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On understanding the "code" of recommendation letters
This question deals with letters of recommendation written for students in the humanities, and in particular for those on the job market or those submitting to dissertation grants and fellowships. The question may also apply to letters of recommendation in the sciences.
On this site and in conversations with current faculty members, I have surmised that letters of recommendation are usually written in a kind of "code" (one post here described these letters as a "second language" you have to learn). Since most letters are invariably positive, I suppose that the code is just a subtle way of signaling the true value of a candidate's work or the true extent of their potential. Those who know the code are able to see through any hyperbolic language and decode a letter-writer's real estimation of their candidate.
A common warning about asking for letters of recommendation is: make sure you ask someone who already knows how to write them, or they could end up doing more harm than good. It makes sense that, if someone doesn't know the code, that person won't be able to communicate whatever it is that committees want to see in the letter.
This is all just my ignorant explanation of what I've observed, however, and I would like to ask for more information. I am especially interested in knowing:
-Is it true that letters of recommendation are written in such a clandestine way?
-If there is a code, what is it like? What kind of signals does it have? How do you know when you are reading about a candidate who really is great, versus a candidate who is just fine, when their letters may contain similar language?
If it turns out I am off base on this, I'd appreciate hearing about that too.

Just as an example, taken from this site about two minutes ago: "From what I have seen, it is quite common for far more subtle and hidden negative messages to be put into an academic reference than what you have described. In these cases the references are not used because the letters are there to convey a warning." (https://academia.stackexchange.com/questions/96205/bad-reference-vs-no-reference)

Not an answer, but an explanation of why one may be counterproductive: Take the premise of the question as given - that there's deliberate obscuring of meaning. If the code is explicit then the people that the letters are about all immediately know it too, and then it's the same as speaking very plainly about them (even if they don't see it, they may hear brief phrases from it in interview, for example). Writers would then immediately require even more obscure language, negating the point of spelling it out in the first place! We'd have an even faster form of Pinker's euphemism treadmill

Is OP from germany? If so I think the reason is the same as for employmance reference letters, which have to be "favourable" by law and therefore use this kind of "code" that everyone knows anyway.

One more comment, noticed by a friend in philosophy: http://leiterreports.typepad.com/blog/2017/09/the-differing-codes-in-which-letters-of-reference-are-written.html#comments

I am writing from the perspective of mathematics in the United States.
To the best of my knowledge there is not really any "code" for recommendation letters.  However, there is a quite large amount of inflation, enough so that writing without an awareness of the current levels is a bit like Dr. Evil holding the world ransom for one million dollars.
The process abets this inflation in many ways.  Many grad school recommendations have a bunch of questions asking for the candidate to be numerically rated on a bunch of different metrics -- including things like "honesty", "integrity" and "leadership" -- and you can say things like "The best I have ever seen," "In the top 2%," "In the top 5%", and so forth.  It's more than a bit silly, but having both written the letters and read them I can say that most successful candidates are getting top or nearly top marks in every category...no matter the fact that in most interactions with students, things like honesty and integrity are more conspicuous in their absence than their presence.
To get a sense of the inflationary regime it is very helpful to compare letters written by (many) Europeans to letters written by (most) Americans.  Recently someone whom I have a substantial professional relationship with applied for a postdoc at my institution, and afterwards (he didn't get it, but he got a good one elsewhere) he asked for feedback.  I told him that one of his letters was essentially only one paragraph long (and I told him which one!).  That paragraph was uniformly positive, and I can't point to any specific, factual thing that was missing from it.  However, at the current state of inflation, most letters are two to four pages long.  A one paragraph letter just won't do.  It is not necessarily code for "the candidate sucks".  It might also mean: "I am too busy/selfish to write the letter that I know the candidate needs", "I am not familiar enough with the current state of inflation to write an appropriate letter" or even "In my part of the academic world no one natters on for pages at a time; is it different in yours? What's wrong with you people?!?" In this case, I would suspect the latter.
Added: Inspired by some remarks in @David's answer, let me mention that there are certainly things that will be read in ways that may not be what a naive writer would intend.  I wouldn't call this "code," but others might.  Some examples:

A good letter must explicitly mention that the candidate is both intelligent and talented.  In the absence of this, any other praise may be read as a nice way of saying that the candidate is not intelligent and talented.  Saying that someone is a hard worker without saying they are bright will be read be many as meaning that they are only a hard worker.
Praising someone's teaching must be done carefully, lest it sound like you mean to say that the candidate does not take their research seriously or even does not intend to further pursue their research at all.
Female candidates are often praised for being team players while male candidates are often praised for being brilliant, individualistic and perhaps even iconoclastic.  You should keep this in mind when writing and reading letters for female candidates.  When describing a strong female candidate I make a conscious effort to use the "good male words" like brilliant, gifted and so forth...and also to back them up, of course.

Honestly, I wouldn't be able to write a 4-page recommendation letter even to recommend myself. I'd love one day to read a US 4-page long letter, just to see what kind of mysteriously useful information they might contain. Some time ago, while searching examples of US style letters, I found someone who published what they considered a strong letter (written by someone else) on their website. It was 2 pages long. The writer spent 1 page to praise an (undergrad) engineer for experimental work that I could do when I was 15: does it make any sense? Would I really hire anyone on the basis of this?

(Sorry for the rant, but I'm really struggling to understand this kind of culture)

@MassimoOrtolano Understanding and acceptance are different. We do not choose the culture around us; we can describe it though.

@BorisBukh Given that sometimes I need to write recommendation letters for students of mine who want to go to the US, I'd be more interested in understanding how to write a decent letter for the US standards.

@MassimoOrtolano In my experience, there is less of expectation for a European to write an "American" letter.

I will note that one of the letters (I have not seen the others) that landed me my current TT job was 1.25 pages long, and that was less than 5 years ago.

@Fomite: Well, on the one hand, when I wrote "two to four pages" I meant that in the sense of sheets of paper, not completely filled pages.  On the other hand, it may well be that the length inflation in math is greater than in (other?) scientific fields -- I couldn't know, but it's a vaguely plausible guess.

Is it true that letters of recommendation are written in such a
  clandestine way?

"Clandestine" seems like a very strong way of putting things. But yes, letters are often written in a way where two letters that would both be identified as "positive" using something like sentiment analysis might still have very different meanings.

If there is a code, what is it like? What kind of signals does it
  have? How do you know when you are reading about a candidate who
  really is great, versus a candidate who is just fine, when their
  letters may contain similar language?

In my experience, there are a couple types of signals:

Superlatives: The use of particularly strong phrasing. "I am writing to support" vs. "I am writing in full and enthusiastic support"...
Specifics: Talking about someone in vague generalities is probably a bad sign, even if those generalities are positive.
Phoning it in: If it feels like the letter was somewhat perfunctory, that's also a bad sign.
Damning with Faint Praise: Anything where the reader would come off feeling somewhat tepid, even if the language itself is fairly positive. "X's work is solid..." is not a ringing endorsement.
Comparisons: "My best student..." vs. "Among the best..." vs. "A valuable member of my lab..." can help provide an informal ranking of applicants - presumably hirers want to be pulling from the top of the pool. This also shows up in things like highlighting where they were singled out for something.
Qualities: For tenure track jobs, lots of language emphasizing their ability to work independently, generate new ideas, etc. are good. Things like "X is a hard worker..." aren't good, because you're not being hired into a lab, you're being hired to run one.

There's also more insideous code that creeps in, either intentionally or via implicit bias, like describing a female candidate as having "an impressive track record for a woman."

My experience is in the sciences and engineering, not the humanities, but I'm not aware of any such code.
Many professors believe that a recommendation letter has to be an honest evaluation of students, not just a list of highlights. Honest letter writers are highly valued, and people eventually see through dishonest (sugar-coating) writers that don't tell the full story. Sugar-coating a mediocre student does a disservice to all the other great students you could write great letters for.
Thus, if you ask me for an academic reference as a classroom teacher, then I'm obligated to discuss our entire history and not just the classes you got A's in. That's not me trying to sabotage anyone, that's a reckoning between your future desires and your past performance.
It's critically important that a student asking for a letter as well as the letter writer have a common understanding of what will go into a letter. The letter writer should be upfront about their evaluation and what they can or can't say in the letter. If a writer doesn't feel they can write a strong letter then they need to tell the student this and why. If the writer does not tell them this then the student needs to ask clarifying questions until they are satisfied that the letter will accomplish their goals. There is no shame for the writer or the student to suggest that perhaps the student ought to ask around for someone who can write them a really strong letter if they're not satisfied.
Edit: I will note that there are many subjective evaluations of students, perhaps moreso in the humanities, that would be subject to coding. In the same way that badly outdated houses are called "quaint" or "homely" there is a vernacular that develops about students. The goal here however is not to be clandestine as much as it is to save face and put the best positive spin on a student. Such coding is highly subjective and not a reliable way to convey intent however, so it's best to stick to specifics. For example, if I say that a student "works really hard and stays late most evenings" that could mean that they're (1) a diligent worker or (2) they take twice as long to finish things compared to a normal student. Moreover, I don't know which way that someone reading my letter will interpret that statement, so it's better to leave it out and be precise: "diligent worker, stays late when necessary".

