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Confusion between citation databases: how are they related?
I have seen in some faculties that I have been visiting that they give more importance to some citation databases than to others. About this issue, I have some confusions. I prefer to open only one global question here that cutting it up into smaller chunks because I believe the things I will expose are related:

What is the importance that some journals are indexed in Scopus and some in Web of Science or Thomson Reuters? Does Scopus have a better reputation? I ask this because I saw one faculty that strive to put their publications only on journals and conferences indexed by Scopus.
Is there any relationship between Scimago and Web of Science?
I found in the following link:
http://www.thomsonscientific.com/cgi-bin/jrnlst/jlresults.cgi
that a journal in which a colleague has gotten his article published that appears on this list, does it mean that journal is indexed by the Web of Science? Even though I have seen in the webpage of that journal that it does not mention Web of Science perse.

Any clarification of these citation databases would be a huge help to me. The field that I am working on is Computer Science.

Regarding your last bullet point: In this answer I mentioned the two journal lists showing which journals are indexed in Scopus and/or Web of Science https://academia.stackexchange.com/questions/89060/journal-indexing-thomson-reuters-or-scopus/89062#89062

Web of Science is probably marginally more selective; Scopus is a little broader (I routinely get higher numbers of hits in Scopus for comparable searches). My understanding is that Scopus has also made a deliberate attempt to increase its coverage of conference proceedings, which would mean more significant coverage in those disciplines which are very conference-oriented - ie engineering and computer science - but I'm not a CS specialist so please don't take that as gospel. "Only on Scopus" may be a deliberate nod to this, or it may simply be that that institution subscribes to Scopus and not WoS!
No, they are not connected. Web of Science is based on the "Science Citation Index", but this is not connected to SCImago.
Thompson Reuters were the owners of the Web of Science product. (They sold it recently and it's now owned by Clarivate Analytics, an independent firm not part of any of the major publishers). Web of Science contains a number of distinct databases; the link you give there is a 404, but it looks like it would be some subset of this list. It probably indicates that the journal will be found in at least some part of the Web of Science product, though I believe not all institutions subscribe to all parts of the service. (You can always plug the journal into Web of Science and see what comes up...)

On a broader level than @Andrew's answer: Whether a department uses one database or the other in most cases doesn't actually make much of a difference as far as departments are concerned, as long as that database fairly samples what faculty do. For example, both Web of Science and google scholar will give you a reasonably fair comparison between the performance of professor A and professor B, even though they will yield different numbers of citations.


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Academic Positions: Following a campus visit, when are referees contacted?
I`ve had my phone interview followed by a campus visit for a tenure faculty position. I was wondering if anyone has an experience as for when references are usually contacted?. This is in reference to universities in the U.S.
Thanks,

My (top 5 CS) department automatically contacts referees for all assistant professor applicants as soon as they apply. But practices vary significantly by field. What's yours?

I have recently been offered a more or less equivalent position to assistant professor ("lecturer") in the UK. My references were contacted after they unofficially made me the offer. The official offer will be made after positive reference letters have been provided.

In my experience, with universities that are often considered to be among the top 50 institutions in North America, referees will be contacted prior to a campus visit. Often times the decision to invite someone for a campus visit is expensive - time and $$$ - and universities/departments use as much information as they can get beforehand to decide on inviting a candidate for a visit.

Thanks. I agree. They really spent a lot of money on my visit and this is one of the best programs in my field in the U.S. I`m going to follow up with my references to know if they have been contacted. But at the same time some departments contact the references only after the campus visit. I also heard that some universities contact references after they made the offer.

Are you not being reimbursed for the cost of your visit?

@Change, most places will obtain references ahead of time when they are recruiting for a starting position (Assistant Professor, for example). When recruiting a more senior candidate for, say, a full professor position there may be some reasons to delay the reference request.

@Thomas. I didn't pay anything. The University made the flight reservation, hotel, meals, car and trip insurance and car insurance. Any other expenses that came up, they will reimburse. I still didn't send the receipts for the small amounts because they paid a lot of money already.

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In a PhD dissertation, can one copy the structure of the acknowledgment section from their own or from someone else's prior work?
In the acknowledge of a thesis, we thank all the people who helped our research. E.g.
"First of all I thank xxx, for xxx throughout my Ph.D. period."
For my master thesis's acknowledge, I tried very hard to rephrase the sentences to avoid repeating others' similar ones.
This time, I need to write my PhD thesis's acknowledge. I have download around 10 copies of other's acknowledges. I find it really difficult to work out a sentence structure that is different from all of them.
I mean the peoples we thank are different, but the reasons or the phrases representing how we should thank them are similar among all thesis.
I just wonder if I can stop struggling with rephrasing the sentence structure, and copy & mix the sentences from my and others' acknowledges and just replace the people's names?
Is this an acceptable behaviors? Is this plagiarism or self-plagiarism?
I just think there are so many theses with acknowledges. You probably would never be able to work out an unique sentence structure. You will be similar to others anyway. So why not just copy, mix and change names?

You are probably overthinking this

You're writing a thesis for a postgraduate degree. That means you're pretty smart. Use your brain instead of trying to find rules to govern every situation.

You are overthinking this, indeed. However, the answer is that there is absolutely no standard for the acknowledgment. Copy someone else's if that makes you comfortable.  Or just write whatever you feel is appropriate. I posted mine in response to a past question about this, and if you look that up you'll see that I included both serious and silly credits. You aren't going to be graded on this paragraph. If you must worry, find something else to worry about.

Doesn't this prior question mostly cover the same issue? http://academia.stackexchange.com/questions/24156/is-a-copied-acknowledgements-section-considered-plagiarism?rq=1 As the answers there suggest: it seems a little nutty to try to actively compare one acknowledgments section against another to enforce originality.  As long as you didn't write your acknowledgments section by lifting whole paragraphs verbatim from someone else's thesis, I think it's not worth worrying about this at all.  (And, if it needs to be said: don't write your acknowledgements section in that way.)

First, throw away everyone else's acknowledgements sections. Ignore them.
Second, think of all the people to whom you feel grateful, and write down your thanks in whatever way feels natural to you.
It really is that easy. There's only so many ways to say something, so if it sounds similar to someone else's, so what? As long as they are your own heartfelt words, no one will notice or care.

"in whatever way feels natural to you" And what if you're not a native speaker of the language you write the acknowledgements in?

@JIK: "in whatever way feels natural to you". I doubt anyone will nitpick what precise words you used to thank them, whether they are grammatically correct, and whether they conform to standard idiomatic usage.

@JiK: Anyone who makes it through the writing of the rest of the thesis can make it through the acknowledgments.  If they got help with language issues / translation / writing on the rest of the thesis, certainly they could still get it here.  Or if they wrote it on their own but with effort, then probably something short and simple feels most natural to them.  Writing "I sincerely thank my parents, People A through G, and my thesis advisor" would be an acceptable acknowledgments section, and honestly, those who treat it as an exercise in being clever or funny risk making a worse impression.

The acknowledgements aren't really something you claim credit for. I think on the whole people aren't going to worry about copied acknowledgement sentences, unless you copy something very unique (eg. someone quoting a film/book/their grandfather). I'd very much doubt anyone would care if you copied your own text from your master's thesis (I guess they might interpret it as insincere, but if they know you find the language hard they could probably see past that). You could try mix-and-match, with sentences but also with clauses.
Or alternatively you could write in your own language.

Having a bilingual acknowledgments section is actually a pretty good idea.  You can't fault someone for thanking in more than one language: in fact, it seems quite gracious to do so.

I know of theses where the author has thanked friends and family from their home country in their native language, and everyone else in English. It works well!

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Send updated manuscript before referees' response
Is it common to send an updated manuscript to a publisher before the initial referees' report, if you have fixed a number of typos and ambiguities in the meantime?
EDIT: By fixing ambiguities, I mean for example writing down definitions that were previously just implied, or adding short examples every here and there.
That is, I think the changes I made are likely to help the referee understanding the manuscript.
The manuscript is on a mathematical subject.

if they are not groundbreaking, the refrees are more likely to ignore them while deciding, but they will point out at the feedback.

See edited question. By "fixing ambiguities", I actually meant more than just replacing single letters or words

Is it a journal paper or conference paper? If conference paper, then you cannot alter after the submission deadline. Otherwise, I think it is OK if you change a few things before the reviewing process started.

it's for the proceedings of a conference

There is nothing you can typically do during review -- the reviewers have received their copy of the manuscript that they were asked to review, and as an editor I would leave it at that even if I got an updated version. My response (in different words) to the author would have been "Well, these are things you should have thought about before submitting the paper."
But assuming the first version wasn't terrible, you will get the opportunity to roll your changes into any revisions you make in response to the reviewer comments.

I agree. Whether conference or journal, what's done is done. The exception is to fix typos after providing camera ready copy, at the discretion of the publisher.

