are described here: http://www.ams.org/notices/201103/rtx110300434p.pdf

"Good" for what?  To whom?

Sometimes they are the only citations you'll ever get.

@paulgarrett just a minor comment on your comment: there are two questions and your comment-answer concerns the first question. I was confused in the beginning, somehow, and thought your comment is a response to the last question which didn't fit the picture.

Although it's true that citations are always helpful, there are obviously limits. If the majority of your citations are self-citations, that's usually considered a "red flag."  If your paper that came out two years ago has 10 citations, and two or three are from within your group, nobody's really going to have a problem with that. But if your paper gets cited 45 times, and 40 of them are you citing yourself, that's not so good.
Citation counts not being "in sync" with the journals they're published in are also problematic. Publishing in no-name, third-tier journal X, your paper is probably unlikely to generate many citations. It looks suspicious when such papers get many citations.
But again, much of this can be sorted out by a judicious use of search tools like Web of Science or Scopus.

Which use of search tools like Web of Science or Scopus can be considered judicious?

Judicious as in "sensible," and "using good judgment." In other words, not just looking at cite counts, but going in to the cite counts, and seeing who was doing the citing. Looking to see if the number of citations corresponds with what one expects given the quality of the journal, that sort of thing.

your comment reads (as in "sounds") both sensible and judicious. Thanks.

The ethical rule has to be: cite your work if it's relevant, and don't give it preferential treatment over the work of others. In short: use the same criteria for previous references to your work as you would use for citing others. No excessive citation, no self-censorship.

Unfortunately, some bias is impossible to avoid: the papers I cite are a subset of the papers I know of. I always know of my own papers, but I might never have heard of some other one.

@FedericoPoloni Bias is inevitable, but you can strive to avoid it as much as possible… and doing extensive literature search is a prerequisite for a review.

I hear that as you get older this bias goes away.  But the guy who told me that couldn't remember why it is true...

@DavidKetcheson Eventually you end up where you're going to end up - I think people have warrant for letting their personal ambition fade when that happens.

I think self-citation is not a bad practice in general, specially if you consider how most scientific branches work ("standing on the shoulders of giants", although you can also stand on the shoulders of normal-sized people, including yourself). However, there are two scenarios where self-citation or the lack of it can be seen as a bad practice:

Superfluous self-citation. (already discussed in previous answers). It refers to citing minutiae contained in your previous papers. For instance: "we consider the change of variable $y=x^2$ as in myself (1974,1975,1977,...,2012)"
Not using self-citation in order to inflate your results. Sometimes not citing your previous papers can produce a beneficial result. I have seen some researchers publishing a good/decent result, followed by a sequence of clones and mutant papers that do not cite the big one. This, of course, has a good effect on the child papers since it makes them look more original.

+1 for "sequence of clones and mutant papers," which is a phrase I will certainly be stealing to refer to this phenomenon.

As with all referencing, the referenced works must be pertinent to what is being described in the paper referencing them. If one writes about a specific topic where much of the work has been done by the same researcher or research group then self-citing will be quite common. There is of course a fine line between that and "self-promoting" self-citing. It is impossible to try to draw the line based on number or references or percentages of the total number of references. However, it is not common that most science in a field has been made by the same person so referencing own publications where they are only vaguely related is obviously not a good way.
Having many self-citations is clearly not a sign of widely spread science, either because it is not that interesting or because the field is very isolated (or very new). Citing ones own work will definitely become obvious when looking at the citations as you have done. The normal citation index or h-index obviously does not capture this although it is possible to calculate such indecees without self-citations. But as stated above a certain quantity of self-citation is inevitable since it is likely that one publication follows on many others from the same person or group. So self-citation is acceptable to a point. It becomes less and less acceptable when the reason for the citation is pogressievly less obvious and where other papers would be equally good (or better).

Just to build on that, I would add that self-cites are particularly found mostly where they are citing previous methods or research the current paper directly comes out of.

Citing your previous work can be both good and bad. The biggest benefit is it might make people more aware of your work and how it fits in with a bigger topic. The risk is that people do not understand the relevance and think you are self-promoting and therefore take a negative view of you.
The worst case of this is when a reviewer tells you to cite some piece of work. If it is a big laundry list of articles all by the same author, you tend to get a little angry and think the reviewer is trying to promote that author. If it is a single article that is obviously related and the reviewer clearly states that he/she is an author, I tend to be happy to cite it.
The question you need to ask is: are you citing the previous work to promote it or to help the reader.