I don't see how/why someone should not ask the person that can write the strongest letter anyway. The people I asked to write recommendation letters were the best suited people, the closest supervisors, the qualified researchers with whom I spent most of my time.

@Mark The reality is that many people get to their junior year of college and suddenly realize they need letters of recommendation, and just happen to ask whomever they're currently taking classes with. These are the people you need to gently prod in the direction of someone more suitable. It's also the case that many students don't understand what makes a good letter of recommendation, so they ask someone they got an A in a class with rather than someone who can speak to their strengths as a person.

In my experience, this is absolutely true in the sciences as well.


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Definitions and proofs in extended abstract(mathematics)
I have to submit an extended abstract of my paper for a competition. The extended abstract must be about 2~4 pages, and the competition requires it to include all the methods and results. Of course, specific definitions and proofs are included in my original paper(about 20 pages), but I can't just summarize them all into 2~4 pages without omitting some ideas or methods. So my questions are

I have some concepts that are not frequently used. Should I write them in my abstract?
Do I have to write precise definitions?
How should I summarize my proof? Can I skip the specific processes and only state main ideas? Can I omit proofs of lemmas?

(My advisor said that he has no idea of how to write an extended abstract, so I hope I can get some help from here)

Before you start writing, try to create a 5-minute elevator pitch talk about your paper. Imagine you're describing the results to your friend (or actually invite a friend) and talk through the main idea of the paper. Practice it several times and note which things you keep in, and which you decide to leave out. This will give you an idea of what to include in your extended abstract.
It is simply not possible to squeeze everything from 20 pages into a 4-pages without losing something, so stop trying. Inevitably you will have to omit some results, or simply name them without going into details. You will have to drop some technicalities (which can contain some useful ideas as well) and so on. The aim of the extended abstract is to communicate the core ideas, not fully elaborated proofs and  methods. The elevator pitch technique above helps you to tell what's central and what's not.

source: Stack Exchange

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Professor never sent in recommendation letter
I have been applying to PhD programs and asked multiple professors over a month in advance if they would write me letters of recommendation. For two of the programs, one out of the three professors never sent in their letter. One program is already almost three weeks late and the other is a few days late. Note that they did send in letters for other schools, so this has left me confused. I feel pretty disrespected and hurt as I spent quite a bit of time on these applications as well as over 200 dollars. The professor has not returned any of my emails. Note that I cannot or could not have seen them in person as I was out of the country.
With this said, what would the programs do? Will they just throw out my application?  I've also resolved to email the programs asking if I could have a different professor write a recommendation letter and send it in. If the programs agreed to this, how should I ask the new professor? They're the head of the department where the other professor who hasn't sent in the rec letter for the two schools works in. I don't want my email to be read as "you weren't my first choice for these programs but I kind of need your help". Would saying something along the lines of "Dear Dr. Professor, One of my letter writers for schools A and B never sent in their letters. After emailing A and B, I am allowed to have another letter sent in and am wondering if you would be able to write one for A and B?". Note that this professor did write letters for other PhD programs that I applied to, so I think it wouldn't be too much of a hassle.

Don't explain why, just ask for the letters.  Apologize for short notice and tell the professor it would be "helpful if you could send the letters right away."  (The professor will probably figure it out, but there's no need to make a point of it.)

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Is it ok to ask my professor about a project for a second time?
Note that I am currently an undergrad.
One month ago, one of my professors agreed to let me work on a research project with him. After a few weeks of not hearing anything from them, I emailed the professor asking about the project (1.5 weeks ago). He replied saying that he would be contacting a collaborating researcher (at a different institution) in the project within two days and can discuss a roll for me with them. Based on the language of the email, it seems that he had been waiting for me to email him. He said that he would contact them in two or so days, so 1 week ago, and then get back to me.
I still haven't heard back from them and so I am wondering if it is inappropriate for me to email the professor and ask about the project a second time? (note that based on the current situation, we can only email each other and not talk in person). I realize that many times going through such a process can be a bit slow but I am in a position where a recommendation letter from this professor (who is well known in their field) would be significant, as he could then talk about my academic experience with him as well as my research experience with him.

As a somewhat absent-minded professor, I never mind when students send a polite reminder about something I had said that I would do. Maybe give it a couple of days. Waiting nearly 2 weeks wouldn't strike any reasonable person as a sign of impatience.

I think this is fine! I would email to ask if they got ahold of the other professor and, if so, if they would be interested in setting up a call to discuss further. Here is my availability etc.

First and foremost if you have the option to visit their office, I would highly recommend doing so before sending the second email. Because I have had professor that have lost my email in the dozens or hundreds that they receive daily, and a simple office visit was sufficient enough to clear it up

Professors get tons of emails and a significant proportion of them will slip through.
If you can not go in person then: Yes, write again but be careful about the tone. Make sure that it does NOT sound like an accusation ("You promised to write within 2 days but you didnt!"). Better along the lines of: Sorry to be bothering you again but I was just wondering if there are any news on the project we had in mind? etc I want to again express my strong interest into this project and I would be really happy to work with you on it.

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Team conflict in a large research project
I am an undergrad working in a large research project (1 PI, 5 grad students, 15 undergrads). The project has 5 main facets, each of which is the primary responsibility of a single grad student. The undergrads are distributed as: 7, 3, 3, 2, 0. I am part of the 7 undergrad team.
Now while the grad students are the "leads" the PI treats us all equally.. because some grad students came in after the undergrads started the project (is the case for my team, I have been involved longer in the project than the grad student who is the lead).
The problem is there was an email sent by me, written rather quickly, and the grad student twisted some of the words I said. Sent a team wide email to the undergrads in my team, the other grad students, and the PI suggesting some malicious intent on my part.
Should I explain my side of things in an email? Or wait until the meeting the PI has called for? I want to do this before people start forming their own conclusion, but I'm not sure if I should wait or not.
I said: "not everyone has put in the same amount of effort in this project"
which was twisted as if I said: "I did all the work, no one else did any work" (i.e. the most extreme interpretation)

This question does not sound too academia- or research-specific; it might be more suitable for Workplace.SE.

Deal with the issue head-on: send an email apologising for the ambiguity and saying that you weren't trying to be critical or suggest others weren't pulling their weight. That you wrote the email in haste and didn't phrase it well as a result.
Don't wait for others to draw their own conclusions. It's very easy to misunderstand a terse email.
It's probably also worth talking to the grad student in person, if you haven't already done so, to make the same points and defuse any ill feeling.

Agreed, it is important to note that while OP may not have meant it that way, his e-mail could have definitely been read that way. Using 'twisted' implies malicious intent on the part of the grad student, while it just might have been a misunderstanding. I would encourage OP to indeed apologize and make sure to take the blame for the ambiguous wording, and refrain from saying things like your words were twisted


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Why do PIs say no to students working during grad studies?
Professors in my department frown upon students working (part-time or full-time) during their MSc or PhD. Even extra TA hours are looked down upon...
The rent on-campus is ~$950/month and we are paid ~$18000/year. So there is enough money BUT the on-campus housing is very limited so students usually have to find off-campus res ... which is ~$150 more per month. Again, while I can make it work w/ $18k, I'd like some extra income to help pay off undergrad loans.
What is the reason behind saying no to students working while doing graduate studies? I'd like to understand the PI's perspective.
Does working while doing graduate studies affect the student's performance negatively?
University: top-20. Area of study: life science, computer science.
(Unrelated question: how many hrs/week should students put into their lab?)

Would you please clarify that $950/month include meals and utilities or $950 is just for the room? Also, what do you mean by $150 more per month, that include meals and utilities?

@scaaahu One dorm room with internet+heat+hydro+other stuff included. Mentioned that only to give an idea of expenses.

The whole purpose of my question above is to figure out if $18000/year is enough to cover the living expense.

@scaaahu it is but only bare minimum. $18000 gets me a room, food, and $100/mnth in other expenses.

maybe bcs all point of PhD is to study and work on research project???

If you had a full time job and started an other (part-time, full-time) job, do you think your first employer would be happy? A second job means that you cannot change turns easily, you are probably going to be much more tired and less productive.

Extending @Bakuriu's comment.  If you had a full time job and started another job with better compensation and benefits do you think your first employer would be happy?

If the pay is unacceptable to you, why did you sign up for this program? Did you not know about the pay when signing up? Were you misled about being allowed to take on side jobs?

Btw, in the U.S., often undergrad student loan payments can be deferred (I believe interest-free) while in grad school...

He just does not work his free slaves to spend their energy on something else. 18k a year in US is way below poverty line.

@Superbest being optimistically informed about costs (or interpreting advice optimistcally) is a common problem.  In this case the OP could have been led to expect that they would be able to be housed on campus, only to find they were in a small minority that couldn't.

Personal Investigator?

I'd suggest you look into tutoring outside the university.  You can determine how many hours you work, get paid reasonably, and you don't have to tell your PI.  @SuperBest, coming out of undergrad it is hard to know how much you need to live on, your comment is not constructive.  Also, only for specific loans will the interest be paid by the gov (https://studentaid.ed.gov/sa/repay-loans/deferment-forbearance).