@FredDouglis I disagree. It's probably not worth it in a conference paper but, if you notice a problem with a journal submission, it's certainly possible to submit a revised version. There's no point unless the error would cause actual problems for the referees but why waste the referees' time by making them try to figure out something that you already know is wrong and already know how to fix.

@DavidRicherby , As an editor, I don't know that I would accept an update once it was in review. I think it speaks badly of the work.

I agree with @padawan's comment elsewhere... if it were so soon that reviews hadn't commenced, it's another story.

@FredDouglis I'm confused. Isn't the goal to increase human understanding by disseminating high-quality papers? You seem to be operating as if the goal is to grade the submitted manuscript as if it were an exam. I've reviewed at least one paper where, after a couple of months, I've received a new version from the editor because another reviewer had asked (via the editors) the authors to clarify something they couldn't understand and the authors' response was, essentially, "Oops, you can't understand it because it's wrong. Here's a fixed version."

@DavidRicherby, I think it's at the discretion of the editor.  Generally my experience is not that a reviewer goes back to the authors to ask for explanation.  They review the paper as provided, and if there's an issue, they reject it.  With journals, they can usually be sent back for "major revision" and that's the time to fix things.  But if it's totally bogus, it may result in outright rejection, and they don't get the chance.  Anyway, I've been an EIC and I've served as assoc. editor for ~100 articles.  Never seen update in place.

I think it speaks poorly of both the paper and the author if the author thinks of problems shortly after it's been submitted already. It means the author didn't think things through properly and submitted stuff that's half baked.

My reason for not wanting an author to submit a revision is (i) because it puts a burden on reviewers who may have already read through part of the paper and now need to start from scratch, (ii) because it sets a precedent that I don't want to hold: that you can amend things, at your own pace, and as often as you want.

I think there's room for negotiation, or for a query.
Write the editor describing the changes. Note that they improve readability but don't really affect the results (assuming that's the case). Do apologize for not having caught typos before submission.
Then ask the editor whether s/he wants to send the revised version out, or wait. If the papers went to referees just a little while ago they may not have started work and the editor may decide to send on the revisions. It's the editor's call.


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Why are Macbooks so ubiquitous in Science, if they are status symbols
In Biology, I was told, you will almost not be able to find a professor that does not have a Macbook. And as soon as they have enough money, students and scientific staff will follow.
But also in my own field, mathematics, I have seen lots of highly respected professors with Macbooks.
Now, I have never worked with a Macbook myself, but I have helped out colleagues with problems a few times and I have really have not encountered any advantages over a regular and half as expensive Windows laptop, or an even cheaper Linux laptop.
Those that I know good enough to question their choice of laptop confirm exactly my suspicion, saying they thought it was pretty/everyone in their lab had one, or swear by it but never had a different laptop.
Is there something I am missing about Macs? Maybe some recent convert out there?
If not, why are academics so keen on status symbols? Isn't academia the one place where content should count, not looks, or even worse, depiction of wealth?
EDIT: while I agree that this question is prone to flame wars and the question about mac vs. anything else is also not really new, I DID want to know about the specific situation for scientists and the two answers so far are exactly of the kind that I wished when I was posting the question. Now of course mentioning that Macs might(! "if they..") be regarded as status symbols attracts attention to my question ;)

Honestly, that's a boat programming question. This is just the good, ol' "Mac hardware is twice as expensive and has no advantages" discussion all over again, with the suffix "for scientists". I see no value in re-hashing this argument again and vote to close.

@xLeitix In all fairness, the suffix "for scientists" does raise some valid points because we do often have very specific needs in terms of hardware and software. It might be a boat, but there's lots of us in it. The problem is that questions about Macs are often either poorly researched, or written by trolls.

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I don't think questions of the form "Why is X more popular in academia?" are boat programming if X is indeed unusually common among academics.  It's a legitimate question. What I don't like very much about this particular question, though, is that it sounds exactly like the usual trigger of a mac vs pc/linux flame war, i.e.,  Why are Macbooks so popular when they shouldn't?! They're overpriced! They're status symbols!! You shouldn't buy them!!! I'm not saying that this was OP's intention. But I think it could use some rephrasing, if s/he wants it to get reopened.

This question presupposes that academics would by some magical power be immune to status symbols, which seems plainly absurd.

@Calchas this question presupposes that academics purchase Apple products as a status symbol, rather than as perfectly good tools of trade, which seems plainly absurd.

I also suggest that the premise of this question should be more thoroughly specified or referenced, if the question is supposed to be reopened. While I have not paid much attention to what people from other places use, among all the computer science professors at my own university, I only ever saw one (!) use a MacBook, and he explicitly stated that his only reason was that it's such a niche product that there is much less malware targetted at it than at other systems.

I remember the transition point, which happened in the middle of my grad school, with the major shift happening across approximately 2003 - 2006.  What happened was OS X.  Before that point, scientists generally faced a nasty computing dilemma:

Use Windows, and have a terribly difficult time using lots of Unix-based scientific applications.
Pick a Unix flavor, and have flaky hardware and driver support, no access to proprietary applications like PowerPoint and Word (which are often required for US government interactions), and a lot of time required in being sysadmin to your own machine.

Once OS X stabilized and picked up sufficient application support, you could get a Mac and have the best of both worlds: proprietary software, Unix (BSD), and minimal sysadmin time.  The elegant design was a plus, but the big thing was the capabilities.
Over time, both Windows and Linux have started catching up---particularly Linux, where there are now much more sane graphical interfaces and it is no longer a crapshoot whether you'll be able to make the drivers work on any given laptop.  Mac has remained very strong, however, especially with things like their increasing lightness and lengthening battery life, though, and so I expect it will be widespread for some time to come.

Linux may be much more functional than it used to be... but my top three deal-breakers are TextMate, Time Machine, and Spotlight. Sadly, I doubt they will appear on Linux any time soon :(

@Moriarty Ubuntu 14.10 has 'search bar' functionality almost exactly like Spotlight. 3rd party tools are still needed in lieu of Time Machine and Text Mate, but there are (free) comparable alternatives.

@ChrisCirefice Speaking as someone who's used many different versions of MacOS, Windows, and Linux, I've never found anything nearly as good as Time Machine.  It's a backup program that supports bare-metal restore, snapshots, hot backups, is free (assuming you already have the OS), and takes about 4 button clicks to configure.  I challenge you to find any backup program for Windows or Linux that is easy to use, costs less than 500$, and supports bare-metal restore, snapshots, and hot backups.

@PatrickM BackInTime is the backup tool that I use and after my laptop basically caught on fire and died, I was able to restore to a brand new laptop without a hitch from my external hard drive. I don't know what your fancy terminology (bare-metal restore, snapshots, hot backups) means, but if I can restore to an entirely new machine and only lose 3 hours of work (because incremental backups were taken), then I'm 150% sure that for 99.9% of users, it is just as good as TimeMachine.

@ChrisCirefice It sounds like it does what I was talking about.  "Bare metal" means that you can restore from a blank hard-drive without the need to reinstall your OS first.  It means that you are restoring from nothing but metal.  (No existing software.)  "Hot backups" means you can backup the computer without shutting it down, and booting off a separate disk.  "Snapshots" basically means that when it makes new backups, you don't need to save a copy of everything, and you can delete old backups without breaking your new backups.

@ChrisCirefice BackInTime seems to have the second and the 3rd, but it looks like it's missing the first.  With Time Machine, I can boot a new mac off of the install disk, and it will restore the entire OS exactly the way I left it.  Correct me if I'm wrong, but it looks like, with BackInTime, you have to reinstall your OS and apps which will make the restore process much longer and involved.

Rest assured that there are reasons enough for using good quality hardware. Those of us who purchase a Mac do not do so because they are a "status symbol". We do so because they are the best tool for the job.

In many fields, using Windows is simply not an option. We need UNIX.
Linux is a good operating system, is free, and can be installed on a wide variety of hardware. However, Linux is nowhere near as refined as OS X in terms of its overall usability. We can often be much more productive on an OS X machine, and reserve Linux for use in virtual machines or on a powerful desktop when we need software stability or heavy-lifting power.
The other side of the coin is hardware. Until recently, there was very scarce competition in terms of hardware quality. Macs are built well, thin and light, and have long battery life – great for conferencing. Now, other manufacturers have caught up and are making hardware that is at least as good – but a high quality Thinkpad or Dell XPS is still just as pricey as a Mac. I repeat: comparably high quality Windows hardware is just as expensive as a Mac.

The money spent on a good machine pays for itself in productivity.

(and if you think Macs are expensive, wait till you see the prices of some of the lab equipment we use. A small dichroic mirror can easily cost several hundred dollars)

In a university context, I would add the dreaded phrase preferred supplier. At my (UK) institution, a MacBook Air is comparable cost to significantly lower quality alternatives, hence my recent switch after 10 years as a happy Linux user.

