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Do I have to cite common CS algorithms?
I'm working on my final thesis for a CS grade course and I want to use a common sorting algorithm (quicksort for the curious ones). Do I need to include a reference to this algorithm (cite or quote)? Or it is so common that I don't need to? Take into accout that it was first published on 1961 and it is extremely used and known by almost anyone in the CS world.

It is really up to you (and your advisor perhaps). In any case, chasing down the reference for quicksort, and even some of the quite voluminous bibliography on it's analysis, isn't that much work, and a handful of references will hardly lead to overrunning any maximal page count...

What does "use" mean in this context? Are you writing a program, or just describing the algorithm itself?

Does it matter what particular algorithm is used, or is the important point the fact that your data gets sorted somehow?

If you need to cite a specific thing (e.g. a lemma used in the original proof of correctness/complexity for example) then definitely cite it no matter how well known it is. If you are simply defining a new algorithm and one step is "sort this array using quicksort" then a citation may not be needed (in fact at this point you may consider just saying something like "sort the array using any O(n logn) algorithm" if you don't have more specific requirements about the sorting algorithm).

@Abigail it depends if you end up referencing 200 algorithms or not

Whatever you decide, make sure you cite this stackexchange article for justification ;)

If you're doing college homework, the only real answer is to ask your instructor -- this isn't an actual academic paper, so the rules for grading are up to them.

Just cite a classic book on Algorithms which explains quicksort (almost every book does contain a section on Sorting Algorithms)

Do I have to cite common CS algorithms?

No.
The fact that it was first published [in] 1961 isn't relevant, you needn't cite it because it is [widely] used and [well-]known by almost anyone in the CS world.
That said, although a citation isn't necessary, you can provide one at your discretion. Such a citation is probably more important for a final thesis than for an academic publication, since it may be considered important for students to demonstrate they can cite.
Beyond citing the original source, you may like to cite your favourite textbook(s) on the topic (rather than citing the entire volume, reference a particular section, e.g., \cite[Chapter 4.3]{Textbook} in LaTeX).

In particular, it could be worthwhile to cite the relevant chapter of Introduction to algorithms by CLRS.

I was told that citing a textbook is "unprofessonal", that a "professional" article should always cite a research article or a monograph. Not sure I buy that, but at the time I had to change the citation.

@sds Eh. I think one should look at the purpose of the citation. I don't think there's anything wrong with citing textbooks from other fields (e.g., I'm a computer scientist and have cited textbooks from mathematics), or where you need some obscure detail that's presented in one (I've cited Knuth for a specific fact about the performance of hash tables). The problem comes when you're citing a textbook for something that's common knowledge and, there, the problem is more that you're citing at all, rather than that you're citing a textbook.

@sds Following the previous comment one should look at the purpose of the citation: Sources beyond the original manuscript can offer additional insights which are useful to the reader. You may even choose to signpost such sources, e.g., "Knuth summarises topic X and provides a detailed performance analysis."

@Basile What's the point of such a citation? I mean every self respecting computer scientist will have read CLRS and have a copy in reach, so what value is it adding to the paper? If you can point to any specific detail that's important, sure, but just a "hey I used quicksort and as everyone here knows you can look it up in that book" seems unnecessary.

@sds I have cited textbooks in a paper and the paper got in to a good conference. None of the reviewers said anything. That's just one data point, but citing a textbook when required is definitely not unprofessional.

@Voo If you read my whole answer, I explain. It is also explained in comments above.

I agree with most of the body of your text, but - you're reaching the wrong conclusion with it...

@einpoklum Your comment seems useful, but isn't... #reviewerTwo

@user2768: See my own answer.

@user2768 You say he shouldn't and then backpedal with "you can provide one at your discretion" and say you could include it in a final thesis, because it demonstrates that a student can cite. But nowhere do you name an actual good reason for why it would improve the actual paper to include the reference, which is what I'm wondering about.

@Voo I say you don't have to, not you shouldn't; I don't back-pedal. I name an actual good reason [for citing] e.g because it demonstrates that a student can cite. I'm unsure what you're wondering about; your comment seems to address your concerns. (My answer doesn't explain why citing textbooks is useful, comments do e.g https://academia.stackexchange.com/questions/134582/do-i-have-to-cite-common-cs-algorithms/134585?noredirect=1#comment358595_134585 & https://academia.stackexchange.com/questions/134582/do-i-have-to-cite-common-cs-algorithms/134585?noredirect=1#comment358598_134585.)

@Voo "I mean every self respecting computer scientist will have read CLRS and have a copy in reach"
You should also consider students or recent graduates. Also not everyone is American or can afford to buy expensive foreign textbooks.

If the specific use of the algorithm is important to the work, then you should cite what specifically you used or implemented, and also citing the broadest/oldest class of algorithms would be strictly optional. Using the example of quicksort, there are many dozens of varieties of it that have the same general idea but have different characteristics and performance. If you used the 1961 paper as a reference for your implementation, then of course you would cite it. If you used the Java or C++ sort function (which are different and have changed between versions - mergesort, timsort, hybrid, etc.), you would just say so and don't need to hunt down what that was based on.
On the other hand, if sorting is not an important part of the work (it matters only that it was sorted, not how you sorted it), it is common and accepted not to bother citing every last little detail like this. In most cases how something was sorted is so unimportant that it isn't even mentioned in text at all, but of course if your work is on sorting algorithms (and in a thesis) you should be more detailed and cite liberally.
As this is not for a conference but for a thesis, and possibly part of a graded course, you should probably just cite it anyway, possibly both the original and whatever source you actually used for reference (textbook, code library, whatever). Especially at the less-than-PhD level, instructors are much more likely to prefer heavy use of citations, and I've known many professors to ding for lack of citation of things that one would not bother to mention or cite in an actual paper.

Cool answer also. I understood that this topic is a lot about context, nature and audience of the publication.

This is the best answer I've seen. Regarding the second paragraph, I think omitting any citation when you only care that something is sorted (or analogous other outputs) is reasonable insomuch as it's obvious that sorting is possible. If it's not obvious that a particular arrangement you need can be obtained from an arbitrary input, you should cite the result that proved that it is possible.