Can you get a roommate? My apartment in grad school was $1000/mo, split between two people wasn't too bad. Of course it depends where you are geographically and YMMV. FWIW, when I was in grad school, having another job wasn't just frowned upon; it was expressly forbidden by the department.

I have the impression that you are pretty aware of the main reason why PIs tend to frown upon outside jobs - they take time and mental energy, and most PIs will expect you to commit as much as you can of both to your grad school project. Hence, working on the side will typically  affect the student's performance negatively.
There is also the added problem that outside jobs often provide unwanted rigid commitments, which tend to interfere with the somewhat unstable nature of grad school workload. It is exceedingly annoying for a PI if a major paper deadline needs to pass, because the student also had important duties at their day job that they could not get away from.

"outside jobs often provide unwanted rigid commitments" - indeed, and such commitments are considerably easier to handle when they are imposed internally by the same PI who wants the student's research to go on.

At the risk of criticising the management skills of some PIs, "working the side will affect performance negatively", whereas "pulling a few all-nighters back to back because we're behind on our paper deadlines", sure, that's all positive, you should totally make sure your students are free to do that whenever you like ;-) If PIs treated sleep as a fixed commitment then they might be better-placed to manage their way around other fixed commitments. The issue with work really is, I think, that it's a commitment the PI disapproves of. If it was childcare you might (might) get more sympathy.

@SteveJessop Not that I am disagreeing, but the OP asked why people disapprove of outside work, not whether this is justified.

@xLeitix: I suppose my insinuation is that (for PIs who aren't especially effective managers) the PI's actual feelings about it and reasons for refusing it ("aargh! I don't know if I can cope with this!") might differ slightly from their stated objections ("it will interfere with your progress and your responsibilities as a student") ;-)

I actually did try working parttime during graduate school for the reasons you give. In my grad work, I was paid for 20 hours a week of research (I had a research assistanceship) officially.
This doesn't sound too bad until you:

Add in time for classwork

Both homework and attending the class

Add in time for breaks (lunch, etc)
Add in buffer time for busy seasons for my grad work

Additionally, there are a few other factors. First, you greatly benefit in graduate school by having time and flexibility to ponder/investigate things without feeling time stressed.  This is harder to do if your entire week and evenings are full.
Second, most graduate research jobs are effectively a "fulltime" job. I was paid for 20 hours a week, but my advisor/PI's expectation was more to treat it as a fulltime job, between all the above factors (homework/classwork/etc).
YMMV on hours expected. Some assistanceships will be incredibly focused on 20.000 hours a week, no more no less. Many will not, particularly research ones.
Graduate school tends to be more loose and spontaneous than work, too. Each department/PI will have their own feeling here, but in my experience graduate school is a lot more likely to spontaneously decide to have a meeting or cancel/reschedule something than the working world in such a way to inconvenience you. At work, moving a meeting from 10am to 11am has minimal impact since I'm at work all day anyways. In grad school, if portions of my schedule are blocked with work, it's really hard to do this effectively.
Ultimately, I ended up finding myself frazzled to the point where I couldn't keep up in graduate school, so I quit my part-time job.

Fantastic, I was really looking for someone with this type of experience. I am leaning towards not working part-time unless I have total flexibility.

@player87 I hope it's helpful.  Graduate school can be intimidating and in many ways is intimidating.

"Second, most graduate research jobs are effectively a "fulltime" job." This. In the dark, I would suspect any supervisor that downplays this to be lying to you.

This may not be totally relevant to your question, but I think it should be noted that there exist PIs who don't think the same. For instance, my professor does not have a problem with me having a part-time job, as long as I do my main job. The reason is, as he told me once, life is hard enough for us and if we are prohibited from making some money, although we would have more free time, but our mind would most likely be occupied by financial concerns and primary needs, which results in declining the overall performance. He made his point by saying that a PhD degree is on top of Maslow's hierarchy of needs while food and shelter lies at the bottom. And it is really hard for a human mind to ignore the bottom and focus on the top.

There are several possible reasons for your supervisors to frown upon your involvement in non-academic work.
I think the most probable concern is that you will end up being overwhelmed by the cumulative workloads of research and flipping burgers, which might prevent you from making a significant enough scientific contribution to deserve a PhD. Most supervisors care about the career prospects of their students.
Of course there is a corollary: your commitment and output to the lab is smaller if you're invested in a side activity. A student is a significant investment in money and effort for PIs and they naturally prefer focused and high performing ones.

The PI wants to pay you for 20 hours/week of work and get 40-80 hours/week of work out of you.
If you get a part time job, or any other commitments really, you won't be available to work 40-80 hours on the stuff the PI wants you to do.
A really bright student working 40-80 hours/week on the PI's projects will both help the PI advance their own career, get the things that the PI wants done done, and is (very slightly) more likely to be a student who graduates and goes on to become a useful contact for said PI in the future.
They don't want to pay what a really bright person who is competent in computer science can earn outside of academia on a 40-80/hour schedule.  Instead, they pay 18$/hour for a fake 20 hours/week 50 weeks/year and hope for 40-80 hours of work.
Initially, you may be spending the extra hours/week on classroom instruction, but that tends to fade rapidly.
This is similar to the internist trap in other industries like publishing.  Underpaid or unpaid interns at the start of their career are expected to donate their effort to produce things of value to prove themselves.  A percentage of those are then invited onto the next tier (postdoc), where they are still underpaid (after all they compete with the previous tier somewhat) in precarious contracts for a period of years.
A percentage of those are then invited onto the next tier (tenure track in the academic case).  Some percent of those are still winnowed out, with the remaining fraction of a fraction of a fraction of a fraction going on to get tenure.  Most of those who get tenure are at some small university with limited research opportunities, and only a small fraction end up being the kind of professors that are imposing the above constraints.
With tenure, your promotion/salary increases are then tied to your ability to do the same to the next generation.  If you can convince dozens of new grad students and postdocs to work 40-80 hours/week on your research you'll be co-author on all of their work.  When they graduate, they'll cite your papers, granting them a high impact factor.
So why does the PI frown on outside work?
There is an oversupply of overly optimistic people who want to be academics, caused by the lottary nature of the system and the fact that each layer is selected from the people who "won" the previous layer.  They can use this to convince you to work extremely long hours for little pay.  Those who do not buy in are not as useful to the PI.
Or, because the PI can.
Now, if you really want to become an academic, or really want to focus on your research problem because you want to solve it, this is in your long-term best interests as well.  A chunk of the payoff for the PI is having those students who graduate and go on to do great things, and by putting in the hard long hours you are more likely to make it out the other side of the pyramid intact.
Still unlikely to make it out, but less unlikely.
Now, I know of at least one Computer Science grad student whose PhD project (with their supervisor's work as well) turned into a commercially semi-viable startup, which then sold for a few million dollars.  They then semi-retired and started working on fun projects (what others might call work) outside of academia.  Being paid enough to eat while working on such a project may be economically reasonable.


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What are the expectations of bioinformatics Masters students?
Country: Looking for answers for US/Canada/UK/Germany, ideally Canada.
Subject: bioinformatics

I am starting a bioinformatics MSc degree in a biology department of my university (no bioinformatics dept exists).
Until this point, I've talked mostly with grad students pursuing biology degrees. The expectations for bio MSc student have been described to me as produce data for 1-2 figures. PhD students are expected to produce good data for an entire paper, i.e. 5-6 figures.
Similarly, what are the expectations for MSc students in bioinformatics?

For masters, is it possible to take an open source tool and build on top of it to solve some issue it has?
Basically there is a tool that has two components A and B. Component A is fine as it is but component B is done poorly - so many people can't really use it. Can I take this tool, scrap a part of it and redo it?

That depends a lot on your university, and you should possibly have some university guidelines of what is expected from Master students. Differences can be tremendous, up to the point that some universities require original research and some don't.

Are you interested in "research" MS programs (i.e., a thesis requirement) or "professional" MS programs (i.e., no thesis, but maybe a report or other capstone project)?

@RichardErickson I am interested in a research, thesis based MSc programs.

As @svavil said, it depends on your university and thesis supervisor. There are many different fields in bioinformatics and many different options to do a thesis. We have had students help building a specific tool (where the basis already existed), work in a research collaboration and develop a method to analyse their data (this is what I did), do part of a complex analysis, develop a browser tool for some smaller task, and so on. It depends on what currently is interesting for the supervisor and what is interesting for the student. There are more informatics based thesis and bio based ones.

When you asked the bioinformatics students this question, how did they respond?  When you asked your prospective advisor this question, how did they respond?  (You did ask those people, didn't you?)

Hopefully I can help - graduated a similar Master's in EU.
At least here, a PhD student is expected to produce 3-4, not 1 paper, so it is reasonable to expect contributions equivalent to one paper from a Master's student. Of course, time is limiting, so students usually finish the actual paper later on (sometimes even during the PhD), but I would suggest working with that goal (i.e. 1 paper) in mind.
Now, as to what constitutes a paper in this field: improving a tool is fine, as long as you provide proof of the improvement. Proof usually comes from simulation studies, or it could be a demo of application using some publicly available data (I assume your tool is somehow connected to data analysis). In my field, this might be one of the best known examples - improving the efficiency of a popular tool from O(n^2) to O(n) is a direct way to Nature Genetics and hundreds of citations.