"We can often be much more productive on an OS X machine" I think with we you probably mean "those of us who purchase a Mac" but definitely not all scientists and academics.


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Letter of recommendation from Professor who I have not done research with
I had a meeting with a well respected professor to discuss issues in the research field (biomedical engineering) I am interested in. I am not seeking to do a PhD with him as I intend to go overseas for my PhD studies. During the meeting I asked him in depth questions about why things are the way in the field, and received good answers. He also suggested potential PhD advisors in the research field who are doing good work. I felt the meeting was productive and he may have a little impressed with me (knowledge of the field).
At the end of the meeting he suggested that he could write a letter of recommendation for me, because he knew all these professors.
However I had not done any research with him. That meeting was the first time I met him and my only interaction with him.
I mentioned this to him and he said, that's ok, he can still write a letter of recommendation based on my resume and transcript.
My question is will this letter of recommendation be helpful? Is it a good idea to submit this as a 4th letter of recommendation? Is the worst case scenario that at most the letter just counts as nothing?
Some additional information:

I have funding for my PhD studies
I am tangentially related to this professor, he was the boss of my supervisor, but he has sinced moved away and that was the first time I met him.
I may only have 2 good letters, from people I did research with. The third letter is from my programme tutor

Whether it helps or not depends quite a bit on where you are applying and what admissions system is used. But I don't think it will hurt. The personal touch is welcomed when appropriate but it is probably more of a letter of introduction than real recommendation. But that, alone, is good.

Here is a student I've recently met that you should take a look at. They have some pretty good ideas for research that seems to mesh with ours. They want to study in ...

In a lot of places this wouldn't do as a formal LOR, but as a message, out of band, to a professor would be useful to you for when you arrive at a new place. It gives you a basis for a first conversation.
But, in terms of admission to a program, you are probably better served by letters from people who know you better and can attest directly to your background and your likelihood of success in the future. I don't think I'd recommend replacing a letter from this person for one that is more relevant.
But, in a place in which a professor's role is to hire researchers directly and has a heavy influence on admissions, such a letter would be much more relevant. They get a letter from someone they trust who puts their own reputation directly on the line by writing it. I think it will be strongly considered.

For context I am applying for US PhD positions. Is it useful in that system?

In the US, you choose a dissertation advisor only after some coursework and maybe passing comps. You don't normally start research until a bit later. So, not so useful for admissions, but still an introduction that might be useful later.

@Buffy Even in the US, different departments are different. PhD students in my department are expected to start research on day one.

@JeffE, even if they come with only a BS? And do they get to choose a dissertation advisor on day one? And is it research toward the dissertation or just more general experience? Your simple description seems pretty unusual for CS in the US. Can you expand?

@Buffy Yes, even if they come with a BS.  In principle students can choose a dissertation advisor as soon as they're admitted, but students are encouraged to work with multiple faculty before choosing an advisor, so that everyone can make an informed decision. Early research is mostly intended as experience—research is a skill that has to be learned by doing—but in practice dissertation topics are "chosen" only after the student has enough research results to cover a coherent topic, so first-year research often does become part of the dissertation.

@Buffy I'm a bit surprised to hear that this is unusual, but perhaps I shouldn't be.

@JeffE, what you describe in the clarification here is more "usual" I think.

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PhD Germany with British conversion MSc IT
I would like to relocate to Germany and obtain a PhD from a German University. I have a BSc(Hons) in Psychology, which is obtained from Edinburgh Napier University, and MSc in Information Technology from Aberdeen University. I really enjoy IT and I would like to stay in the field and combine it with academia and research. Specifically, I am interested in web development and human-computer interaction. My questions are:

where can I check if my qualifications meet German PhD admissions criteria?
are the PhD studies being paid in Germany? (I am married so I cannot afford lack of any salary)

Welcome to Academia SE. Unfortunately, there are a few problems with your question: 1) You are asking more than one question. 2) Question 2 is a so-called shopping question, which are off-topic here. 3) The remaining questions boil down to how PhDs work in Germany, which has already been answered, as far as I know.

That’s still two questions. (Note that it’s perfectly fine to ask separate, related questions.)

To find out if your degree is recognized in Germany you can check the Anabin database here: http://anabin.kmk.org/no_cache/filter/hochschulabschluesse.html
From what I can see your Universities are listed as H+ which means they are recognized but I was unable to find anything on the individual degrees. However, as others have stated the usual approach would be to apply for a doctoral position directly to the professor these are often advertised. I would check the Die Zeit Stellenmarkt for example for doctoral positions.
Good luck.

+1 for "Die Zeit Stellenmarkt" which is one of the goto places for academic positions including PhD. You should also checkout jobvector.

To obtain a doctorate in Germany, you must have a qualifying degree from an accredited institution. Nowadays this is always a Master's degree with a thesis (Master's degrees without a thesis are effectively worthless if you intend to pursue a PhD). It should be in the field you are intending to obtain your doctorate in. If your degree is from an applied institution such as Napier, expect to have considerable difficulty finding a PhD program that will take you. (Though it is not impossible and things are changing.)

Don't expect the German system to be much like the British, as they are culturally and technically different. In Germany, you do not apply to a PhD program; you establish a relationship with a professor who is willing to supervise you, and the admission as a doctoral student follows from that. That is very difficult to do if you are coming in cold from outside the country. There are some EU-sponsored programs which explicitly solicit applications from other EU countries, but they are the exception.
How is your German? Anybody suggesting that you can get by in Germany without a decent command of German is not being totally honest with you. Even though PhD candidates here are often foreigners and the international language of many disciplines is English, you will be working in institutions in which the administrative language is German, and not being able to speak it will put you at some disadvantage. If nothing else, the competition will be much harder if you can only speak English as your second language, particularly if you are expected to teach.
Your best chance might be to apply to another academic M.Sc. program at a research university in Germany and get your foot in the door that way; this will expose you to professors and give you a chance to establish a relationship that could lead to a PhD.

The Friedrich-Alexander Universität Erlangen-Nürnberg long had a good reputation for computer science. There is also the Karlsruhe Institute für Technologie or the Leibniz-Universität Hannover. Freiburg is also an option. Note however, that these are the better institutions and the competition is strong. You may not be in a position to be too selective. Cast your net wide and look at all institutions with a computer science department.
PhD candidates are generally hired on as "WiMi" - Wissenschaftlicher Mitarbeiter - on time-limited contract. Pay varies but 1500 €/month is typical. How far that takes you depends on where you are living. In Munich, it will barely cover your rent if you have a family. In some east German cities (Dresden, Leipzig, Halle, Magdeburg, Jena) you might yet support your family and live decently. The situation in Berlin is changing rapidly and while it is currently just affordable, it won't stay that way.

Thank you for your answer! My MSc degree is not from Napier but from University of Aberdeen.
Your suggestion to apply for second masters prior to trying to get a PhD position sounds sensible. I am open to such option as long as I can make it work financially. I do not want to make it sound like money is my highest priority, which is not. But it definitely is a necessity. To my knowledge, at leats most of the German postgraduate master courses last two years. What are the funding options there?

Yes, it is true that my education and experience comes from the UK however, at least I think that I have a realistic view of German culture and expectations of the life there. Regarding my German language skills I would describe them to be at B1 level, at the moment. However, I am working on it and I learn the language both in my free time and by attending evening courses.

@BystrikOndica Before you do something as drastic as getting a second masters, you should try your other foot-in-the-door options. Number 1 should be to ask your MSc advisor for help. He might have contacts to possible advisors in Germany. With a recommendation from him to them you have a real chance to get a position.

You made a valid point there. However, I know that my department does not have any relationships with German universities. What I may do is obtaining a letter of recommendation from those professors whom I had most contact with and who know me best and then find and approach professors at some universities in Germany.


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Can I trust a paper that hides implementation details?
In Computer Science, sometimes we're assigned to reproduce the results presented by a paper that already have been published. In many cases (most of them) the code is not available, making the task more difficult.
But this questions is related to the cases where the code is available, however, many things author do in his code are not described in the published paper.

Is this ethical?
How to proceed when many things presented in the code are not explained in the original manuscript?
What if the code disappear from author's page? Will the results exist in the universe once again?

Disclaimer

This is not about minor details in the code, but huge holes of dark matter.
Let's assume that we're talking about Journal papers with more than 10 pages.

Blame journal page and word count limits, which make describing everything that the software does completely impossible.

Let's blame the journals and make them full of things that people will never be able to reproduce.

@schester I think your point of view is very interesting, and all the discussion in the thread is being very helpful. I'm trying to understand the situation. Thank you all for the answers!

Blame journal page and word count limits — I've never heard of such things in computer science.

FYI: Why do so many publishing venues limit the length of paper submissions?

Are you sure its the same code from the paper?  Does it have a timestamp?  I have ran into a similar issue, only to find that people update their code after the publication, which may use a different algorithm, whether or not the old ones worked.