text:
How do I continue my PhD research project as a Postdoc?
I was wondering if I could get some advice about how to go about continuing my PhD project as a Postdoc. I'm actually from the UK not the US but I think that your answers and advice will still be applicable and really helpful.
So here's a bit of background about myself: I really enjoyed my Plant Science PhD, and even though I came out of it with more questions than when I went in, I managed to get two papers published in two very respectable journals (both of which are still cited today). At the time I wanted to get experience working in other fields, so after my PhD I found a Postdoc in a different research area of Plant Sciences; however, I didn't really enjoy this research area and due to unforeseen circumstances that were out of my control, I came out of it with only one paper, which I am still trying to finish. At the moment I'm employed in Science Services so for the first time in years, I am in a position where I can be choosy about my next job.
What I would like to do is apply for funding to continue my PhD project because I would like to get back into this area of research; I think with the new technologies that are available I could make a lot of interesting discoveries. My PhD supervisor has since retired and has given me his blessing to approach other researchers, and I assume I have to do this before I apply for funding.  Is this correct?
I have no idea how to go about this and if it is even feasible, so any advice you can give me would be great.
Many thanks,
Kate

May I ask how did you find your last Postdoc position?

I just applied for an advertised Postdoc position on the University's website. That's the norm in the UK.

Take a look at my answer at this question: http://academia.stackexchange.com/questions/58020/how-to-find-an-academic-mentor-as-a-professional/58083#58083 // By the way, I have the impression that there are a good number of Britishers participating here.

In the UK there might be one or two early career fellowship schemes that you could apply to. Some have restrictions on when you finished your PhD and require the hosting university to provide some percentage of the funding. They are competitive of course but it sounds like a good fit for your situation - you have a good idea and relevant experience and all you need is someone sensible enough to fund you.

Thanks for your answer Phil. Unfortunately it's been too long since my viva to be eligible for most Early Career fellowships, but after your comment I did a search and noticed that RCUK offers a grant for postdocs at whatever stage of their career (as long as they are not PIs). I may try applying to them.

that might depend whether or not you could justify your current job as a 'career break' of some kind from research. Some universities also have local schemes where you might be able to convince them to let you apply. At least for EPSRC, you have to be a full-time member of academic staff to apply for a grant, but if you can team up with one then you can be named as a researcher-co-investigator and win your own project like that.

I don't think I can justify it as a career break because really it was just due to some bad decisions on my part. Oh I didn't see that but to be honest since I'm not attached to a University I kind of thought that this would be the only way of getting the grant funded i.e. being named as a co-investigator and then applying for the project.
I think I might approach some PIs that may be interested in the project as they may have better ideas of funding than I do. Plus they may know if there are any local schemes, as you suggested, that I may be able to apply for.  Many thanks for your help


text:
Explaining undergrad transfer on application to grad school
I'm applying to PhD programs in math.  The thing is: I went to a great school coming out of high school, but it didn't work out.  (No GPA problems thankfully; just personal stuff.)  I ended up going to an engineering program, where I eventually understood math was my calling, and everything has been going swimmingly since then.
The question is: do I need to explain myself?  Every program I apply to will be getting the transcript from my first institution.  It seems to me I should explain why I left and how I've gotten to where I am.  That said, only one school I'm applying to actually requires a statement about this kind of circumstance, which has left me a bit confused.  Presumably my having transferred will raise questions that I should strive to address in my application, rather than letting the admissions committees' imaginations fill in the gaps.  That said, I feel as though anything I can say to explain the situation will detract from the positive developments that transpired after I transferred, particularly given the prestige I chose to give up.

If there were no GPA problems at the first school, then there's nothing in that first transcript to look askance at; hence, no explanation needed.
However, the specific change you made, from engineering to pure math, might help your application.  Perhaps a small anecdote will help me explain why.
When I took my Calculus III (multivariate), it happened that my fellow students had no patience for proofs.  They were overwhelmingly engineering students. One of them became a self-appointed spokesman for the impatient majority, and would interrupt the instructor in the middle of a proof of a major theorem: "Excuse me, Ma'am, could you skip the proof, please, and go straight to the applications?"
Not all engineering students are like that; and to be fair, the large number of credit hours they are frequently expected to take per semester isn't conducive to stopping to smell the roses.
Conclusion: a brief mention in the essay or cover letter of your change of major from engineering to math might help your application.

I feel it's difficult to give an elaborate answer to the question without knowing the specifics, but I'd say you don't have to be too straightforward with it.
Consider the following:
You want the admissions people, whether that is the HR department or the group leader him/herself, to not be suspicious about your transfer, but you are not sure whether you should justify the transfer to them in your application. Justification sort of implies that something out of the ordinary (or something that requires explanation) has taken place, which puts you in a rhetorical weak position.
Instead of trying to formally explain your choice of transfer, maybe you can take up the subject in a non-direct way in your personal letter or letter of intent or anything like that, which I presume you will have to write anyways.
You can explain where/how you started, briefly touch upon the transfer reasons and work your way to the core: how your transfer caused you to find your calling and how it has contributed to your intellectual development. That way you not only explain that you have transfered and why, but also what positive effects it has had on you, without being a bit uptight about it by writing a separate letter or a specific paragraph about it.
Of course it is possible that I misunderstood your question but that's my two cents :)
Good luck