This may be a tad late, but as someone about 6 weeks off from defending my MSc in Bioinformatics (and having watched a couple of people from my cohort complete), I may be able to give you an idea of what I've seen at my institution (a large multi-hospital research institution in the US).

What are the expectations for MSc students in bioinformatics?

I'm not sure I'll be able to frame the requirements as you have. That said, for the MS, our guidelines state that our thesis project can consist of, and I'm paraphrasing here: a novel implementation of software to an existing problem (i.e. your software improves on existing solutions in some way), a significant improvement to an existing software, or the application of current software to a novel problem. Fortunately, being a large clinical institution, we have no shortage of novel problems to solve.
So, what does that mean regarding the breadth of the project?

For an MS, we often don't generate our own data but may instead take data that already exists from research done by a lab on campus, a lab at an institution we're collaborating with, or public data sets (e.g. TCGA, ENCODE, ClinVar, Reactome Pathway Database, Uniprot, etc.).
We'll then mine this data to get at our biological problem of interest, use it as a development set for an algorithm or method, etc. Another approach may be to generate a novel data set by combining multiple data sets in a clever way.
Keep in mind, there are a number of highly respected bioinformaticians, Atul Butte at UCSF comes to mind, who have launched successful companies by mining public datasets and combining their domain knowledge and experience – there's a lot of public data out there waiting to be transformed into knowledge.

For masters, is it possible to take an open source tool and build on top of it to solve some issue it has?

As you may have guessed by now, I'd venture a yes – provided your improvements enhance its value in a significant way (particularly in terms of reproducibility and validity, but usability matters too) and is already a widely used tool for a specific problem or (ideally) class of problem. That said, whatever improvements you make should target a specific problem and improvements should be measurable in some way.
Regarding figure counts, I wouldn't worry too much about them. For an MSc, they're less relevant given that you probably won't be producing your own data rather than conducting a deep analysis. I've generated hundreds of graphs, tables, etc. throughout the course of my research in an effort to understand the underlying complexity of the data and the problem at hand. Visualization is a necessary and powerful tool. I'll likely include somewhere between 8 and 12 in my final thesis writeup.
Hope this helps.

In its core the same expectations apply to all types of masters in all countries.
You need to find a subject of intrest and either contribute with something noone else has tryed before or redo some other persons work from another angle.
It doesn't matter what you choose to work with, as long as the questions you try to answer is of acedemic interest. And likewise there is no final answer to how much data you should produce; it should just be enough to answer the questions you focus your work on - no more, no less.
There is no problem in rebuilding on top of an open source tool. However, if the persons who originally developed the to tool, proved that the tool can do whatever it is supposed to do, the core question cannot just be "can I make this tool better". Instead you could eg. ask the question "by applying desing-principle K to component B, in tool X, can we make more people use tool X?". And your work would then both concentrate on redesigning/rebuilding component X and proving that more people will use it.


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How to deal with scooping when doing open-source tools development?
I am developing a tool for bioinformatics ... it is an application that will be open source when finished. It is something that has use outside of bioinformatics as well.
I am also using some open source tools to develop my application. When I need help with the open tools I'm using, it's kinda difficult for me to get the help I need without telling the people what I'm using it for.
I asked my prof if I could make the app public while it's in development, and he suggested it might be a bad idea to do that because of the potential of someone scooping the work and publishing it before we get a chance to do so.
My questions are:

How serious is this problem? Do people really just take someone else's work and publish it as their own? And do journals really allow this?
My prof mentioned this in terms of someone developing the tool on their own and then publishing it (i.e. take the idea but not necessarily the code). Is there anyway I could have my cake and eat it too - i.e. make the tool public and still guard against scooping?
How does your lab deal with open source tools? Do they get released to public before the publication?

Are the other open source applications you are using GPLed? MIT? What are they licensed as?

Would you be releasing something that's already in somewhat usable form?  Or will it basically be mostly broken code (presumably so you could ask for advice on how to make parts of it work)?

Actually, since you're going to eventually open-source it anyway, what's the tool basically for?  Is it database-related, a computer algebra system, a graphical interface, data analysis via AI, etc.?

I have all my code on github simply out of convenience. If anyone ever looks at it, I wish them luck with that mess...

"it's kinda difficult for me to get the help I need without telling the people what I'm using it for" - You may have to re-think your way of seeking assistance. Have a look at stackoverflow.com. Millions of questions related to programming problems and very few need to publish more than, say, 20 lines of code plus some description of what one is trying to achieve and what does not work in this snippet. Sometimes people also produce artificial sample code to illustrate their problem w/o disclosing the actual code. Isn't that feasible for you?

@chessofnerd haven't thought of that yet, but it'll probably be "do whatever you want with it, with attribution"

@JimmyB Unfortunately, no. It requires the open tools' development cycle to be altered in a small way so I'll need to explain why .. and in doing so I'm giving away the idea.
The open tools' developers didn't think of the way I'm using their tool. I'd love to tell them if not for this scooping concern.

"My prof mentioned this in terms of someone developing the tool on their own and then publishing it (i.e. take the idea but not necessarily the code)" That's a risk with any piece of software. If that wasn't a possibility you'd probably be looking at an anti-competition lawsuit. Even after you publish there's nothing to stop someone looking at what you've created and doing it better.

If you use GPLed code, unfortunately you won't be able to do a "do what ever" license. You will need to be careful to respect the third party licenses of the libraries you use.

Having developed academic open source software for 20 years, I have never heard anyone getting "scooped" by putting code out there. And I know lots of people who do all of their development out in the open, often years before they have it all together to make it into a publication.
I believe that the reason why this never happens is that it's difficult to take someone else's code and understand it in sufficient detail without the author's deep familiarity with the subject. Certainly to understand it at a level that would allow that person to write up a publication about it and claim that it's their own invention. (That's in addition to the fact that everyone knows that that would be unethical.) It's so much easier to collaborate with the original author if one had to add something because then one would have the person who understands it all help you with it.
So I wouldn't worry about this. Put stuff out there and see that people use it. You'll build a reputation that way, and that's what you're going for. If you keep things secret, nobody will know it but you also aren't going to gain any reputation points for it.

That's not to mention the sheer amount of time it takes to do this research. (You researchers know this all too well.) If someone was already trying to do the exact same thing they might be able to trim off some days by grabbing some code, but I think the time they spent monitoring you to FIND the code you put out in the open would set them back more than it would help them.

I suggest to edit your answer to include that some consultation with the prof. is arguably a good thing to do before publishing anything. I.e., "Consult your prof., convince him, and then put stuff out there and see that people use it. Don't go blatantly against what (s)he said, at least not after discussing it."

@Clément -- of course, communication and finding agreement is always the first step!

Maybe you want your contributions to explain what you will be needing it for. So that if someone invested the time to copy your work you could have a history of steps you were taking to solve the problems you found along the way. And it will be easier to put the spotlight on the unethical person trying to claim your work.

In response to your third question, my group actively pushes to make our work open source. This is particularly important for our more refined/developed tools, which I believe are closest to your own work.
The reasons behind this push are many but a primary incentive is the increased visibility and collaboration opportunities. Making our code available and open to all is a great way to increase uptake.
We also believe that performing science 'in the open', as it were, improves the quality of the science done. Our group actually requires that all of our papers are published as open access, open source is therefore a natural extension of this.

I would like to echo Wolfgang: this just isn’t something that happens.
But more to the point, your professor seems to misunderstand what “publishing” means:

he suggested it might be a bad idea to [publish the application during development] because of the potential of someone scooping the work and publishing it before we get a chance to do so.

If you made your code public, you published it. Sure, this might not be the very academic type of publishing that your professor had in mind but that’s irrelevant here: for the purpose of scooping, it establishes a clear priority. If somebody actually took your code/idea and tried to pass it off as theirs in a scientific journal, this would be plagiarism and there are mechanisms to catch that. (Admittedly these mechanisms occasionally fail but they would probably at least help you getting your results published as well.)
In summary: not only is scooping not a realistic concern with Open Source software, but early publication actually mitigates the risk of being scooped.
In practice, most bioinformatics labs — particularly the famous ones — usually open-source their code way ahead of formal publication in a scientific journal. This is true for most recent bioinformatics software that you’re likely to use.


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Making the most of having two group affiliations
I am co-supervised by two PIs and I am spending half my time each week in one lab and the other half in the other lab.
My question is, how can I make the most of this situation? What are the pitfalls? How does this differ from being supervised by one person and therefore spending all of one's time in one lab?
I am a PhD student, but I suppose this could also apply to post-docs. If it matters, my field is biology.

When the two PIs are at different universities, you could perform your thesis as a double degree (something I did myself), assuming that both universities allow this. One aspect that needs to be taken into account is that if you do so, you need to adhere to the regulations of both institutions, which sometime leads to conflicting requirements. Also you need to align with the bureaucracies of both institutions, which certainly results in some overhead for you.
Anyway, even when the PIs are at the same institution, you can profit from their (hopefully somewhat complementary) expertise. Also you will have a larger network. You will need to balance your time between both research groups, and align their feedback, which is a potential pitfall, but also a learning opportunity.