Maybe CS is different, but I thought the paper is the primary contribution, and the code only exists to justify the results in the paper. So IMO the important question should be, does the code produce the results that the paper claims it does? It seems like you're asking something different, namely whether the paper completely explains the code.

@DavidZ There have been several outstanding contributions to CS that were simply made available on the web rather than published in a journal, sometimes specifically because the author(s) felt that it was unacceptable to publish without providing code and/or that limiting access behind a paywall was harmful (the ACM has had some interesting back and forth over that particular issue since the advent of public access to the internet). Unlike, say, materials research or genetics the tools necessary to reproduce an experiment in computer science are often literally at one's fingertips.

@zxq9 indeed, but in cases where one does decide to publish a paper and release associated code (which is what I'm talking about), and where the point is to show a new algorithm or technique rather than to promote a software product, I would think the paper is primary.

@DavidZ Depends on the perspective of the reader more than the author, imo. When an author writes a new paper and is explaining a new technique, what the tradeoffs are, how the concept came into being, etc. then sure, the paper is primary. Source code, however, is a form of complete specification, and if the purpose of a reader is to implement a solution in another language or refactor it in an exactly equivalent way the source may be the only unambiguous definition of what "exactly equivalent" may really mean. (This relates to the RFC inexactness problem.)

@BenVoigt I have seen that even in the "extended version" published in the ArXiv or the author's homepage. Some of the offender sentences were "[the features are...] and some physicochemical properties", "some of the features are averaged"; while they devote a full page to explain things like what is an RBF kernel. In these cases, the code was available only as binaries.

If nobody can reproduce their results with the material given -- article plus code that is unavailable, unreadable and/or not sufficiently documented -- then no, that publication is no good.

Binaries are enough to reproduce the results, why do you want the code?

@SylvainPeyronnet Because very often the code specifies something slightly different than the authors thought it did or intended it to (logical bugs are a thing). That means the binary may be a result that was unexpected and generally, but not always, meets some expectation that is different than expected. This is pretty much every logical bug ever. Code documents intent whereas the binary is only a raw implementation of one outcome of one compilation on one platform. This doesn't even touch on incidental differences in binaries, such as differences between compilers.

As a researcher, I'm generally very keen on including as many implementation details as possible. However:

There is rarely the room available in a paper to describe every detail of an implementation.
Describing every detail of an implementation in prose often takes substantially more work than writing the program in the first place. The meaning of code (which is written in a formal language) is generally unambiguous; the meaning of prose (which is written in natural language) can often be ambiguous. Resolving the ambiguities in the prose takes time, effort and care -- it's often harder than writing the code.
Researchers are generally both very busy, and under a lot of pressure from above to produce quick results and move onto new projects. Resisting this pressure to bring existing work to a tidy conclusion is a good thing, but there are limits to how long you can spend doing this, and sadly the reward structure in academia provides little incentive to do it.

There is a reasonable case to be made that implementation is not valued in academia to the extent that it should be. However, even if it were appropriately valued, and even if there were no page limits for papers, there would still be an opportunity cost for individual researchers when it came to producing copious documentation describing the implementation details of their code. Human lifetimes are finite: the time spent describing every detail of old code could alternatively be spent coming up with and implementing new ideas. Some old code is so useful and valuable that it's worth spending a lot of time describing, but that's certainly not true in all cases. A lot of code (particularly hacked-together research code) just isn't that valuable in the long run: time spent describing it could be better spent on something else.
To directly answer your questions, then:

Yes, it's ethical to not describe every detail of your implementation -- most of the time, you can't, and of the times when you can, a decent proportion of the time it's not the best use of your time. Having said that, I'm of the school of thought that says you should at least make a reasonable effort to write good, clearly-documented code, to publish it on the web for all time (e.g. on GitHub) and to at least describe how the method works in a way that will enable someone reading the code to know what's going on.
If things in the code aren't in the original manuscript, start by reading and running the code to see if you can figure out what's going on. If it's not clear from that, do some reading around to see if other sources can give you any hints. If all else fails, and it's crucial that you understand the details, email the authors. If they ignore you, give up on their method and use something else.
The code can disappear from the author's page for a variety of reasons -- maybe they stopped paying for hosting, for example. If you need the code in that situation, email them. As mentioned above, good practice involves putting your code in a public repository so that it will hang around, but it's not unethical if you don't (just unhelpful).

I couldn't agree more in the area of implementation details. I couldn't tell you the number of times that I have read an academic paper (or part of a textbook/etc) where it seems like the actual algorithm in the algorithm is left as "an exercise for the reader"

Thank you for the answer! I'll mark it as the best answer. I'm very happy with all the insights given by this topic.

Short answer: You are at the cross road situation of blaming the game, the player, or neither. Show the paper/journal to your supervisor or someone in a senior position if you can; to help you with your decision.
Longer answer: It all comes down to one thing: whether writing a piece of code is a contribution or not. Well, it is actually a grey area. I would judge a computer science paper/journal, with code, like the following:

Know the Context and the Promises: What is the context? Is it just a tool that demonstrates something? Or a language that promises that it does wonders? If it is heavily code oriented, then the code should be presented clearly in the publication.
Semantical Backup: Do the author(s) prove their promises with semantics? How deep do they go into their semantics?
Clean Links Between Semantics and Programs: Do they clearly demonstrate the relation between the semantics and the program? If not, it is a red flag in my opinion. Something is lacking here and the authors are hiding something.
Track Records of The Authors: You can also simply look at their records as well, see what they did achieve so far; and base some judgement on this as well.
Some extra work: You could also look at their code as well, if they provided a link. It is not hard to compile any mainstream languages, most likely a one line command will compile the code and you can see for yourself. You can even copy/paste part of their code into a search engine box, and take it from there.

Conclusion: You see all these points are not hard hitting rules that help you with judging an implementation part of the paper. It is the best to get a helping hand by a senior academic (e.g., supervisor) to look into it to help you with your decision.

It can be extremely hard to build code, depending on things like the language, what dependencies are needed, and how the build has been set up. Research code is actually often quite hard to build, because little effort is put into setting the build up properly (often it's only easy to build on the machine of the original researcher).

@StuartGolodetz I know that, however this should not be an excuse for the author of the paper to provide a crappy code that can not be run. They can easily contain all their code and all their dependencies into one zip and write a bash for it or to use third-party containers. Again, this is a problem in CS domain and some people unfortunately take an advantage of it. This is a grey area that you need to take a decision, for the faith of the paper, with a senior lecturer.

@StuartGolodetz Also... look at big main stream languages/operating system that are open sourced which you can build them up from the source with all their dependencies. In my opinion (that might be extreme to some academics), if the code can not  be run or demonstrated, then the researchers did not their job. If they want to publish a paper on just theory then thats another ball game.

Most computer scientists can't write quality software, because they don't have the training or the experience for it. Even worse, research code is usually written by the least experienced members of the team. By the time people start learning best practices, they usually advance to higher-level stuff, and the programming tasks are assigned to new students.

@DaveRose: I was primarily arguing that your assertion that "it is not hard to compile any mainstream languages" is by no means always true. In general, setting up cross-platform builds that work reliably on all setups (including those to which you may not have access) is not trivial, even if you have a reasonable amount of experience. Many researchers (particularly early-stage ones) don't have that experience, and their code can be hard to build as a result.

@DaveRose: For the record, I'm not arguing that their code should be hard to build -- I spend a lot of time trying to help people improve their build processes -- I'm merely arguing that it sometimes is. That may be because they haven't bothered to set up a decent build process, or because they don't know a better way of doing it. The underlying problem in both cases is that building things reliably, particular things with lots of dependencies, is not easy. (That comment's based on a fair bit of time spent automating builds of third-party code.)

Is this ethical?

I don't see this as a question of ethics. Is it unethical to write a bad or not useful paper? No, it's simply the best that some people are capable of (or interested in) achieving. By not including implementation details, the paper's authors are clearly limiting the usefulness and future impact of their papers. Nonetheless, the paper may still have some usefulness, so I don't see why anyone would think publishing such a paper is unethical. The only exception is if the authors are dishonest about their claims of what the algorithm can do or how well it works, and are deliberately hiding implementation details to prevent their dishonesty from being exposed. Obviously that would be unethical.

How to proceed when many things presented in the code are not
  explained in the original manuscript?

Do your best to fill in the holes. If it seems too difficult or too much work to reconstruct the missing implementation details yourself, talk to your professor -- he or she may not realize that they've given you an unreasonably difficult assignment, and it would be their job to figure out how you should proceed.

What if the code disappear from author's page? Will the results exist
  in the universe once again?