Note: Java's standard sorting implementation used by most of its sorting methods is timsort since Java 7. Before that, it used to be mergesort.

@VictorStafusa Ah, mergesort, my memory failed me, thanks for the correction!

"Quicksort" today rarely refers to the 1961 version; the algorithm has been improved since then. If you're going to cite, you should of course cite something that's relevant to your thesis. As others stated, if you just needed an algorithm to get things sorted, that doesn't need citing. But if your thesis did depend on the details of sorting, then is suddenly becomes important to cite, and cite right.

I'll take what appears to be a surprisingly contrarian position on this:
Yes, you need to cite the implementation you used, in a scientific paper.
It is far too common that scientists working elsewhere trying to reproduce results fail to do so, and waste a lot of time trying to make sure their setups and steps are just the same as what they're trying to replicate.  Too often, the issue comes down to a particular bug in a software package that one lab or the other is using, or a different choice in an implementation detail nobody knew mattered.  By citing the specific implementation you used, including the version number of packages where available, you can eliminate a potential source of frustration (and/or false fraud accusations!), at relatively little additional cost when writing.  (Note that sometimes, that "other lab" may be a future you!)
If you are using a quick implementation found online, citation may also be required by the license on the source.  For example, you could say "I used the Java implementation of Quicksort found at https://en.wikibooks.org/w/index.php?title=Algorithm_Implementation/Sorting/Quicksort&oldid=3562350#Java" (note use of the "oldid" parameter to tie to a specific version; click View History and then the latest date to get that in the URL).  That attribution is arguably required by the license; similar story for what you find on Stack Overflow.
This also provides a means of credit for those who may have spent a lot of time (that they could have spent on something else) writing a software package that is useful for the broader community.  The credit aspect is probably more important for academic developers than commercial ones.  In those cases, there may be a paper announcing or describing the package, which you can and should cite for this purpose.

No, if the algorithm has a well-known name that means that it is assumed that you are not the author and that readers can get familiar by using that name as a reference. In a similar way when you are writing a math paper, you don't need to create a reference every time you use terms like Hamel basis, Lagrangian, Gaussian distribution, Fourier transform, etc., because it is well known like QuickSort, TimSort, simplex method... using a specific name is enough reference for the reader.

I was just thinking about this the other day. What one person considers "well-known" or common knowledge, isn't so for another person. QuickSort is a great example. Most people who have studied any computer science would know it. However, the average person on the street wouldn't. For example the person at the grocery store checkout probably wouldn't. So when deciding to cite something as a reference, does it come down to if it's considered "common knowledge" given the topic of the work?

"Every time"? No, just the first time. Certainly in a thesis. See my answer.

Isn't the name itself a reference? If I say Fourier Transform everyone would know that I don't get a credit for that and the name is a reference to the formula/work that everyone can find out easily (even more than having a link to a paper from 1800s)

@Celeritas "common knowledge" within the target audience of the paper.  Whether an academic paper is properly cited for, or even meaningful to, most grocery store checkout staff is not an interesting question.

Do I have to cite common CS algorithms?

Generally, and in a thesis, yes.
Why?

You may consider it common, others may not; not everyone is in the same sub-field of Computer Science.
You may be using a variant of the algorithm which is less ubiquitous; or a specific implementation, as @WBT suggests.
If you're using terms from the definition or specification of the algorithm, it may be useful for the reader to have access to some textbook for reference/inspiration/whatever.
Actually, it's rarely a bad idea to find an excuse to refer to a nice textbook. Pick a good one!
It's a thesis, it's not as though your pressed for space or anything.
Better to err on the side of caution with citations.

Specifically for quicksort - mmm, maybe not, can't say for sure; depends on the specifics.

If your results depend on some property of the quicksort algorithm, for example on its typical or worst-case performance, then you should cite a paper that demonstrates that the algorithm has those properties. For example if you deliberately chose an algorithm that works well when the data is already sorted, it might be best to cite some paper that compares sorting algorithms and demonstrates that quicksort is a good choice in this scenario. (I don't recall whether that's actually true, it's just an example).
If any sorting algorithm would do, then you don't really need to justify your choice; indeed, you don't really need to say what algorithm you chose.
Personally I don't think you need to cite a paper that explains what QuickSort is; it's more relevant to cite something that explains why it was the right choice for your particular application.

In case of quicksort, everything depends on how the pivot is choosen. Most of the implementations I've saw have some pathological cases that makes it vulnerable to O(n^2) behaviour. A frequent case of those is when the list is already sorted. A simple case that defeats many of the naiver defenses against O(n^2) is when the list consists solely of a bunch of repetitions of a single element.


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What to do (years later) with otherwise good student who has accidentally plagiarised part of PhD thesis?
Here's a not so hypothetical situation. International student x is very talented but comes from a background where technical writing is not taught or understood very well. She writes a great thesis with a good literature review and nice results. However, the results are based on two key papers from previous students in the group. She decides to give credit to the papers in a special chapter, which she starts by saying "I need to give credit to this and that paper" and proceeds with copying paragraphs wholesale to describe what those other students did.
This was a few years back; X is now faculty at a good school and she contacts me (past advisor) in teary-terrified voice to let me know that she plagiarized in her thesis. I am now in a panic as well. How could I miss those? And how could she do that?? We both risk losing our jobs, and she is at risk of losing her degree as well (which, by the way, was a very strong thesis with a good number of top journal publications).
As far as I know there's no process for revising a thesis after it's been submitted and I don't know what else to do short of turning ourselves in - which I feel morally obligated to do.
Please advise.
Edit
Thanks all for weighing in on this. I spent the night going through the thesis and there appear to be three more sources that are suspect of being plagiarized, all in the same wretched chapter; one is a thesis of a colleague, the other is a textbook and the third is a book I wrote a while back. So this is more serious than I thought.
She has unfortunately not used quotes for the material, i.e., instead of saying "[paper i] says «this and that»," she just went on with "[paper i] says this and that."
She has not been accused of plagiarism by anybody. I am guessing that she has finally come to grips with good writing standards and upon looking through her thesis she realized that her "summary" was actually plagiarism. I have every reason to believe that she did what she did in good faith (she has proven her honesty on many occasions).