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How do I get LOR from a project mentor who's still pursuing PhD since she doesn't have an official email or access to the University letterhead?
I plan to apply for Masters. I am currently working as a research intern at a reputed University in my currently. I was assigned a Ph.D. mentor on joining the project by the Professor. Ph.D. mentor guided me on a daily basis and has a better understanding of my work and abilities than the Professor. The professor has little knowledge about my capabilities and I'm afraid he'll give me a very weak LOR if at all he agrees to give. Is it advisable to get a LOR from my Ph.D. mentor considering she does not have an official University email address or the University letterhead?

Ask the professor and your grad student mentor to write the letter together.

It strikes me as odd that a PhD student/candidate does not have a university-linked email. What country, if I may ask?

@paulgarrett I'm in India. Planning for Masters in the US. I found it a bit strange as well. When I asked, she told me that all her official University emails were sent to her Gmail address. I am trying to get the professor and the mentor to write the LOR together. But the issue is that the Professor is often traveling and uncooperative.

I think the "travelling" part is not a huge obstacle to writing a letter, but "uncooperative" could be fatal. In any case, get the PhD candidate's letter. Letterhead and email addresses are not usually considered critical factors here.

Although it looks more professional to have a faculty email address on a letter of recommendation, it is not a must.
The person that you are asking might have left the university, and also they might not yet have started in another university. This would not prevent you from having the letter of recommendation.

It is not advisable to get a letter of recommendation, even for a masters program, from somebody who is still a graduate student.  Letters from graduate students are generally given very little weight in admission to U.S. graduate schools, and there are good reasons for this.  Graduate students cannot be relied on to have the experience to evaluate students skills, relative to other typical graduate school applicants, or necessarily to judge whether a student is ready to complete a program of graduate studies.
Whether the letter from the graduate student is on official letterhead is of very little importance in comparison.

True, but a good letter from a PhD candidate is better than no letter from senior faculty, etc.

@Buzz My Ph.D. mentor was previously an associate professor before doing Ph.D., so has some experience of mentoring students.

@Ish She was an assoc. prof. before a PhD? That's not possible.


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Creating bibliographies, 25 years ago
I'm interested in the academic history of creating a bibliographic reference list. The time period is early 1990s. I want to understand how former researchers have done their writing.
Introduction
25 years ago in the year 1993 scientific publishing was not done with Internet but somehow else. From the history lesson it is known, that the first electronic OPAC systems were invented and they were used in many university libraries. The OPAC catalog didn't contain the fulltext article but only the bibliographic references, for example author, title and year. The technology behind the early OPAC system was perhaps a desktop IBM PC, but I'm not sure. It is also possible that no electronic OPAC was available but only the good old card based catalog. In any case, the cards were not handwritten but with a typewriter, so the user of the library were able to find the correct book in a short amount of time.
Question
After the short introduction for explaining the general environment in the early 1990s there are some open question which I wasn't able to answer alone with literature research. So perhaps somebody has a personal experience and knows the details. The problem is, how the researcher can write his manuscript with a mix of a card based catalog and an early digital OPAC. The problem with the OPAC in that time was, that no copy & paste was possible. Suppose, I've found an interesting title on the screen, whats next? Should I write down the bibliographic reference direct in the manuscript or can I send the information to somebody else? A similar problem is given with the card catalog. Suppose, the researcher found an interesting looking entry. Probably it was not allowed to take the card out of the catalog and insert it in the own bibliographic references, so how has the researcher in that area solved the problem?
The next question is the sorting of the bibliographic references. Suppose, somebody has written down all the entries and want to insert a new entry alphabetically. What is the best practice method for doing so?

I speculate that the answer to all your questions is "manually".

You made your alphabetic reference list with a pencil and paper, once you had them all in the correct order you wrote or typed the final list - one friend put all the reference books in order on his desk and wrote the list from there...

BiBTeX was initially released in 1985...

And before BiB TeX some of us had written straight TeX macros to do it...

And that ignores the various tools available with nroff, troff, etc...

From your questions, you seem to consider the 1990s a kind of mythological era where (former?!) researchers used to perform arcane rites. But let me set this straight: if we couldn't use the cut & paste function, we would simply sit at the desk with pencil and paper and copy down whatever information we needed to copy. And, yes, in the 1990s we had LaTeX, BibTeX, drawing tools, CAD tools, symbolic and numerical tools, etc. So, it wasn't exactly the stone age.

Even as early as 1993, many researchers had access to the internet, email, ftp file transfers, and the nascent world wide web.  You could submit papers to some journals by email.  You could go back 10 years before that and find a small community of researchers who had access to the internet.

how the researcher can write his manuscript with a mix of a card based catalog and an early digital OPAC --- My Ph.D. thesis had a bibliography of about 1000 items, and I simply typed them in. But LaTeX was available, so alphabetically inserting items wasn't an issue. Some of the references were handwritten on paper before I went to the "math graduate student computer terminal room" for writing, but most were photocopies. with holes punched in, that were inserted in the numerous loose leaf notebooks I had of papers, and I just typed the information in from the paper. (continued)

Of course, papers before a certain time (some journals it was early to mid 1980s, other journals it was before the 1960s) did not have the journal's name, volume number, year, etc. information printed on the first page of the paper, so I always wrote that information myself at the top of the paper's first page right after making the photocopy, before putting the journal volume on the bottom shelf of the re-shelving library cart where I put "finished volumes", after which I reached for the next volume I had on the top of the re-shelving library cart to photocopy.

Incidentally, at the beginning of writing my thesis I was using index cards for bibliography entries. Each card had the title, author, journal information or book publisher information, some possibly important-to-me things about the paper/book, and the LaTeX citation code (written on top right corner, in red ink to easily see at a glance) I was going to use for the paper/book. After about 40 or 50 cards, I stopped making them. For the LaTeX citation codes, I wound up using stapled print-outs of the bibliography of the LaTeX code as a "dictionary" to look up citation codes when I needed them.

Oh my. We are quite a history-less field, aren't we, in computing? I programmed an OPAC system in the 1980s and we were not the first by any means. What you mean by "bibliographic information" is called metadata. There were many different systems (MARC - Machine-readable Catalogue) around. We argued about things like having multiple of the same tag for all the different authors or having different tags so we could model the order of the authors. In Germany the art of cataloging literature goes back more than a century. There is the Regeln für die alphabetische Katalogisierung (RAK) that was put forth in the 70s to get away from that horrible Preußischen Instruktion used since 1899 or so.
We used index cards for keeping track of references in our own publications. We used pen and pencil to write on the cards, or even typed them up on a typewriter. The cards were very easy to sort (and re-sort), so the last thing you did was type up the reference list. Or you used BibTeX, if you had access to a machine that could run it. There were lots of computers before the IBM PC, they just weren't personal computers. If you didn't have access to a computer, you used a typewriter and lots of Tipp-Ex. Or you ended up retyping every page when the number of errors got to be too many.
I suggest reading up on the history of library catalogues (VOX will point you to a book in English on the subject) and then about OPACS if you want to look a bit deeper into the history. But you need to go back more than 25 years.

The typical incomprehension of "old times" among 20-somethings is hilarious. In various situations, I do manage to provoke my (math, in the U.S.) grad students... often in response to complaints that something (computer/internet-related) is "down" or "not reliable"... by recalling the days when there was no wifi, no cellular phone system, no internet, and long-distance phone calls could easily break one's budget. Preprints had to be sent by physical mail... "Card catalogues"! "Index cards". Typewriter font?  :)

Remember when a Citation Index was an actual index you had to page through? :-)

@aeismail, and nothing was "searchable" ... :)

"Back in the old days, we had to alphabetize things BY HAND..." :)

Consonant with many of the comments and Debora Weber-Wuff's answer, you may find a goldmine in Umberto Eco's How to Write a Thesis from 1977. Not only does it explain index cards, but it also factors in what books are available at the library. (The last time I mentioned this book, Massimo Ortolano confirmed that it is an Italian standard resource.)
First published in English in 2015, the guide is even advertised for the throwback factor, on the "overview" page by the MIT Press:

Of course, there was no Internet in 1977, but Eco's index card research system offers important lessons about critical thinking and information curating for students of today who may be burdened by Big Data.

For what it's worth, this does sound like an interesting technological transition time period to study, particularly if you are able to figure out who was more likely to have access to newer technologies and compare their workflow/productivity to people without. You may also find that some learned societies' journals or newsletters from the time have editorials or columns that explain newfangled bibliographic tools to their readers. That is, if you can muddle your way through the archaic language you are likely to encounter (like "synergy" and "sea change" and "dynamic" and "World Wide Web").


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Journals that only publish online. How reliable are they?
There are lots of journals that only publish online. However they are indexed by scopus and ISI so they are unlikely to be predatory journals. Are they safe? What are the chances that some hacker erases the journal’s database and all the records of publications are lost?
Surely it’s better to have printed copies of volumes and stuff. At least that way there is always proof that one’s article has been published.