Again, it's up to the author to decide how much work they want to invest in ensuring their paper has a long life and makes a meaningful contribution. It's also up to the journal editors and reviewers to enforce some minimal standards. But at the end of the day, if the author doesn't care enough about their work making an impact to deposit their code in a repository that would outlast their personal web page, that's really their decision, but it doesn't reflect well on them, and potentially limits the cumulative usefulness of their work to the community.
To summarize, what we are seeing here is an example of short-termism, which is something you see in all walks of life. Some authors write a paper just with the goal of getting the short-term reward of getting their paper published (and the attendant professional rewards the academic environment will give them for such a publication: jobs, promotions etc.) and will just put in the minimum amount of work to achieve that immediate goal. Others care much more about the long-term impact their work will have on the research community, which will also eventually translate to a personal benefit to them since they will develop a reputation as better researchers. It is the researchers who belong to the latter group whom you usually hear about as the famous, super-successful authorities in the field whom everyone admires, so I certainly recommend trying to follow that approach yourself.

" Is it ethical to write a bad or not useful paper? No..." I think you want one more, or one less, negative there somewhere.

Got it, and fixed, sorry for the carelessness.

No. It's not ethical.
If we stick to Eliezer's scenario, I cannot trust a paper that posits wonderful things, but fails to at least outline how they were accomplished.  I've read several papers extensively detailing mathematical models for stuff, and the enormously successful results achieved thereafter, but left the code implementation out.  Obviously I can't confirm the non existence of associated code.  It might have existed once, somewhere.
There is a very well known web site in my sad sphere of interest that is held in high esteem by all.  Except me.  It features detailed information of what it does, and published analysis of it's output (even some in real time).  It doesn't publish any actual code of how it does it.  Hmmm.
Facetious example:  I've just invented true Artificial Intelligence.  Hussar!  Here's the kit I did it on.  Here's the conversation I had with it that passed the Turing Test.  The (easily understood Java) code I wrote is on my web site for you to read.  Including the bit in (opaque) compiled machine code that I happened to use.  Do you believe me?  People believed Volkswagen.

Do you believe me? I'll try to believe you if you delete your another answer which is absolutely non-sense.

Paul, I think you are confusing between not ethical and not useful. Ironically, that makes your answer not useful (although it is not unethical), illustrating exactly the same distinction.

Clarification to my previous comment: your "facetious example" does actually represent unethical behavior, since in that case I assume (based on your reference to Volkswagen) that you are referring to a researcher who fraudulently claims to have developed AI code that passes the Turing test when in fact he hasn't. I agree that is clearly unethical, and said the same thing in my own answer. However, if you did in fact invent true AI and didn't provide full human-readable code or documentation (which seems closer to the OP's scenario), then again that is not unethical, merely unhelpful.

I think it's entirely understandable that details of a code example will be undocumented.  Let's say, for example, that the paper is about exception propagation in an instruction stack.  In the example code, the author does some tricky little obfuscated sorting of an array, which will be iterated over to produce an example exception.  Is it relevant to explain that little sorting routine?  No...it's just some example code that gets you to the meat of the problem.

This answer isn't really consistent with the OP's description of "huge holes of dark matter".

@DanRomik...let me introduce you to my dear friend, "rampant hyperbole."  I've never met a new coder looking to refactor existing code that didn't declare the thing to be a "rat's nest of ungodly spaghetti."


text:
How to manage publications on a local computer
I would like to find a better way of naming publications which I store on my local computer as PDFs. So far I have been doing something like this:
Albano R., Sole A., Adamowski J., Mancusi L. (2014) - A GIS-based model to estimate flood consequences and the degree of accessibility and operability of strategic emergency response structures in urban areas.pdf
This presents a couple of disadvantages:

Titles can be extremely long. This causes problems in certain operating systems or software such as OneDrive. You can only have so many characters in a filename...
Not all publications can follow this format. The above is OK for journal papers and theses, but not so much for books or other kinds of publications.

I would like to have a consistent way to manage such a database. I thought of keeping the publication metadata such as authors, date of publication, type of publication and type in a separate text or excel file and naming the PDF files by ID, like 1.pdf, 2.pdf, etc. This could work, but it would require referring to and managing a spreadsheet which would contain all the meta data.
Is there a simple method or perhaps lightweight software that I can use which can help me with this sort of task?
EDIT
I didn't really like the way @Jonas Stein's script is set up, though I do owe him the inspiration and indication to use JabRef. Here's my alternative script:
import bibtexparser
import os
from shutil import copyfile

filename = 'db.bib'
out_folder = 'out'

with open(filename) as bibtex_file:
    db = bibtexparser.load(bibtex_file)

for entry in db.entries:
    print(entry['file'])
    id = entry['ID']
    file = entry['file'].split(':')[1]

    copyfile(file, os.path.join(out_folder, id)+'.pdf')

print('done')

It's much more compact and does the job.

Some people suggested to use a dedicate software for that matter. Absolutely recommendable. Another possibility is Zotero. It can automatically import all your PDFs allowing nice organization of your library, full text searching, producing bibliography, etc. Works with LaTeX, Word, ...

Do you write in LaTeX? If so, a bibtex file will already take care of storing all the metadata. Then I suggest filenames corresponding to bibtex citation keys, and I follow the convention "turing1936computable", "shannon1948mathematical", etc. (Last name of first author only.)

For me it is usually important to know if the paper is single-author, two-author, or multi-author. Therefore I go for the jabref recommended author1999 / authorA.authorB1999 / authorA.etal1999 format. Nothing more. The rest of the details can easily be found via your bibliography manager (I use jabref on bibtex files).

If using WIndows, why not use tagging (and Details, etc.) available already within the file folder structure? See e.g., "How to Tag Files to Tidy up Your Windows 10 Files" https://www.laptopmag.com/articles/tagging-files-windows-10. This way the info is right there in the good old file explorer and not having resort to open a new SW.

What @TasosPapastylianou says. The cool thing about JabRef is that is automatically generates keys if you hit CRTL-G, disambiguating as needed ("Foo2019" vs. "Foo2019a"). If you then simply name the files with the keys, JabRef autolinks to them, and you can open the PDF (or other filetype) with a single click from the JabRef entry. Very good.

I manage publications with JabRef in a bibtex database.
It is possible to add a link to the filename with JabRef in the bibtex database.
A python script pybibtexcleaner transcribes the special characters in the title and moves all sorted files to one folder with file names in the format
bibkey-title.pdf

The script will generate from a bib entry
@Article{Stein2017a,
  author    = {J. Stein and M. Baum and S. Holbein and T. Finger and T. Cronert and C. Tölzer and T. Fröhlich and S. Biesenkamp and K. Schmalzl and P. Steffens and C.H. Lee and M. Braden},
  title     = {Control of Chiral Magnetism Through Electric Fields in Multiferroic Compounds above the Long-Range Multiferroic Transition},
  journal   = {Physical Review Letters},
  year      = {2017},
  volume    = {119},
  number    = {17},
  doi       = {10.1103/physrevlett.119.177201},
  file      = {:../included/119.177201.pdf},
  publisher = {American Physical Society ({APS})}
}

the new filename
Stein2017a-Control_of_Chiral_Magnetism_Through_Electric_Fields_in_Multiferroic_Compounds_above_the_Long-Range_Multiferroic_Transition.pdf`

and copy the file to ../articles/ and also adjust the path in the .bib file.
It is very useful if the filenames start with the bibkey.
You should always use all digits of the year.
The script can also transcribe chemical formulas in a readable way, if they are introduced with \ce as in \ce{H2O}.
You can keep track of your work with git and you can restore old versions or synchronize the literature database on your different systems.
ps: I use the old stable 3.8.2 version of JabRef, because the new versions 4.x were less stable when I tried them. The user has better control on the rename process with the short python script and can easily adjust it to the needs, but recent JabRef versions are shipped with similar functionality.

Jabref is great. Once you have your library you can search and manage it. I have added an extra field for my own notes on the papers that i've read.

Yes, @Ivana. You can also use a group for printed or read papers.

I like your suggestion. I downloaded JabRef and tried downloading your script from github. I made a 1 document JabRef database, modified the pybibtexcleaner.ini file according to my own setup and tried python pybibtexcleaner.py. However re threw an error: `re.error: bad escape \m at position 1. The problematic line is line 29. What do you think might be the problem? Thanks.

@user32882 oh yes there was a bug. Please pull the latest version and try again

It seems to work now but I don't really get the purpose of this script. You are parsing through the .bib file, extracting the titles and then rewriting  the file in another folder as bibkey-title.pdf. What is the point of that? Also why append the title? Some titles can be super long....

@user32882 the purpose is to have files with unique filenames that can be used by a human to see directly which pdf is linked to a \ref{}. You can limit the length of the filename simply by cutting the string after n characters.