Perhaps there is some form of mechanism for adding errata or clarifications to a thesis? Googling "errata phd thesis" results in quite a few such documents.

Bitwise, thanks for looking this up. I feel that errata would probably be acceptable if it were for only a few words or equations. Not sure about doing an erratum for a lot of material.

Any text which is attributed is not plagiarism. If I write, 'John Smith wrote ""', then  is not plagiarism. What is going on here is alleged plagiarism. Fight the allegations. Find out how they are substantiated and strike at those arguments. Simple as that.

what makes her -after few years- think that she plagiarised? I can't see the plagiarism.

Ideally, what is needed here is to obtain a version of the paper from the accusers which is properly annotated with clear indications where the alleged plagiarisms occur, down to the starting and ending word of each one. Each one should be given a number or identifier, and then discussed in attached notes.  There should be one final version of this annotated paper which everyone involved signs off on, so that the accusations of plagiarism are not an unfair, moving target.  Then the instances of alleged plagiarism can be dealt with calmly on a case-by-case basis.

Do you have any reasons to assume it was in good faith (e.g. verbatim instead of 'in own words' of an otherwise cited material, because of lack of exposure to the contemporary culture of scientific writing)? Are the plagiarized people aware of it? If so, what is there stance?

Thanks all for weighing in on this. I spent the night going through the thesis and there appear to be three more sources that are suspect of being plagiarized, all in the same wretched chapter; one is a thesis of a colleague, the other is a textbook and the third is a book I wrote a while back. So this is more serious than I thought.

So, I know this isn't very constructive, but .. As you say, how did you miss this?   You read your student's thesis and didn't notice material plagiarized from your own book?   I mean, I'd think you might recognize the work of your colleauge or 'other students in the group', but your own work ...   Did you actually read the thesis before it was submitted?

Out of curiosity, how did the tale end?

I think this happens much more often than people (with English mother-tongue) realize. Most students, especially from Asia, don't even realize that it is something considered wrong in the US. I am saying this based on experience of 10+ years at Far-Eastern higher education, before someone would like to label me racist.

I'm confused why "Bob says the sky is blue." is career-ruining plagiarism but "Bob says 'The sky is blue'." is an honest innocent attribution. Both make it pretty clear whose idea the blueness of the sky is. Was this really the entire story?

This is common enough that someone has written Important Tips On Writing An Apology Letter For Plagiarism

The second to last paragraph is unclear; the two things looks the same to me.  Maybe because you're quoting quotes?

Did any of the plagiarized material make it into journal papers, or was it all literature review that was never published outside of the thesis?
If some of it made it into papers, then it's important to contact the journals and publish corrections.  This is more straightforward and predictable than dealing with the thesis itself.  If the plagiarism is confined to background material, then I don't think retracting the papers would be necessary.  Instead, I expect it would be possible to publish a correction that indicates the plagiarized portions and provides citations.  This would be embarrassing and would hurt her reputation a little, but it would solve the problem as far as the papers were concerned.  It would also strengthen the student's case for dealing with the thesis if she can say she voluntarily corrected the publications and did not need to retract any of them.
If none of the plagiarized material was published elsewhere, then it's trickier.  Once all the original results are published in research papers, I doubt anyone will read the thesis and discover the plagiarism.  Even if they do, they might take pity on the student and ignore the plagiarism.  (I once ignored some mild plagiarism of my writing in the background sections of a thesis at another university.  The student had already graduated, and I found no evidence of plagiarism in any of his research papers.  If I knew for sure he could just file a correction to the thesis, then that would make sense, but I wouldn't want to potentially destroy his career over this mistake.)  So she might well get away with it if she doesn't say anything.  Still, I'd advise her to officially confess to the university.  Turning herself in is likely to lead to a much better outcome than being caught by someone else.  Plus it's the right thing to do, and it will save her from years of worrying about getting caught.

We both risk losing our jobs, and she is at risk of losing her degree as well (which, by the way, was a very strong thesis with a good number of top journal publications).

Unless your university is extraordinarily strict, I don't think your job is in jeopardy.  On the other hand, the student's degree or job might be, depending on how the university handles the situation.  Based on your description, I think it would be unfair for her career to be ruined, but I can't predict what will actually happen.  I hope your administration's sense of fairness is the same as mine, in which case a correction will suffice.
The hardest situation will be if she decides to remain silent.  In that case you probably have an obligation to turn her in, and it would look terrible if anyone found out that you knew but didn't say anything.  On the other hand, turning her in would be a tough decision.  Much better for her to turn herself in voluntarily.

Good points, Anonymous Mathematician. The plagiarism was limited to background information. None of the material made it into publications. It really wasn't the literature review (which she did in earnest), but the chapter after the literature review, where she specifically cited the initial papers on the topic. I agree that coming clean is the only thing to do and realistically her thesis is very strong otherwise. I would just hate to see her career ruined since she did very well as a PI so far.

First off, just to make it clear, this is plagiarism. Providing a reference and then long string of text implies that the text is YOUR description of ideas of someone ELSE. To give full credit to someone else requires some sort of formatting distinction (typically block indentation or quotation makes). Potentially the plagiarism was accidental, but it is still plagiarism.
Supervisor
A doctoral dissertation is generally a single author piece of independent work. Plagiarism in a dissertation should have little direct impact on the career of the supervisor. It might have some indirect consequences like people questioning how you can be so unfamiliar with your students work that you do not catch plagiarism, but I think most people would be pretty understanding about this. If the thesis was not single author or if the work was published with your name on it, that is a different story since co-authorship implies you have BOTH plagiarized.
Failure to report academic misconducted (whether it is your student or not) can impact your career. At my university we do not classify failure of a student to report academic misconducted of another student as academic misconducted. I don't know the disciplinary process when faculty are involved. Personally, I would say that we all have a responsibility to the scientific process to report ALL cases of academic misconduct that we are aware of.
Student
At my University, the penalty for plagiarism by a current student is zero on the piece of work. This would mean the student would have failed her dissertation. As a department we would deem this penalty too severe and push that she would be able to re-submit a new dissertation that reuses the non-plagiarized material. The University would push back and ask for a completely independent dissertation. I have never experienced this with a PhD student, but this occurs regularly with our final year undergraduates and about 70% of the time the student is allowed to reuse the non-plagiarized material.
I don't know what would happen if the plagiarism was found after the degree was given. My guess is the University would have to retract the dissertation from the library and any electronic database. They may revoke the degree, but they could also look at other work and count those towards the dissertation.
The current university may try and fire or penalize her, but this seems harsh compared to the typical penalty of plagiarism in a dissertation of not getting/delaying a degree.