What happens if some crazy person burns the journal's repository of paper documents?

I asked a similar question about [arxiv]
(https://academia.stackexchange.com/questions/47416/what-are-the-archiving-policies-of-arxiv).

There are journals that still publish on paper??

The printed versions would be distributed internationally to authors/readers/institutions. Obviously It would not be in one location.

@JAB Somebody would have to be pretty crazy to burn down all the copies in university libraries, too.

Well, one of the endless discussions one can have is backup. - A good backup is offline/regularly detached, or on write only media. If I had to guess, I'd expect some kind of tape storage on which additional information is stored only. If the IT staff are competent, the damage any hacker could do to the actual paper content is pretty much negligible (except possibly for papers currently under review). It would be inconvenient, but not a major issue.

What's the difference between printed copies of journals in people's offices and copies of pdfs on their hard drives? Surely these days one would be more likely to obtain the second one from others after a catastrophic incident than the first one...

On the long term, paper has some merits regarding sustainability of information – at least that is what we deduct from history. If nothing bad happens, a piece of paper keeps its information for a couple of hundred years. Compare that to a floppy disk from the 80s – IT is a cultural nightmare. True story: Our universities registrar proudly keeps enrolment documents from each and every student since 1791, the year the institution was founded. With the exception of students who enrolled between 1971 and 1988, when the first electronic enrolment system was in charge. This data is past recovery.

@Daniel: the "cloud" is a possible solution to that, indeed very real, problem. The idea is that the medium is not the interface to your data anymore - the protocol to access it is. The way data is stored can be changed in the background to accomodate for current/practical/cheaper technologies without the end user knowing. The protocol may chnage but the essence of the data will not.

A little too broad, not very clear question.

Any reputable online-only journal will have a plan for data retention that goes beyond what's visible to the user. There will be backups somewhere.
Print journals may have the advantage of having a physical repository copy existing, but even those are not necessarily of "archival quality" (that is, printed on acid-free paper and using techniques that promote their long-term preservation).

I would be incredibly shocked if the print journals did not have a digital backup plan strikingly similar to online only journals, and just general "how to survive a nuke" scenarios that most large organizations with data to protect use.

This answer says it all, but I would like to recommend The Keeper's registry, that tells you WHERE the archive (or backup) of a journal are: https://thekeepers.org/

It seems the ArXiv stores its data on Amazon S3 cloud servers. I would assume Amazon has a data safety and backup policy that is as professional as it gets.
Presumably also most journals don't store their data on their own servers, but use one of the large file hosting services.

I may be wrong, but it appears to me that Wiley uses Amazon Web Services to serve papers (the URLs seem to suggest that to me).

Being online-only is orthogonal to the issue of journal quality. Any new, quality journal will almost always be online-only these days, for economic reasons. Any new or existing predatory journal will generally be online-only, for economic reasons. Probably the best working guide to a journal's quality is "Do I read and cite papers from this journal?"
On the issue of archival security of publications, you should look for explicit statements on the journal web page about that. An open-access journal that takes this issue seriously will have plans that involve archiving content on at least one third-party, independent, and ideally distributed, service. Some other answers here have mentioned technical issues, such as using well-regarded storage services such as Amazon S3. But the quality of such services is not relevant if the company using them goes out of business and no longer pays to maintain the service. Archival security should persist even if the publishing entity itself does not.
For example, many open access journals in the medical field will archive their content with PubMed Central, a service of the US National Library of Medicine of the National Institutes of Health. Until recently, that might have seemed like a gold-standard of stability and security, so additional facilities that are international, collaborative, non-profit, and ideally distributed might provide additional peace of mind. For example, look at the CLOCKSS and LOCKSS initiatives.
An example of an online-only, reputable journal that pays attention to independent archiving is PeerJ. Their page here gives an example of the attention paid to these sorts of policies, which you might compare with when seeking a journal in your field that takes these issues seriously.
Such information is not always prominent on a journal website however. In a comment to another answer, user @Emilie points to a very useful central resource: "the Keeper's registry, that tells you WHERE the archive (or backup) of a journal are: thekeepers.org".

Probably the best working guide to a journal's quality is "Do I read and cite papers from this journal?" - Another good indicator: The amount of exclamation marks you get in their mails. They also get your name and title wrong Example: Greetings to you !!! Mr I Ian

@Ian So that would be a journal you're willing to submit to then, right?

@sgf Personally, I find the amount of exclamation marks combined with the amount of spaces before punctuation inversely correlated with my willingness to have any kind of contact to that journal.


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Forgotten to answer question
Seeing Forgot to answer exam question and thinking back to my exam that I wrote a day ago, I think it might be me who forgot!
I recall the last few exam questions but not answering them!
Should I speak to the professor to see if anything can be done or should I leave it be?
(all the details match me... A+ so far and also submitted a draft earlier...)

Maybe you should be proactive and post the correct answer to the question(s) you forgot to answer here. Who knows, the professor might be impressed enough with your brilliance they’ll accept the late submission.

The professor has to mark what was submitted. They may possibly decide to make an executive decision to remove the last question as many students did not do it then that is their choice.

@DanRomik this could be potentially bad for both professor and student. By making the question and answer public, they risk exposing themselves and maybe violate confidentiality of course material. We can't know.

If you want an A+ then of course you could ask. Maybe he will consider the previous draft, maybe he won't; but it never hurts to ask.
You should be aware, though, that he is not obligated to give you points for it; it is completely your fault for forgetting to answer the questions. Therefore, don't demand points but ask nicely if there is any chance to consider the draft, you will have better chances this way.

How does a professor distinguish between a student ‘forgetting’ vs not having time to get to those questions?


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Professor didn't write recommendation letter on time, what should I do?
I'm applying to graduate school programs, and for a few applications due yesterday only 2/3 of the professors I asked to write rec letters for actually sent them in. Will I be removed from consideration from the programs where the third person didn't send them in? Note:they did send them in for schools that had their due date a few weeks ago. Is there anything I can do? Or is it all out of my hands. I emailed them a day before with a reminder and also a day after asking if they will send it in.
Thanks

Are "professors I asked to write" the same as "professors who agreed to write?"

Well yes, I asked all my letter writers about 1-2 months in advanced and they all agreed.

It sounds to me like you're in the US and I'm going to answer this from a UK perspective, but I expect the situations are broadly the same. I'll first discuss a similar thing that happened to me, and then give some advice.
So, this exact situation happened to me last year with two different universities, and two different letter writers. All the places I applied to required a minimum of two reference letters, so in each case, I was down 50% on letters.
In the first case, the university notified me that I was missing a reference letter and I had time to find someone else who was willing to very quickly write me another letter. My application there was ultimately unsuccessful, but not because of this (it's the best uni in my country and my application was wildly optimistic).
In the second case, the university didn't notify me at all that they had only received one reference letter in support of my application. In fact, I didn't find out until they mentioned it in the interview, after which they subsequently gave me an offer, still only having seen one reference letter. So it didn't matter in this case either.
My advice to you is the following: contact the schools which are missing letters. Ask if it matters that your letter might be arriving slightly late-- I expect it probably won't. People working in academia are aware of the time constraints that academics have and will likely be lenient in this kind of situation. I also don't think it will reflect badly on you, as you have done what you can to rectify the problem.
Secondly, send another gentle reminder to the letter writer in question, or, if possible, pay them a visit in person. Chances are, it was an honest mistake and they just forgot.
Good luck with the rest of the applications!

Not all is lost. Maybe send a very friendly reminder to the person who missed the deadline. People are busy and a Recommendation Letter is not that important to them. Also, if you included email and phone number they may contact your reference and ask them directly.
In my experience it is much more important who wrote the letter than the content of it.


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Uploading paper drafts before first-time publication
I am half-way through a Masters degree in Logic and Philosophy of Science following a BSc in Astrophysics. Although I've dreamed for years about getting a paper published, I still haven't submitted anything for publication. The reason why I hadn't submitted anything was very clear to me as an undergraduate: I chose to pursue theory over experiment right off the bat and, although I got to fiddle around with very ground-breaking mathematical techniques, I quickly realized that my knowledge of modern physics was not up to par with the foundational work I was pursuing. I intend to pursue a Ph.D. in theoretical physics focusing on quantum gravity and want to wait until I have taken the relevant courses in particle physics and general relativity before putting my old research results in the context of the current consensus view.
In the meantime, I pursued a detour into the philosophy of science because I am fascinated by and very passionate about the foundations of physics. My experience in philosophy has been remarkably different. Besides my application essay, I have written two term papers that I am very proud of. I deem them to be of publishable quality because I went beyond the mere expectation of "meeting the examiner's criteria" and actually took a deep dive into the literature to produce novel research. I think they are ready for the peer-review process, but am hesitant about what to do with these drafts.
I first came across ResearchGate, and later Academia.edu, while doing literature searches, but quickly realized that a number of my current and former professors are active in these sites. I've been seriously considering uploading my drafts namely because I feel that I've been too secretive of my ideas for too long and it's time to get them out. I do, however, have some reservations. These lead to my question:

Would uploading my papers to "social media sites for academics" interfere with the peer-review process of reputable publishers? (e.g. Elsevier, Springer) I understand the purpose of these sites is to share ideas with as broad of an audience as possible, but they do not carry the weight towards career advancement that a publication in a "good journal" gets.