I think your script is over-complicated. Please see my edit for something super simple that just works and is easy to debug

For the filename, I use a system that I plagiarised from my PhD supervisor:
aaaadd_xxxx_jjj.pdf
where:

aaaa: name of the first author (variable length)
dd: 2-digit year of publication (fixed length)
xxxx: first word of title, minus articles and other small words (variable length)
jjj: abbreviation of journal of publication (variable length, but short)

I then use the same without the .pdf as my bibtex key (with an added :).
For example:
T. Penguin et al, a Survey of Antarctic Leasure Activities, Journal of Improbable Results, 2025
would be
penguin25_survey_jir.pdf
with the bibtex key penguin25:_survey_jir.
I like this system because:

I'm used to it
Filenames remain compact and UNIX shell friendly
The encoded information is usually enough for me to identify the paper

It doesn't cover tagging or categorising.
This applies well to journal articles.  For conference proceedings articles or books, the journal acronym is replaced by an acronym of the conference or the publisher, or perhaps the full name of the publisher; I'm not fully consistent there.  But I don't usually have entire books as PDFs anyway.

What are the advantages and disadvantages of this format?

@FedericoPoloni Added a few bullet points addressing that question.

Do you have a mini Y2K bug in your format, or doesn't it matter?

A problem with that format is that you only see the surname of the first author, and sometimes it is the last author's name which means much to you.

@AaronF Until I get papers published by authors with the same name, same title, and same journal, exactly 100 years in-between, it doesn't matter.  I don't have many papers that are >100 years old.

@DmitrySavostyanov In some fields the last author has an important meaning.  That happens not to be the case in my field.  Of course a lot of information is inevitably lost condensing author list and title to a form as short as I described.

"I like this system because I'm used to it". Well, that's gotta be an argument for any system

@infinitezero You can be used to something and not like it ... like getting up before 8 AM

There is lots of software out there which can help (e.g., Mendeley). I used this (and others) but found it would take more management than I would care to give.
Personally, I just had a publications folder with nested sub-folders for different topics. I would then simply name the .pdfs using the last name of the first author and the year of publication, that is: lastname_2019.
I found this had several advantages:

It's easy to remember. In discussion with peers I could easily refer them to a paper by lastname in 2019. It's great to be able to do this easily and helps your reputation. The alternative is discussing with peers who just vaguely remember the contents of a paper but can't remember the title or authorship.
It's easy to search for the paper using (for example) spotlight in macOS. I just typed in the last name and all their papers would come up. Also helps in memorising the authors last name. I relied on this heavily and never really searched the publications folder.
If using LaTeX, I could easily remember what papers I wanted to cite and as I set the bib reference to the lastname_2019 format, I had no more information to remember.

Of course, if a person publishes multiple papers in a year, I would just append a letter to the add. To be honest, I think I only had to do this once or twice for my field.

Then Mendeley is your friend as you can assign publications to different folders. In my field the first author is always the most important, and either if it wasn't I don't think it matters for referencing, in no way is it assigning credit.

I think this works well in some fields like math. I did something very similar there. Presumably it doesn't work very well in other fields, where most papers have lots of authors and the average number of papers per year and researcher is much bigger than one.

Mendeley is not bad, but so proprietary (

I use mendeley with automatic folder scanning. I download a paper with a filename like SI90234023499-II.pdf dump it into one of my watched folders, and it is automatically sorted into ~/Literature/FirstAuthor/Year/Journal/Title.pdf and added to the Mendeley database. You can customise the directory location from any combination of metadata, but for me is doesn't reallly matter because I only ever access stuff via the Mendeley App anyway, so I rarely handle the PDF files directly.

Note, that Mendeley is a proprietary database. Users of such cloud based systems invest their time to create a database they do not own. These systems are designed for a strong vendor lock in. I suggest to use free and open source solutions, where the community keeps control on the own data and can fix bugs.

If such a system existed, I would use it, but I've yet to find a system that works to automatically take in my documents with no manual intervention, reliably scrap the information, automatically rename and file the PDF and automatically make it available on all my devices (2x desktop, 1x laptop, 1x android phone, 1x iOS ipad) and will integrate with MS word.

@IanSudbery Zotero, combined with the plugin Zotfile, will do all of that except for the mobile devices, and for that interface with Dropbox etc. And it's open source, so you know your data will never be locked in with Elsevier. Not too much of an issue if you're just using it for keeping annotation data, but a Really Big Deal if you take notes in the system.

For books you can use Calibre, which is a free e-book management program. Easy to use.

Agreed. Calibre for file management and Zotero for references.

How about plain old Excel.

Start by naming your PDF documents using a naming scheme like what @gerrit has suggested (or some other mechanism that results in manageable/recognizable file names).
Create an Excel worksheet document.  Make Column A very wide. Each row will represent a single file
Select a cell.  Choose the Insert tab and press Link
Paste in the full name of the document (in whatever format you want) into the "Text to Display" field
Navigate to your PDF file in the file browser, select the right file and click OK

You now have a searchable document that contains your publication titles and clickable links to your documents
If you want to be fancy, you could have several columns (publication date, authors (or maybe primary author and other authors), title, etc.).  Put some column headings in.  Now, it's not only searchable, but it's sortable and filterable (particularly if you create it as a Table (play with the Table button on the Insert tab.))

Every startup should consider: can your product replace Excel.

I recommend you name the papers as you say 1.pdf, 2.pdf, and have corresponding metadata files 1.txt, 2.txt which you can structure however you want.
Then the crucial part is this: use grep (available for both Linux and Windows) to search through the content of all the text files in that folder. This will find you which txt files contain the searched terms.
Searching is as simple as this (this will show which text files in the current folder contain the word "Adamowski"):
grep -r "Adamowski" .

I think this is the simplest way.

pdfgrep could be useful for this solution: https://pdfgrep.org/

Is there a simple method or perhaps lightweight software that I can
  use which can help me with this sort of task?

Although it is a bit over the top, JabRef can maintain bibliography and rename files:

Renaming of files is now part of the “Cleanup Entries” feature (brush
  button in the toolbar or Ctrl + Shift + F7). Then, you can rename
  attached files based on the BibTeX key. You can change the format
  (pattern) under Options → Preferences → Import, by altering the
  pattern under “Default PDF file link action”.

And the patterns are diverse, and it is possible to consistently abbreviate journal names, titles, and combine author names, for example:

Author-related key patterns

[auth]: The last name of the first author
[authors]: The last name of all authors
[authorLast]: The last name of the last author

Title-related key patterns

[shorttitle]: The first 3 words of the title, ignoring any function words (see below). For example, An awesome paper on JabRef
  becomesAwesomePaperJabref.
[veryshorttitle]: The first word of the title, ignoring any function words (see below). For example, An awesome paper on JabRef becomes
  Awesome.
[camel]: Capitalize and    concatenate all the words of the title. For example, An awesome paper on JabRef becomes
  AnAwesomePaperOnJabref.
[title]: Capitalize all the significant words of the title, and concatenate them. For example, An awesome paper on JabRef becomes
  AnAwesomePaperonJabref.

Modifiers
  Generally, modifiers are applied in the order they are specified. In
  the following, we present a list of the most common modifiers
  alongside a short explanation:

:abbr: Abbreviates the text produced by the field name or special
  field marker. Only the first character and subsequent characters
  following white space will be included. For example:

[journal:abbr] would from the journal name “Journal of Fish Biology” produce “JoFB”.
[title:abbr] would from the title “An awesome paper on JabRef” produce “AAPoJ”.
[camel:abbr] would from the title “An awesome paper on JabRef” produce “AAPOJ”.

My method is to name each PDF file as:
year, authors, title.pdf

E.g.:
2020, Abc Def Ghi, The letters of the alphabet.pdf

I work with Ubuntu and never had problems with these filenames, although they contain spaces and commas.
Putting the year first makes it easy to sort papers by year in the file explorer.
Putting the title in the filename makes it easy to immediately see in file explorer what the file is about.

You are lucky, if you had no problems with spaces and commas in the filenames. It is calling for trouble. How do you transcribe the names of authors with non latin characters?

How do you limit the length of the title? Most filesystems and programs have a very limited filename length.

@JonasStein there is no need to put the exact names (with non-latin chars) or the full title - just put a sufficient amount of the title such that you understand what's inside.

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


text:
Should I ask for each recommendation letter separately?
I will be applying for a PhD this year. So, I would like to ask for recommendation letters soon. Should I ask for each recommendation letter separately, or may I group email all the letter writers? Is there any general benefits or caveats in either approach?
My primary supervisor would like me to stay for a PhD at my current university. So, the group email might make the case seem "more decided". I'd like to avoid any further discussion on staying, since I thought to do so earlier (kind of promised) but have changed my mind since. It might negatively affect the letter to some extent.

I would recommend that you do not send a group mail to professors you plan to ask for help. It will look somewhat lazy, and some may be offended that you were not willing to take the time to write a separate email (which should barely take any time). Another reason why this is bad is that hopefully each recommendation will not be saying the exact same thing, and you may want to reflect differences when you ask for the letters.
In fact, I would probably recommend approaching the professors (or others) that you plan to ask in person first. Of course, this depends on your relationship with the professor-- if they are very busy and have already previously agreed to write a letter then this step might not be necessary. However, when asking professors for letters it might seem a bit impersonal if you do not ask in person, and you also will not be able to gauge their reaction to be asked if the correspondence is online.