"people questioning how you can be so unfamiliar with your students work that you do not catch plagiarism, but I think most people would be pretty understanding about this." its not Master's fault ;)

Well, here is the responsability of two persons: the advisor and the student, but the amount of responsability is somehow lesser for the advisor. I am pretty sure that your past student has signed a non-plagiarism form or put an statement that she was not plagiarizing anything in her thesis work, so she was doing that on purpose. It seems harsh my opinion, but it seems that way.
The only solution is to tell the truth to the Dean and for what I know, the penalty will come sooner or later. According to what you reply, that person plagiarized about 10 pages and also parts of the appendix, so in that case the only way out is to inform about the accident.
I do not think that she will lose her degree, remember the scandal that happened in Germany a few months ago?. The worse thing that could happen is that she get somehow "banned" from the journals that she has been cited, but only for a certain amount of time. About your case, I think that is not so probable that you will get into trouble.
Wish you the best.

So any experience on how such cases are handled in the US vs Germany?

In fact, in the scandal in Germany, several people lost their PhD degrees. It's very well possible in the German system, even decades after the PhD was awarded, such as in the case of the former minister of eduction and research http://en.wikipedia.org/wiki/Annette_Schavan

Um, I'm not sure it is worth bothering about.  She gave credit for the results,
it was in the context of describing other people's work, it seems to only involve
the language.  This is not a literary topic, so I would tell her to not worry about
it but learn how to write.

An author owns both the written ideas and the language they used to express those ideas.  Failure to identify the original author of the ideas and/or the language is plagiarism and should be treated seriously.

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How much does TA experience impact acceptance into PhD programs?
Obviously being a teaching assistant as an undergrad or a masters student looks good, but how good does it look?  Is it merely a nice little bonus, or does extensive TA experience have a large impact on one's acceptance?

From my perspective admitting students to CS PhD programs:
TAing for CS classes will be a small positive signal that you did well in those classes and were well thought of by the instructor (who presumably asked you to be his TA, or at least accepted your application). It might also let you get to know the professor teaching the class better, which will be helpful for your application if he/she can write you a letter of recommendation. But beyond that, it won't be a huge bonus in and of itself -- its mostly a signal correlated with other good things.

It may depend on:
Where?

For instance, teaching is compulsory in most American universities while in the UK you are only "encouraged" to teach, with some exceptions.

PhD on what?

It may not be that important if you are going to do a PhD in theoretical mathematics  or a more "industrial topic", while the opposite may happen if the PhD is in Education.

how good does it look? It looks good, but it doesn't represent a huge advantage. In my opinion, as long as you get all the requirements, the most important part of the application are the reference/recommendation letters.

Updated my tags (computer science, US).

@SteveP. My last comment still applies. Get good reference letters, nothing else matters.

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Employment history and graduate admission
Why do some graduate schools require an employment history for their application forms?  Additionally, is it likely that they verify said history via one's social security number?

Is it possible to verify employment history with an SSN?

Thanks for your comment. I know that it is possible. But wonder if it the department or admission office cares to verify it. For example, I might not be interested to share one dramatic employment history..So I wonder what if I don't mention it

@trxw The only way I know would be for someone to have access to the IRS or SS databases. Unless that information is reported to the credit bureaus (as an employer I never reported any of my employees anywhere other than the IRS, state and federal, and SS office). For some reason, you seem to think that with someone's SSN everyone has access to all information about that person's past. If you have evidence of that, please cite it because I do not believe that to be the case.

It is much more likely they will use your SSN to verify your legal status.

They could pull a credit report to get employment history, but that’s illegal (without permission) in the US and the hard way.

Why do some graduate schools want to have employment history on
  graduate school application forms?

I can think of a few things:

If you're not coming directly from undergrad, they want to know what work you've been doing.  In some cases, it may be entirely irrelevant, but nonetheless, they ask.  While references are typically obtained from academic institutions, if you've been in industry for a while, one of your recommendations may come from your employer...
If you are coming directly from undergrad, you may still have been employed during school or have completed some number of internships.  Again, while they may not be relevant, there's no reason not to ask, especially if they can positively affect your application.
Either way, employment, depending on what you did, could demonstrate responsibility, leadership, potentially research ability, etc.

Is it likely that they verify it with SSN?

This almost seems like you're trying to determine if they can catch you in a lie--they do not need a SSN to do that.  Don't fabricate anything.

Agreed. Also, the people who make decisions on your application probably will not even get your SSN. As an example from a hiring committee I was on, my university wanted SSNs (or equivalent) to verify the applicant could legally work in the United States and to verify that the applicants did not have something nastily criminal in their past. Human Resources did that before we got the applications (and presumably did not forward us the problem applications). We did not receive SSN information.

Thanks for your answer. I am not trying to tell a lie, rather I want to keep some of my work history private. That is a right for privacy, I think.

It is unlikely that something will be verified but still its best for you not to write anything which is not true.
And your employment history tells a lot about you, here is a list of some points apart from those mentioned before:

It shows that you have the capability to handle industry environment
If its a really good company then it shows your excellence because you got through a very difficult interview process
It shows your communication skills and people management skills
It shows your ability in analytic tools also.

So it will be good if you mention all your employment history, be it in a education institute.