There is also a related follow-up question:

Is there a right time to get out a first publication? I used to be intimidated by people who published one or two papers during their undergrads, but these were mostly collaborations with an established research group. Conversely, I have friends who didn't publish their first paper until they completed their P.h.D.

Am I overthinking all of this?
Thank you so much for your time.

Be aware that in some fields, journals won't consider your paper for publication if it has appeared elsewhere. In others, that isn't a problem and authors are actually encouraged to upload preprints to, for example arXiv. So, investigate the journals in which you might want to publish eventually. Since you seem to be on the boundary between fields, it might make a difference.

Good question. In some fields like mathematics and cs there is no problem AFAIK to publish papers that are on arxiv. Also in physics I think it is fine.

Thanks. I guess I should treat it as on a per-journal basis. The journal that seems best suited to two of my papers is "Studies in History and Philosophy of Modern Physics." I should check in with their copyright policy before I upload anything anywhere!

Minor remark: don't assume that people who have a page on academia.edu or ResearchGate are actually active on these sites: they might not even be registered, these sites collect publications automatically to give the impression that many academics are there.

Would uploading my papers to "social media sites for academics" interfere with the peer-review process of reputable publishers? No. (This question has been answered already, try searching this site.)

In my view, you're overthinking all of this.
Unless you've got strong mentors collaborating, your first papers are likely to be terrible. Your work might be wonderful, but writing scientific papers is a specialized skill, and you haven't really practiced that skill yet if you haven't had a paper go through scientific peer review.  So if you want to publish, you should start submitting and start building those skills.
My strongest advice here would be to try to start working with one of your professors as a mentor (and likely co-author).  They are likely to be much better able to assess what is needed to make a good publication out of your work. If you've actually accomplished something interesting, they are more likely to offer such mentorship.
If you have a very strong ability to withstand rejection, you could also go ahead and just submit your papers to what you believe is an appropriate journal (make sure it's actually reputable, and not a predatory piece of junk!).
Finally, the biggest red flag to me in what you've written is talking about being secretive about your work. Even if you're onto something wonderful, you should be thinking about this as not as your magnum opus but as just the first in a very long series of publications that you will make over the course of your career. Being secretive is often a trap, which causes people to think their work is more important than it is because they aren't getting outside feedback on it.
Let go of the fear, find a mentor co-author or send in your manuscripts yourself, and learn from the (likely harsh) feedback that comes from the reviewers.

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


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How to publish analysis work of an approach worse that state-of-the-art?
I am currently working on an engineering problem for which I have developed a new and quite effective solution.  My research field is electronics (if that matters).
The problem is quite complex as it revolves about using a single circuit configuration for multiple voltage ranges (conversion of ac voltage to high dc voltage).  State-of-the-art circuits offer unacceptable performance for input voltage range A and reasonable performance for input voltage range B.
My solution offers reasonable performance for voltage range A but the performance for voltage range B is slightly worse than state-of-the-art.
Since the problem can be broken to two individual parts (low voltage range and high voltage range), I plan to publish the first part on its own (e.g., novel high voltage step-up converter). However, I am debating how to publish the second part that on its own does not offer better performance than state-of-the-art. I have spent half a year developing, evaluating, and optimizing the circuit and I believe the engineering society would benefit from this work.
I am thinking along the lines of "Analysis and optimization of ...".

Perhaps it would result in a paper that is too long to publish, but you might consider, at least, putting the two results into the same paper and giving an analysis of each case.
Show how and why it works for one range, but, in a later section, show why it fails to work for the other.
The overall suggestion here is that the analysis of the result and the possible insight it might bring to the general case is more important than each result individually. That is the perspective of a mathematician, anyway. The insight of the analysis/proof is more important than the theorem itself.

However, I am debating how to publish the second part that on its own does not offer better performance than state-of-the-art. I have spent half a year developing, evaluating, and optimizing the circuit and I believe the engineering society would benefit from this work.

(emphasis added)
Why do you believe the engineering society would benefit from it? What does it offer over the existing approaches? If you can answer that question then you know how you should proceed with writing a paper for this second part.
You seem set on defeating the state-of-the-art performance by a particular metric, but this is not the only way to publish. You can pick your own metric to evaluate; you can even say that you do not perform as well, but your approach is novel because of X, Y, and Z. Perhaps you are the first to apply a certain technique in this domain, and you show that the technique is promising because it achieves almost as good performance as the state of the art. Or perhaps you can argue the the problem you are solving is more difficult or more general.
There are lots of ways to pitch a research contribution, not necessarily just based on evaluating the performance of your method. The success of publishing the work will depend on how well you can convince others that the work is interesting.

Why split the result into two papers since they are obviously quite closely related? It seems like salami-slicing and makes both papers weaker than they would otherwise be together. If it would be overlong to pack both voltage ranges into a single paper, you might consider putting the "worse than state of the art" range in the Supplemental Material, stating that the design gives acceptable performance in range B (since you say the results are only slightly below state-of-the-art) with the added benefit of a wider operating range. Getting a single paper out of 6 months work is already pretty good!


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PhD supervision in the Netherlands: what ranks can supervise?
I've heard word that in the Netherlands only a professor/hoogleraar can supervise PhD students but I've found little to solidly confirm this. I've also heard that in practice, other arrangements are often made. Can anyone comment or confirm that a universitair hoofddocent (equivalent to a reader or an associate professor) cannot supervise PhD students? How do full professors handle the workload of supervising all the PhDs?

There is a difference between supervisor and promotor. You need a promotor, who is going to sign off your thesis. This needs to be a full professor (not associate or assistant - edit: nowadays at least at some universities in the Netherlands, associate professor is the rank needed to be the promotor, not professor - see answer by GrotesqueSI and comments). However, your main supervisor can be any PI (comparable to assistant/associate professor). Your daily supervision can even be handled by postdocs, and to some extend even by senior PhD students.
Depending on the status of your PI, if he or she isn't full professor (yet), a promotor may not be involved in a PhD students work at all.

Aha, I think I'm following. How about for non-Science disciplines where there really isn't usually much of a 'PI' role? I'm mostly just trying to sort out if I'll be able to accept PhDs in the Netherlands...and figure out what to do with the ones I already have.

I should clarify, I'm not a scientist. I am a PI of a big project but it doesn't fund PhDs. My PhD student all do projects that have their own funding and are related to my research interests but are not directly associated with my research projects. Thus I'm not their PI.

As long as you have a PhD and are connected to a university, you should be fine. You would just need to find a full professor who signs the documents as promotor - but this should be easy. If you are not at a university, I don't know how things would work, same if you do not have a PhD yourself.

@Mark If OP is supervising potential PhD students but is not at a university himself, he definitely needs a university to collaborate with this. Only a university can grant PhD titles.

@quarague Gendered assumptions are terribly offensive, bad for academia, and are often wrong. What about my post made you think that I was a "he"?

In 2017 law was passed to allow associate professors to act as promotor. Although the implementation is up to the universities, so whether this is practically the case may differ among them (but at least some of them have implemented this in one way or another...). You can ask and/or check the promotion regulations of specific universities you are interested in.

@Mark, I think technically it is not required to have a PhD to act as co-promotor (i.e. act as supervisor). In fact, you technically do not need a PhD to act as promotor. For example, a hoogleraar without a PhD (they are rare but do exist) would still be able to act as promotor.

To add to this, my own question, for anyone looking, what Mark said is almost but not quite right. The "promotor" comment is mostly correct, but at least at some universities in the Netherlands, including mine, Associate Professor is the rank needed to be the promotor, not Professor.

Thanks. I included this information in my answer. Seems like this was changed after my time in NL.

Is it the same im Austrial?

It might be good to add the info from J. Doe's comment that this is due to a fairly recent (2017) change in the Dutch law. Prior to 2017, Mark's answer would be correct.


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Should I have a fourth recommender in PhD Application
Due to some technical issues, it took me a couple of weeks to hear back from one of my potential recommendation writers for my Business PhD application.  I reached out to other reviewers in the interim and have filled all of my required slots.  I just heard back from the first person, and I am wondering if I should add a fourth letter for a few schools.  I think this professor can add some unique perspective since I traveled with her for a two week immersion elective and the experience informed the topics I would like to research.  Will the additional  perspective be helpful?  Or will a fourth letter just indicate that I didn't pay attention to the requirements or was worried about the strength about my other letters?

Provide the number of letters of recommendation requested.
Some systems will not allow you to add additional ones. Even if they do, I agree with the assessment that adding further letters won't reflect well. Either you didn't follow the rules, or you didn't figure out who'd be your best recommenders.

Also some schools (including ones I've worked at) will just toss extra letters, etc without consideration. You're just giving the admin more work to do, plus you won't know which ones were filed in the wastepaper basket.