One of the things professors want to know as recommenders is, "What makes me particularly qualified to write a letter for you? That is, why should the recipient of the letter value it over a letter from someone else?"  You probably cannot answer that question adequately in a group email, and so you will diminish the quality of any letters you may get from such an email.


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How many professors should I mail in a single university?
This is a funny dilemma that's been bugging me for quite sometime now. I plan to pursue a PhD in Synthetic Biology and when I visit the faculty directory in a university, I see many profs working on it. Now my question is how many profs should I apply to for a position. They all seem equally good. However, I fear that if I apply to all of them, they might meet over a coffee and come to know that I have been mailing to a lot of them and that would put a bad impression on me (Is it not?). I would want my chances of getting into a program to be maximized. I know there are rotation systems in labs and the program would send my application to potential supervisors(I don't know which ones), that's why I am planning to ping every lab possible which are of my interest. Kindly enlighten me on this.Thanks.

A lot of very similar questions have been answered here, so you might try browsing through old question on this site. In the meantime, what country are you in? The answer depends highly on that.

@Anonymous I am from India but I would be applying to the US universities mostly. I would be grateful if you could post the links here! I saw a few questions, bit similar but they were mostly about getting recommendation letters from multiple professors, so mine seemed different.

In the US you don't apply directly to profs, you apply to departments as a whole. Your first step, before you ping anyone, should be to thoroughly read the application instructions for the universities to which you intend to apply.

This isn't an answer to your question, but the remark that professors might meet over coffee and find out that you emailed a lot of them seemed funny to me. We do meet over coffee and chat. But you have to recognize that (i) we're people too, with families, kids, etc, and when we have coffee, we often have better things to talk about than students emailing us their applications (we might also be talking about actual science, gasp!), (ii) we get a lot of emails from students applying, and the likelihood that we would notice that one of them has emailed a lot of us is very small.


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Advice for switching PhD programs back to my undergrad field
I'm a first-year PhD student who switched from field X in my undergrad to field Y at my current university. The program I'm currently in is ranked #1 in field Y. I am genuinely unhappy here and am looking for advice on switching programs.
I joined this program because I had done research here before and enjoyed it, and it's an excellent university, so I figured it'd be a no-brainer. I was a little worried about switching fields, but everyone said things like "classes don't matter" or "choose the PI, not the school", so I figured this decision would be best. Unfortunately, I was mistaken.
I'm quickly learning that I do not have interest in many of the required courses (I think I wrongly convinced myself that I would), and there is a large amount of classes I need to take (about 12). I'm not enjoying the material I'm learning, and I'm also finding that I don't have many pre-requisite classes I need to truly excel and understand the material. I am sitting in on lower-level classes and giving it my all, but this is just adding on more and more time between myself and what I want to do -- research.
In all, I do not find myself happy here. I am very passionate about research still, and I think pursuing a PhD in my undergrad field at a different institution would be a better fit for me.
Does anyone have any advice about how to do this most effectively? I plan to be up-front with all those involved, and I intend to briefly but clearly explain why a new program would be a better intellectual fit than my current one without bashing my current university. I can get a strong letter from someone at my current university, although he is actually in the field I want to switch to, not the one I'm currently in. I hope my letters writers understand if I explain my scenario to them.
I imagine this will be a sticky situation, since I doubt I'll be funded to stay in the program next semester if they know I plan to leave, and I'm definitely not going to pay out of pocket. But I'm not going to lie by omission!
If anyone has been through this process, I would be eager to hear any advice. I just want to do this in the best way possible, for myself as an applicant and for others involved. I plan to re-apply to some universities I got accepted to in the past as well as other universities I didn't apply to before but think would match my interests.

Are you tired from attending courses? And you want to go elsewhere, so you can attend other courses? This does not make sense.

I am not tired of attending courses. I'm tired of attending courses I am not interested in and do not have sufficient background to fully grasp. I was told I'd have a sufficient background for the courses, but I am missing fundamental classes that are absolutely required. Also, the programs I am interested in have fewer course requirements (typically around 5 or so, compared to 12 or so in my department).

I understand your concern about spring semester funding.  Why don't you put in some applications and wait until you get an acceptance before informing your current department?
I think your department will be glad you've got the self-awareness to realize when something isn't working.

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Why doesn't the academic year start on January first?
The academic year starts somewhere in the middle of the normal calendar year in almost all schools. Even if the courses are divided into semesters, the Fall term is essentially considered to be the beginning of a new academic year. It is also true for the financial year in most places.

Why doesn't the academic year start in January?
If the reasons are so prevalent, then why didn't the normal calendar year start in the month of August, for example?

I am in northern hemisphere, much like most of the world!

I was going to post a cheeky comment about how most of the world lives below the equator, but it turned out that only ~12% does.

Aside from all the places where it does start in Januray (iirc, Hong Kong being one), my understanding is that the key point is harvest - it was all-hands-on-deck in the summer, so the long break goes then.

Ever wondered why the fiscal years do not usually end in December?  :)

Yes! I did. It is mentioned in the question as well "It is also true for financial year in most places." That makes it all the more confusing. Why shouldn't the calendar year start when the fiscal year and academic year start? It's like yeah our year starts in January but we will do everything as if year starts in August!

Note that the new year only starts on January 1st in the Gregorian calendar: even in Europe, this goes back less than 500 years!

@jakebeal True but the academic year starts in September/October in many more countries than used to have the calendar year start in September.

I believe it does start in January in Argentina and Chile, but don't quote me on that.

Boring but true: the academic calendar follows the calendar of primary and secondary schools. A new year begins when the students get their high school graduation and are ready to enrol, move, and start with their undergraduate studies.

@ArturoTorresSánchez, in Chile the academic year starts in March. Just like the Roman year used to start, before Julius Cesar decreed it start in January to keep some bureaucratic date "at year beginning" and not interfere with travel to/from the capital. Yes, "the foo year starts on..." is just arbitrary.

@MateenUlhaq: See the Southern Half at xkcd.com for a image

@Maroon I misremembered (it's been a while). Singapore and Malaysia are January, according to Wilipedia.

FYI, in Japan, it starts in April, as the cherry blossoms then symbolize the start of an (unofficial) new year.

@FedericoPoloni Great. So why do they start in September? It can't be turtles all the way down.

@DavidRicherby Well, you can ask that question on primaryschool.stackexchange.com, when it opens. :)

Because September is nine months after Yuletide - historically the time of great feasting and celebration. Since most births occur in late (Northern) Summer, children turn the magical school-age together in September. As has already been pointed out, January 1st is a relatively modern idea for the "start" of the year.

In my country, South Africa, schools always start early January and Universities always start in February. :). The reason the latter starts in February, is because in our schooling system, in the final year of school, you write an external (departmental) exam. This results are only received early January, and hence university only begins a month later in February, giving students who just finished high school enough time to prepare and get ready to start their undergraduate studies after receiving their "matric" results.

Actually fiscal years are all over the place and some do start in January, so I am not convinced there is a direct relationship with the academic year. In any case, possibly a question for history.SE?

Basically because schooling is the inverse of farming. That is: Historically farming and feeding the family (and community) took precedence over all other considerations. This is primarily a job that takes place through the spring, summer, and fall -- with little or no activity possible in the winter. Therefore in most cultures the original calendar year starts in the winter and so spans one farming cycle, i.e., spring-summer-fall (in the original Roman calendar, the winter period didn't even have assigned months!).
When schooling historically started to be of some value, it came secondary to farming, and occurred only as farming allows. So the winter is an excellent time for it, because no useful farming can be done. On the other hand, the harvest season, around August-September, is the busiest time for farming, and critical in traditional communities to have "all hands on deck" for that work, and thus schooling would not occur at that time. And therefore the main school schedule would begin after the fall harvest, and run through to the summer of the next year.
In short, the fact that schooling and farming have an inverse schedule is not too surprising, because traditionally the former only occurred in the time not being used for the latter. Having grown up on a farm in the U.S. in the 1970's, I still experienced some tension between my family and school, because I would need to be out of school for about a week in September for a particular job that we were expected to do with our livestock at that time.

This is interesting! I could have never imagined farming coming into picture. Kudos!

There is another explanation in my country. Usually we have floods in the summer (not in the cities of course), so we should wait for them to leave before schooling. The bottom line is that the start of the academic year depends on the weather.

where do you live @Saurav?  of course the academic years are delimited by the "summer vacation", whether the students were working on a farm or traveling or at summer camp.  if the academic year is short enough, it is possible to have the two semesters delimited by the Christmas break.  most secondary schools divide the two semesters at some weekend toward the end of January.  some colleges have a "4-1-4" system where there is a special, one month "Jan-term" in January.

It looks like this might also explain spring break (planting).