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How to leave a collaborator after being offered to join a new group?
How does one leave one collaborative group for another, prior to the start of the research? This relates to switching project teams for graduate course work, switching research labs, or basically dropping any collaboration. How does one do so politely?
My specific situation:
I have been asked today by one of the best teams to join their group for our major University project. However, I have promised my friend 2 months ago that I will join his team.
How can I join the better team without jeopardizing my relationship with my friend?

Before people vote to close, please consider that this is highly related to graduate school and research collaborations as well.

I don't agree with the reasoning here, but I'd like to see others vote to reopen rather than doing it unilaterally.

First make sure that this is what you want. This is a very important thing to do. Being in a better team is a chance, but also a burden. They will expect you to cooperate at a certain level, which means: stress, lots of work and being on time. If you think that's worth the result and that you are willing to dive into that, then do it.
If your friend is a good friend he/she will understand. I'd suggest to invite your friend for an activity that both of you enjoy a lot, then bring up the topic. Make it clear to your friend that you value the relationship and how difficult it is for you to take that decision, but also can't put down the chance. Ask him/her what he/she would do in your position to get your friend to see it with your eyes.
True friendship will survive that. And if not, then knowing that you took the right decision will help you getting over it.

I will do that. I am not afraid to work hard - i actually want to. The problem is that my friend is lazy

It seems you already make excuses for "dumping" your friend. You seem to think, it is his fault (he is lazy) and not you for breaking your word.

Some people legitimately are lazy. Personally, I would not be willing to risk my success in grad research by collaborating with someone who might hold me back, unless it was in an intentional effort to help them improve.

Make sure that if you are going to do this, it leaves him enough time to find a new group (assuming this is related to a class or an undergraduate/masters project and not a phd collaboration). Going back on your word is one thing (subjectively unethical), but it would be extremely unethical to go back on your word if he does not have the time to adjust to your news accordingly.
If you two have already formed a project idea together, view every idea you have told him as his. Absolutely do not take anything from your current project idea to the new team (especially if he is unable, or too lazy to, find a new team that has their own idea)


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Should figure captions include the "take home message" that the figure conveys?
Should figure captions only describe all of the necessary components (e.g. the meaning of axes, etc.) or can the figure caption also include a brief sentence about the main conclusion drawn from the figure. For example, say the axes are labelled "speed" and "time". One caption might be "Speed of a giraffe in meters per second as a function of time in seconds from when it first starts moving." It could also have the additional sentence "... Note that Speed is increasing with time." For the previous example, this is probably unnecessary, but for more complicated "take home messages" the point of the figure may not be as obvious. So should comments describing the main result behind the figure be only put in the text body or is it OK to put it in the caption as well? I think this might be field dependent.
The justification for wanting to put the main message of a figure in the caption is that it makes the paper easier to skim, as, anecdotedly, I've heard quite a few people say they skim the paper and focus most of their effort on the figures before ever looking at the results.

You should definitely point out the point of the message if it is not immediately obvious.

@user37208 unless, gods forbid, that your figure is a bitmap figure, thereby denying many the ability of interpreting the figure.  The caption is then a textualized summary of what you are missing.

@PålGD: If the figure is a photo, what is wrong about making it a bitmap figure?

@O.R.Mapper I don't know why you would take a photo of a graph lest the deadline's approaching quicker than you'd like it to.

@PålGD: Since when are all figures graphs? What about real-world photographs of test setups or user studies? Screenshots of running software? Photos of prototype devices? Paintings or photographs analyzed or processed by something described in the paper? etc.? As a random example: Count the figures in this paper that are photos and that could just as well be shown as a vector-based graph.

@O.R.Mapper I'm not saying all figures are graphs.  I'm just replying to the question.  Cute pictures in that article.

There are different schools of thought about this; how much information to include in a figure caption depends largely on personal taste.
Proponents of minimalist figure captions put forth that

It needs less space.
It says in one brief sentence what the figure is about.
Having a long block of text below a figure is ugly.

In contrast, proponents of long figure captions state that

People who (if only at first reading) only skim over the paper and just look at figures do not have to search in the text what each figure is about. The very points found within the figure are explained in depth in the caption.
When looking at a figure in detail, readers do not have to switch forth and back between the descriptive text and the figure, as a concrete description is right below the figure.

Personally, I consider the points in favour of an extensive figure caption more convincing, and I usually go for those as long as space restriction allow so.
An additional benefit is that you can use the paper text for an abstract description of some aspect of your work, and then use the figure caption for an equally detailed, but more concrete description of the example shown in the figure. This way, you improve comprehensibility of your paper without making it seem redundant or repetitive - as a certain degree of overlap (or even exact repetition) between text body and figure captions is acceptable.

+1 for your last paragraph, I had never thought about doing it that way.

A short comment in a caption is ok. But generally captions should stay descriptive of what is drawn in the figure e.g.

Fig. X: estimated airspeed velocity of an unladen European swallow.

They should also ideally not be too redundant with legends although sometimes it helps to say things like "shown at various headwind velocities". The place to draw attention on a specific aspect of the data shown in a figure is the results section.
These are customs and not strictly-enforced rules, nothing bad will happen to you if you take a few liberties. Worst case scenario, you'll have to make a few minor edits during revision.

"The place to draw attention on a specific aspect of the data shown in a figure is the results section." - who says that any part of a figure must be a result?

I strongly advocate for captions that are as self-contained as possible, saying not only what the figure is but also the essence of what the reader should take away from it.
Yes, this introduces some minor degree of redundancy, but I believe this minor inelegance is well worth the benefits that can be obtained.  Figures are extremely salient for a reader's attention: there are relatively few of them and they each have a strong visual impact, going through a different set of cognitive pathways than text.  Many readers first impression of a paper will thus be formed by its figures, as they flip through a paper deciding whether to read it (and many journals explicitly encourage this with "online previews" that show only the figures of a paper).  Even once somebody has decided to read a paper, they may not read all of the sections in depth, but may skim some and read others.  Finally, even for a reader going in depth, the cognitive availability of the information associated with a figure is increased when the reader can pull key points right out of the caption rather than needing to go to some more distance part of the text.
As such, I believe that insofar as is possible, figures and their captions should provide a complete sketch of the paper narrative.  Doing this will significantly increase the impact of your papers by helping readers at many different levels of commitment to reading.