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In the absense of writing experience in my target field, how do I find assignments and evaluate them?
A while ago I posted a question wondering if a CS major would be accepted into a Political Science MSc programme and it turned out possible. I am starting next October.
My goal is now to get into an interdisciplinary PhD, I have already scoped some and most of my targets ask me to demonstrate my writing competency as part of their application process. I will also have to write research proposals.
I don't have high steem for my writing, as I have not produced many essays in my undergraduate program. The application deadlines are as early as December and a good proposal can take months to write.
What guidance can I follow to start writing? Especially when I have no assignents and I have to be self-driven. Should I aim to write for a specific online outlet? Even then, how can I get feedback so I can improve faster?
I'm not sure this is the right place to ask, but I don't know where else to turn.

Your question is possibly a bit too specific to your personal circumstances, but the more general question --- how can a prospective academic from a background that involved very little formal writing prepare for (or adapt to) a different academic area in which a lot of formal writing is required --- seems entirely appropriate to me. Also, your title somewhat suggests that you want experience in evaluating/grading other people's writing, which is not what you actually want.

The obvious way to get experience along with feedback is to enroll in a formal writing course. But try to find one in which the instructor is amenable to you making suggestions about general areas and topics. But any writing will be better than no writing.
A second, but riskier way, is to publish a blog somewhere in which you express your thoughts but allow readers to comment and give you feedback. The world is full of trolls, of course, so be prepared for that, including a way to shut them off and/or back out of the whole project.
Even writing here on this site you get some feedback in the comments.

I don't know why this was downvoted, unless it was thought that a formal writing course is unlikely to be very useful (or available in such a short window of time) for the purpose of writing application essays and research proposals. Maybe @FaureHu can try searches such as blog + to + improve + academic + writing and "graduate school" + "application essay" + "social science" + "examples".


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Paper based on Master Thesis - Disclaimer necessary?
Making my Master Thesis into a paper.
I've recently come across a paper that put a disclaimer into the introduction:
This study is a continuation of work presented in the PhD Thesis ....
I wanted to know if such a disclaimer is necessary if my paper is based on my Master Thesis.
Thanks.

Such disclaimers aren't necessary, but they might appear in the "related work" section to provide additional background. (I would discourage inclusion in the introduction, unless that is where the related work section appears.) If the paper will be co-authored, then such a citation will help distinguish your personal contribution from your contribution in collaboration with others.

It doesn't seem necessary to me (this may be field dependent), but it seems like there's no harm so it's safest to add a footnote to this effect.

I do not see a big problem here. However avoid cutting and paste .Really rewrite the paper keeping in mind that it is now a self-standing piece of work.

Yes, this is necessary.
Self Plagiarism may seem like a strange thing to be worried about, but there are many reasons to avoid it the way you would any other plagiarism:

Some journals use double blind reviewing, so reviewers can't distinguish between self-plagiarism and plagiarism.
You may have received funding for your thesis, which is probably acknowledged in your thesis, but not necessarily in the paper version.
People reading your paper may want to read the full Master's thesis, since theses generally contain more detail and are less space-constrained than papers.

Thanks for the quick reply.
Is a full disclaimer necessary or is merely citing the thesis at some point already sufficient?
Is there some guide online or ethics handbook out there that I could point to for guidance.

But wouldn't self plagiarism require that the thesis was published? I thought you could only plagiarize published work.

@morxa I don't see why this is the case. In the general case of plagiarism, if I read something on a blog, or in a colleague's notes, and publish it claiming that it's my own, it is still plagiarism. For a thesis, it's a big more of a grey area as to what "published" means, but most universities keep an archive of all theses completed, so while not peer-reviewed, they are published (in a sense).

@oldmansaur I'd say that citing is necessary, and a full disclaimer is helpful, albeit not necessary. It will likely put your work into context, which can help potential readers of your paper. I'd view it not as a disclaimer, but as contextualizing the paper in terms of related work.


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Second attempt at PhD
I couldn't complete the PhD at the end of third year because of unsatisfactory progress. That was three years ago. Now I am again thinking of applying for a PhD. The application requires an up to date CV. I am wondering how to mention about the previous PhD study and whether it is worthwhile at all to make such an attempt. I would be grateful for your valuable suggestions.

Mention => I would say "yes", don't lie by omission. Anyone accepting to mentor you could be pretty upset finding out that you already tried a PhD program but "forgot" to mention it. Worthwhile => That depends of many factors, but mostly … of you. What makes you think that you could succeed where you failed previously? What changed? How a different institution / topic / place / supervisor would transform that attempt into a success?

Clément, thanks a lot for your valuable suggestions. First of all I am 42 now. I am not sure whether it is a good idea to start PhD at this age. I am a professional for the last 18 years. During the PhD study, I wasn't very much sure whether to be engaged in the academic activities for long or go back to my main job and I wasn't also enjoying much. Now I want to retire from my job and concentrate fully in study heart and soul. Also I have a plan to select a research approach that fits more with my professional background.

Yes, you must include it in your CV. Concealing it could result in all sorts of trouble later.
Your cover letter or statement of purpose should explain what went wrong last time and what will be different this time around. For example, you could discuss the job vs. studies uncertainty you had last time, contrasted with your current intention to retire and study heart and soul.
For the age concern, see How old is too old for a PhD?. In particular, I did my PhD after retirement, in my 50's, and have no regrets.


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Choosing Recommenders for Physics Graduate Applications
I am applying for physics graduate programs. For context, the graduate programs I am applying to require three letters of recommendation and most of them do not allow more letters.
I have several options for graduate recommendation letters. I plan to send one letter from my current research adviser and one letter from my research adviser from the REU program I did last summer.
For my last letter, I can either request a rec from my research adviser from another summer research program I did two years ago OR from a professor I have a good relationship with who taught an undergraduate class in quantum physics my sophomore second semester. Which final letter writer should I choose?
The reason I am hesitant to go with the professor is because I am not sure his letter will add much. I have a 4.0 GPA and I have no research experience with this professor, whereas I believe the research adviser from my summer research program can write a strong letter and can discuss my abilities to do research.
I have taken additional physics classes (and some graduate courses), but I did not develop a close relationship with the professors and those professors can at best say I got an A in their class and was an engaged student.


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Rule about repeating citations
Sometimes I get papers for translation, larded with repeated citations of publications of the authors’ friends and teachers, two to three times within a paragraph and as often as possible throughout the manuscript….I try to replace with “the latter”, “the former” etc, but is there any tried and tested rule about how often and within which distance references may be re-cited?

When you refer to the authors' friends and teachers, you imply that you see this as simply trying to boost each others' citation indices. However, it makes no difference how many times a particular paper is cited within a single source, so repeated citations are not an issue. In fact, if a work is being cited multiple times in a short space, that implies it is relevant to the current manuscript and not just bolted on as an afterthought.

The golden rule of citation is that you attribute everything that you did not invent yourself to the right person(s).
The golden rule of boring writing is to repeat yourself as often as possible.
Just make sure that it is clear what came from whom. If you say: "In the following paragraph we describe the main ideas of [2]", you do not need to repeat [2] in that paragraph, but if you compare two approaches it might be necessary to mention the papers/people more often.

You could also use "In the following paragraph we describe the main ideas of A, B and C [2]" and subsequently refer to "A, B and C" rather than "[2]" where necessary


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Considering prospective grad schools; professor whose research interests me most may be visiting professor elsewhere currently, how to handle this?
At a certain grad school I am considering, there is a certain professor who I would be most interested in researching under, in fact if I couldn't have him as my advisor I my interest in this school would become diminished, but I read in his bio that he is a currently a visiting professor at a different university. In this case, should I still express my interest in his research in my statement of purpose? How long do visiting professorships typically last? Could I hope that I could have him as an advisor? I'm unsure how to approach this situation.

There is no point in guessing.  Contact the professor directly.  Express your interest in working with him, and ask if he is planning to be back at the "home" university next year (or whenever you'd be starting), and if he would be looking to take on graduate students.
A likely scenario is that he is visiting the other university while on sabbatical, which would typically last one year or less.  However, there are many other possible scenarios and no way to know the true situation without asking.

Well i did but unsurprisingly did nit receive a response. I think the scenario you outlined is likely though


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Should I expect to be invited to visit the grad schools I was admitted to?
I applied to grad schools this year. I haven’t heard from some of them but the one I was admitted to I was invited to come and visit. My understanding is that this is relatively common, but I would like a better sense of how common.
I want to visit the school I choose before I make a decision on where to go. My question is: should I expect to be invited eventually for a visit day for the schools I am admitted to? If not then I guess I should plan a trip myself.
To add to the context I will say that I believe I had a relatively strong application.

In the US context, for most graduate programs in science or engineering fields, at relatively wealthy and prestigious institutions, it's quite normal for departments to pay travel expenses for prospective students to visit the department before making a final decision to accept an admission and assistantship offer.  In some departments, prospective students are invited to visit before admissions decisions are made, which is more like an interview.
For programs outside of science and engineering, or for programs at less wealthy and prestigious institutions, such visits are much less common.
I would ask the department about the status of your application, and if you've been admitted whether they are sponsoring recruitment visits.

It can vary on funding and they don't always invite all accepts.
If you are interested in a school particularly, I would reach out to mention your interest.  Maybe it helps.
Also of course consider to do a visit on your own.