This is a great answer and makes a lot of sense, but I think it could use some sources to back up that this is actually the historical reason.

http://history.powys.org.uk/school1/llanfyllin/scarcity.shtml may offer a starting point, it's a website for children, but contains sources direct from school log books at the time.

This is a fun answer but I suspect other factors, like the fact that people like to take time off during the summer, are much more relevant.

Apparently I can answer but not comment with such a new account. This is really more of a comment to Daniel R. Collins' great answer.
Anyway, in my country, there's a concept of the "summer holidays" when kids otherwise going to school are expected to relax and/or do other non-school-related activities (such as summer camps - note that "winter camps", if any, are much rarer). This is basically June to August (July to August for students, whose classes end later).
As far as I understand it, these holidays are in the summer (as opposed to winter) because the weather in summer is much more pleasant, and thus much more appropriate for relaxationary activities (such as country vacations, or traveling). And, yes, historically (and partly to this day), there's some farming-related stuff too (for the kids to help with at some of the summer camps; this is not much the case today, except in the especially rural areas, but was very popular as recently as several decades ago).

Incidentally - something that did not come up in Daniel R. Collins' answer, or indeed, as I write it, anywhere eise in the comments - the calendar year does not necessarily start in January; in fact this seems to be a (historically speaking) rather new tradition even where it does. (I do not know where it originates; it might have had to do with Christmas.)
In particular, the Hebrew (and therefore Israeli) calendar year starts in September, not much after the academic year. The Muslim calendar year doesn't really start at any seasonally defined point at all; except in Iran and Afghanistan, where it starts in March.
More historically, the British calendar year started in March prior to 1752 (the financial year still does, though it's been moved to April by the change to Gregorian). The Russian calendar year started in September during the 16th and 17th centuries (and in March before that). Of course, as mentioned by vonbrand, the old Roman year started in March (from which the names of our autumn months originate).
Other traditions have yet other starting dates for the calendar year; I've heard somewhere that for every day of the year there's a tradition somewhere that puts the New Year on that day. That much is probably not true, but there are definitely very many. Not many of them, save for the modern Gregorian one, are in January (the traditional Chinese new year almost is, but it's more often in early February); December seems slightly more common (mainly due to the winter solstice).

In addition to the existing answers there would be a strong historical link (as least in the UK and Ireland) to the festival of Michaelmas (The feast of St. Michael the Archangel) at the end of September. Many Universities such as Oxford and Cambridge still use the phrase Michaelmas term to define the term from September to December. It is also the start of the year for the legal system in the UK and Ireland
According to A History of the University of Cambridge: Volume 1, The University to 1546 By Damian Riehl Leader on p29 (can be found on google books) the Michaelmas academic term started from 9 October since the Middle ages.
The Historic UK website gives the following explanation as to why this time of year (late September/Early October) was also adopted for the academic year.

There are traditionally four “quarter days” in a year (Lady Day (25th March), Midsummer (24th June), Michaelmas (29th September) and Christmas (25th December)). They are spaced three months apart, on religious festivals, usually close to the solstices or equinoxes. They were the four dates on which servants were hired, rents due or leases begun. It used to be said that harvest had to be completed by Michaelmas, almost like the marking of the end of the productive season and the beginning of the new cycle of farming. It was the time at which new servants were hired or land was exchanged and debts were paid. This is how it came to be for Michaelmas to be the time for electing magistrates and also the beginning of legal and university terms.

It would appear that the tradition of September/October is linked to early medieval traditions of demarcation of the year which were based more on religious festivals that also had a civil significances such as preparing accounts, signing leases etc.
Here is a useful document on the Organisation of the Academic year in EU states for 2014/15. Most countries follow a August-October start to the academic year.

In Indonesia, there had been an academic calendar start on January (1966 to 1979). Daoed Joesoef (Minister of Education and Culture of Indonesia at that time) changed academic-calendar to start on July in 1979. One of the main reason was following other country academic calendar. Plenty of students who willing to continue their study in oversea had to wait for six month or more.
So, the answer of your first question is: following the rest of the world.
For the second question, Why not "normal" calendar started on August? It's complicated. British adopt January as a new calendar since 1751. (CMIIW)
The Byzantine Empire used a year starting on 1 Sep, but they didn’t count years since the birth of Christ, instead they counted years since the creation of the world which they dated to 1 September 5509 B.C.E.
(Source: http://www.webexhibits.org/calendars/year-history.html)
August is named after Rome Emperor, Augustus since 8 BCE, and I think it's better then sextilish (prior name, the sixth month, but sound like sex-thing-ish).


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What is the distinction between "graduate school" and "professional school"?
I have previously been involved with mentoring high school students as well as undergraduates, who typically don't have a clear understanding of all of the career possibilities available to them and how they might pursue them.
One of the distinctions I typically make is that "Professional School" (e.g. medical, law, physicians assistant, nurse practitioner, dental) is further training past undergraduate studies that prepares you for entry into a very specific profession/job with a terminal degree. "Graduate School" is additional training that prepares you to be an expert in a particular field, but the job opportunities are much more diverse and you may or may not be working toward a terminal degree. One of my college advisors made this distinction to me, and I have carried it forward.
Is making this distinction between graduate and professional school correct?
Is there another more specific or subtle difference that I am missing?
What is the true distinction between graduate and professional school? - Or is there not one?

Given the professions you listed for "professional school", a very cynical part of me wants to say "salary prospects" ;-)

nice comment @tonysdg... I wonder where individuals would place MBA programs or other specialized masters programs?

At least in my geographic region (Texas, or the US southern states), a professional school implies a curriculum that targets specific skills for a particular vocation. In effect, this is akin to my awkward bastardization of several concepts:

"Teach a man to fish and he can become a fisherman ... help him learn
  how to think and he can pursue a career in whatever he wants."

The former refers to a professional/vocational school.  The latter refers to accredited universities with broader range of curriculum missions.  Granted, this reflects my biased perspective: admittedly, vocational schools have a (usually) noble and useful purpose, but proper universities can offer so much more to enrich the whole student, and potentially brighten the intellectual and career outlook for years to come.


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Lack of supervision at end of PhD - how approach publishing?
My PhD supervisor, who was from an external organisation, got my PhD started with initial ideas and guidance, but wasn't an expert in the topic, thus my PhD research has been mainly self directed. About a year ago my supervisor retired, and has justifiably been off travelling and working on other things.
I'm at the late stage where I am writing up the thesis and have two papers almost ready to submit. However, I would dearly like someone to read over the work and check it, as it has quite a bit of mathematics.
How should I approach publication?

Find another supervisor, even at this late stage, and collaborate with them.
Approach an expert in the specific area and ask if they will review the papers before submission. Is this an unusual request?
Submit the papers to journals and trust the review process will identify any errors.

I would do all of those, but I would not assume any of them will find all the errors.

I do not like this: "have a few papers almost ready to submit". This usually implies more than two papers. In a PhD papers are interconnected. So, if paper 1 has an important mistake, does not that make papers 2,3 and ... based on paper 1 also problematic? This is why, in certain disciplines,  you need to publish at regular intervals during your PhD and not at the end.

@Alexandros A few too many assumptions there. :)  I've published a 6 conference papers, the two (question updated) journal papers are based on those. The general method is sound so I would not expect any huge mistake, more like small errors... I just want to get the journal papers right and would like some external feedback. I do regret not publishing earlier, but at the time I felt I was still learning so much that I didn't have the complete picture.

@Alexandros: "In a PhD papers are interconnected." - Some, but I don't think it is unusual for a PhD candidate to always have about 4 or 5 parallel branches of work that are largely independent of each other (e.g. one's PhD research; the possibly disconnected output from one's project grant; a cooperation project with another department that may or may not be integrated with the core work only later; a paper based upon a supervised student thesis that is worth publishing; papers in another community that provide use cases for one's core research, but receive a higher-level view; etc.).

@geometrikal If you've already resolved this, it might be worth adding an answer with how that went.

Your university should have a policy in what happens if a supervisor retires or otherwise becomes unavailable. At this stage it may not produce the ideal outcome, but you should explore it. It sounds as though somebody, either your supervisor or your institution, is not doing their job.

Yes, good idea. I'll check if they have some formal processes, they are pretty good at supporting phd students in general.

AFAIK, usually you cannot defend without an advisor...

I think it might be too late to find a new supervisor. Additionally, finding a new supervisor would take time and this would delay the submission of your paper. You can definitely write to an expert in the field explaining your problem and asking if they would have time to go over your paper. You can also write to your retired supervisor and ask if he knows of anyone who would be willing to review your paper. If you do not find anyone, you will have to submit to a journal and wait for the reviewer comments. There is a likelihood that your paper might be rejected, but you will definitely gain from the reviewer comments. Additionally, there are professional peer reviewing services, which would of course, be an added expense. But some of them are pretty good and are accepted by certain journals.