It's always worth getting someone to proofread your submissions.  All co-authors should anyway, and those less involved with that aspect of the work can be best qualified to judge the clarity of your exaplanations (they can also be most liekly to skim over that section).  Otherwise, you have peers, help each other. The best style partly depends where your figure is going.
In a journal paper, styles vary between journals, even from the same publisher.  Some like dense figures with long captions, or at least, these become the norm when page limits are tight.  Other journals prefer more spacious figures, fewer insets, and simpler captions.  The correlation between cpation and figure styles is only meant to be indicative; I'm sure you could find examples of simple figures and very full captions. Some journals prefer the legend to be given in the form of text in the caption.
In a thesis you'll normally have a list of figures, with short captions in it.  These short captions should give enough information for the reader to find a figure ("There was a figure relating bandgap and lattice spacing, now which figure was it?") while including a subset of the information in a full caption.  Thus the full caption will end up reasonably descriptive.
There are a few other, competing, factors:

Help your reader.  This is a point I often make, but here could be interpreted as:

Don't waste space and the reader's attention stating the obvious...
... but add clarity.
If a figure really works only in colour (and these should be rare), provide enough information so the reader knows this, and doesn't juyst hink your figure is rubbish.
Consider a reader who may not see too well -- give them the information in text to decide whether to print a large copy. (This is an example, but helping this hypothetical reader may help all your readers).

Help the reviewer.  This overalps with helping the reader, but a reviewer will be looking for different things.  By all means say "for a full description of the samples, see main text", but rather than just "Sample A (red squares), Sample B (black circles)" give them a gentle reminder of which sample is which (this of course is easy if it's a treated and a control population).

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text:
Do reputable journals ever conduct peer review entirely by email?
In the comments to one of the answers to this question, the asker points out that he is asked to submit his review of a manuscript for publication via email and that there is no formal online system with checkboxes or text boxes. This struck me as strange, as having reviewed papers for several biology and math journals I have never been asked to submit my review via email to the editor. Even for very small journals published independently, I have always been asked to use an online system, where all contact is viewable by the editor-in-chief and other parties at the journal.
Do reputable journals ever ask reviewers to submit their reviews via email, or is such a request a red flag that you are being asked to review for a scam journal? Do all reputable journals have online reviewer systems?

Is there any reason why they shouldn't?

You misspelled “obscure” and wrote “secure” by accident. Just in case that wasn’t an accident, let me clarify: these online review systems are of course not secure, they’re, without exception, incredibly shoddy pieces of work that would make real engineers cringe.

@KonradRudolph yes I did not mean secure, I was struggling for a word, perhaps "transparent" is better. Basically I mean anyone who should have access to all contact by authors and reviewers can see all correspondence.

... maybe it's worth mentioning that I've heard of social science journals who couldn't do anything with tex or even pdf files, and everything, from submission of articles to communication must be done with Microsoft Word documents sent via e-mail.

@vsz socail sciences? I've seen reputable engineering/computer science/physics journals not accept tex. I cringe

I have interacted with several reputable math/TCS journals, both as author and as reviewer, entirely via email without the involvement of an online submission. I have even witnessed senior members of the community expressing the sentiment that they never agree to the semi-automated referee requests sent by online submission systems, but only to referee requests sent "by hand".
Summary: Yes, there exist reputable journals conducting peer review entirely by email.
Now whether or not a journal soliciting peer review without an online submission system is more likely to be disreputable than one that does, I do not know. I see no particular reason to assume either way.

No, semi-automated requests are not disreputable. We do not have secretaries anymore which take care of our daily chores, as much of that is expected to be handled automatically. Really, as an editor, having to take care of the lists/logistics of reviewed/nonreviewed/undecided papers is pure waste of time if it can be done automatically. Why should it be disreputable if an editor concentrates on the main duties of their job, namely reading papers/reports and making decisions rather than juggling emails, action items and trigger events?

@CaptainEmacs I don't think anyone is claiming semi-automated requests were disreputable? I am certainly not.

I seem to have misunderstood your response that '[some people] never agree to the semi-automated referee requests sent by online submission systems, but only to referee requests sent "by hand"' as a response to the question about reputable journals. I am, of course, not saying that this is your opinion, but interpreted your response that some people do not respond to these as an indicator for disreputability. If not that, what would be the reason that these people do not respond to semi-automated systems? Lack of personal touch?

@CaptainEmacs The stated reason is, roughly, that they get a lot more requests than they could handle, so they have to reject a lot anyway - and then it boils down to personal touch, and maybe "if it is a lot of work for me, I want the editor to suffer a bit, too". I had mentioned this as it indicates that the semi-automated messages should not be read as a sign of more reputation at all.

@CaptainEmacs See this: I will not log in to your website

@ShreevatsaR Ok, there is a mixture of points here. The problem of greedy publishers (which I can sympathise with - but it's not the issue here) and badly written software which forces me to log in and remember stupid passwords that I will only use once, but, when I have to review again, I have to have the login credentials sent again (what a nuisance). Ok, I got your point, I think these websites are evil ;-) On the other hand, there are automated systems which do not require all that effort.

@CaptainEmacs It's not up to you whether these are disreputable or not. If people consider them to be, then they are, however much justification you might have for using them.

@jwg I am not aware to have claimed anywhere that I would decide whether they are disreputable or no (and never would). All I am saying that in answering the question one has to distinguish refusal to respond to semi-automated review requests due to "disreputability" or simply other reasons why people do not like using these systems.

Not long ago all reviews were handled not by email, but by paper mail. I submitted my first paper in 2003 and at that time submission was still by paper. However, I got an acknowledgement that the paper has been received via email, but the response of acceptance from the editor was in paper again. An online system was not in sight at that point.
I would say that there is nothing inherently bad about email communication  with the editor. It may just be that he or she is just old fashioned. These days I still get asked by some editors from reputed journals for reviews in personal emails and send my response via email, too. Nothing bad about this.

"I submitted my first paper in 2003 and at that time submission was still by paper." For that particular journal. I also submitted my first paper in 2003 and I've only ever submitted by email or through web interfaces.

Oh, true - other journals had been "ahead" in technology…

I was also surprised about this. I haven't submitted by snail mail since the 90s.

My experience (in pure maths) is that this is normal for journals that are run out of a university - which includes some very good ones - and only the for-profit publishers have polished online interfaces.

A bit of a plug for the group of open-access journals I'm working for (as a layout/copy editor): although most of them are still using only e-mails and secretaries, we're currently transiting to a customized OJS (Open Journal Systems), while still being free and getting money only from subsides of our universities and the CNRS.

Supplementing the other answers: I myself tend to be suspicious of the legitimacy of automated requests to referee, with someone I know listed as editor... since there are many bogus journals that claim several genuine scholars (for me, mathematicians) as "editors". Some of these requests are indeed bogus. A few are not. When I receive an automated request, I email the purported editor to ask whether everything is kosher. If they say it is, then I do the refereeing.
I think it is not a good thing that refereeing gets automated, and all still without pay, of course. So that traditional publishers need fewer employees, while yet profiting from the good-will volunteerism of academics.
That is, I don't think the issue is "transparency", but, rather, whether or not we (collectively) willingly become cogs in an automated machine that doesn't pay us anything, but charges us (or our libraries) to see the outcomes of our work.

This is another matter.  I've seen a tendency toward rejecting reviews from for-profit journals.  If academia were to embrace that, the for-profit journals would be done for.  Given the tendency toward open access journals, this makes the dichotomy even stronger.  I used to be on the editorial board of a journal run by a for-profit publisher.  At this point I don't think I would even review for one.

I should add, Paul's comment about charging libraries (or us) applies not just for the for-profit publications but for those run by nonprofit associations.  They need to recoup expenses because the publications do provide a service.   But I think there is a big difference in what they charge, and what they provide.

Refereeing doesn't get automated. The editor still has to use their own intellect and experience to choose suitable referees. Honestly, I don't see what difference it makes whether the editor types your email address into the mail client and writes your email (which may well be copy-pasted anyway) or types your email into a different piece of software which sends you a pre-composed email. And the whole "are for-profit journals" a good thing debate is contentious and completely tangential to the question.

@DavidRicherby, to my perception, it is not at all the same to receive an email from software (whom I've not met?), than from a person, especially if the person is known to me. In particular, I am far more willing to do a personal favor for a colleague, than for software serving a corporation. All the more so if I can't just email a report, but have to have an account, a password, and do whatever point-and-click the software demands.

I still don't see the difference. Your colleague either told one piece of software to ask you to review a paper, or told a different piece of software. Your point about needing accounts and passwords and things to use the web interfaces is a much stronger one. (Though, still, compared to the effort of reading the paper and writing a report, the effort of creating an account is pretty negligible, even when you include the effort of retrieving your forgotten password the next time you review for that publisher.)

@DavidRicherby, when I get an email from a friend, asking me a favor, it usually sounds just like that. The software does not attempt to be "personal"...


text:
How to handle unprofessional negative reviews from a journal?
My problem is similar to this this and this question, but still slightly different.
I am facing the problem that my paper was rejected form a journal (with the option to resubmit to the same journal again), where two reviews were provided.
The first review was well written, constructive and shows that the main parts of the paper were read and understood. Nevertheless, the first reviewer suggests to "Review Again After Major Changes".
The second review (who rejected the paper) on the other hand shows clearly that he neither read the paper nor the references listed in the related works section or any background material on that subject (as referenced in the paper or readily available online). Moreover, the review is filled with spelling mistakes, wrong references/citations and wrong claims. In essence, it gives the impression that it was written in a hurry without proper review of paper. But most importantly, the reviewer expects comparisons to concepts with are completely out of date and partly do not fit the discussed scenario.
I am currently preparing a resubmission to the same journal, which will most probably be handled by the same editor and reviewers. My questions is concerning the handling of the second review in the response letter in general and whether it is appropriate to contact the editor right now (few days after the receiving the rejection), shortly before or after the resubmission or not all regarding the review provided by the second reviewer.

@GEdgar That's an answer, and as it says when trying to add a comment: Avoid answering questions in comments. At the moment it can not be discussed properly, edited, voted on, or accepted.

It appears that the editor gave more weight to the first review, or at least gave you the "benefit of the doubt". Since you have the chance to re-submit, and you decided to do so, you should have to respond point-by-point to every comment that both reviewers made. Now "respond" is a deliciously diplomatic word that includes all the spectrum of reactions: from, say, "I did exactly what you asked" to, say, "go find a hole to hide and die, you stupid ignorant".
The main advise I have to give is : keep your judgements to yourself (about which review was helpful to you, whether the one appears sloppy etc), don't differentiate between the two reviews in your response, and don't be more aggressive in your writing style when you respond to the points made by the second.
For example, Don't defend not comparing your work to concept X because "it is completely out of date". Defend your choice because, say, "concept X, valuable indeed when it first appeared in the literature, has been succeeded by etc see reference 1, reference 2, reference 3". You get the spirit. If the "outofdateness" is your opinion and the field does not agree with you,then, you have another paper in the making, one where you will try to convince the other scholars of your field that concept X is indeed outdated.
If you do that correctly, the editor will certainly get the message (and well corroborated) about what you think of the quality of the two reviews, and why, even though nowhere in your response such an evaluation will explicitly appear.

Thank you for your answer. Is my understanding correct that you do not recommend to contact the editor separately regarding our opinion on the second reviewer?

@bonanza Indeed I don't. Let your response to the reviews do all the talking.

+1. Let me just supplement to emphasize that your new version should show no evidence of responding directly to the reviews. Just write a new version using whatever is helpful from the reviewers. Don't mention the reviewer comments in the new version in any way, just change what you believe would be proper to change based on that feedback. Let the new version speak entirely for itself. I don't think you need to complain to the editor about the "bad" review. He/she likely knows already of the problem or wouldn't have invited a new version. You could respond, but not needed, likely.

@Buffy, are you recommending not to mention the reviews at all even in the response letter?  That seems to be taking it too far.

@Buffy I'm confused. Who mentions reviewer comments in the paper? That goes in the response letter. And, as a reviewer, I expect a response to each of the points I made in my review. Perhaps it's because papers are quite long in my field (25-35 pages is normal; 50+ is still quite common), but it woudln't be considered reasonable in my field to just leave the reviewers to figure out what's been changed between the two versions.

@DavidRicherby, no one does this I hope. But in case the OP is inexperienced here, I wanted to make it as clear as possible.

@Buffy OK, I see your point.

@Wildcard, no, not that, responding in the letter (not the article) is fine, but I doubt that it is needed here. It isn't required to justify your decisions, just to write a great paper.


text:
Are Indian assistant professors eligible for tenure-track positions in the US?
Suppose an assistant professor from a reputable Indian university wants to apply for tenure-track positions in the United States. Would he or she have any chance? Assume that his or her publication record is on par with faculty members at top-level US universities.

I imagine the answer here may be highly field-dependent. For instance, I doubt that a nuclear physicist would have much success looking for positions in the US.

aeismail - is this because the field is very narrow or because of national security concerns?

I don't know if other fields are similar, but in mathematics, there are semester-long or year-long focused research programs at places like IAS, ICERM, MSRI etc, for which you can apply to participate. That is a good way to spend some time in the US, get your work known in the US, ask advice from people who will understand your specific situation, and (if you're lucky) perhaps impress people who might recommend to their departments that they should try to hire you.

Is this professor has experience writing US grants, familial with the differences in education, has maybe experience working with grad students?

Yes with caveats -- and the caveats have nothing to do with being Indian and everything to do with being outside of the American educational system:

There are particularities of the application process that are culturally bound and that you may not be familiar with (the style of the cover letter, its importance [or not], the style of your research and teaching statements, the format of your CV, who you ask to serve as a reference).
Your references may also be unfamiliar with American letters of reference styles. I find that foreign letters tend to be much shorter and much less enthusiastic.
Search committee members may not be familiar with your universities and its rank, with the ranking of the journals you've published in, and the significance of your teaching and service. They may be concerned that you do not know how to teach to American student audiences or that you may not be able to successfully apply for grants from American grant agencies.
The provost (who oversees searches) may be unwilling to authorize the search committee to bring in an international candidate due to the cost of airfare.
The university may be concerned about whether or not you will be able to obtain a visa to work. Even if you are able to get a visa, even under the best of cases, an international candidate who accepts a job offer in March may not be able to start by August of the same year because of visa delays. This may have programmatic repercussions (i.e., they need someone to teach CS101 in the Fall).
Rarely, some jobs are closed to non-Americans because the government grants or cooperating agencies require security clearances or have other restrictions. This is more common in the engineering and physical sciences.
In Canada, some positions are required to be offered to Canadian citizens before they are permitted to open to non-Canadians. The same rule technically applies in the USA for immigrant visas, but is not scrutinized as much.

etc.
As you can see, none of these have anything to do with you coming from India, and everything to do with being an international candidate. You'd have much more luck if you were applying from inside the USA (e.g., take a post-doc in the USA for a year or two and apply while on that).

#2 sometimes tends to be a result of letters being visible to the candidate.

#4 sounds rather dumb. The university may be saving a few thousands dollars, but also they are going to spend ~90k$/year for many years just in salary. From any economical balance, it is worth the risk if the applicant may be better.

@Davidmh you haven't dealt with many provosts, have you? Logic is futile. From the provost's perspective, foreign faculty are a source of ongoing cost from the interview to the paperwork for visas to family issues.

@RoboKaren I have had my share of bureaucracy, so I am not doubting it is true. It is just that one wishes they were able to reason in long term economy terms too.


text:
What's the point of a MSc if I can just enroll in a PhD program?
I am thinking about doing a PhD as I am quite interested in research, I really enjoy trying to figure problems out myself and having to find and understand the necessary information I need for my next report or project myself. This is great.
I am currently enrolled on BSc Computer Science and I am in my last year. Its going nicely so far. So long as I do well (at least a 2.1) then I will consider perusing a PhD.
The problem I have is that I don't know whether or not I should go for a MSc first before getting a PhD. I mean whats the point if I can just enroll on a PhD immediately?
I have talked to some other students who have done MSc/PhDs in their respective degrees and a lot of them tell me that I shouldn't waste a year of my life on an MSc, they say if your going to do a PhD, then an MSc is pretty pointless.
Is there truth to this?

This depends on your locale. It sounds like you are in the US. In Germany, you will usually need to have a M.Sc. to be eligible for entering a Ph.D. program. (Which will then not take as long as a US Ph.D. program.)

Dan is obviously in the UK - I don't think American unis give 2.1 degrees.

If you know you're going to continue on to a PhD, then there is no need to pick up a MSc, unless a specific program you're interested in requires you to acquire the MSc before continuing on to a PhD.
Some people want to have the flexibility that comes with acquiring a MSc, but this is a matter of personal interest, rather than a requirement. The danger is, of course, that if you decide to stop your PhD studies, then you run the risk of having worked for several years without any degree at all.

The "danger" you mention may not exist in all programs. In many PhD programs, you can be awarded a masters degree after completing the first couple years of the program (which involves work similar to a masters).


text:
Writing CV's for a "summer school" course
I would like to apply to a week-long master's course offered by a university in another country. The only thing they require for the application is a CV.
Since I have no significant experience in the field of the course or any publications, I have no idea what to include in my CV.
I thought about including (outside basic details) the title of my diploma work, the name of my supervisor and the main subjects (relevant to the course) I've learnt as an undergraduate. But I am wondering if it is too detailed.
I've also taken some MOOCs, but they are not strongly related either. I could include the titles of the conference presentation I've held and my language and computer skills and scholarships I've got.
Which of these would be appropriate to include?
Thanks for the help!

Of course I don't know anything about this particular course, but often, admission to summer school courses is not at all competitive, and there are seats (and sometimes funding) for more or less every serious student who shows interest.  (If it were competitive, I'd expect them to at least want a letter of recommendation.)
So basically your CV has to convince them of the following:

You are an actual grad student, and not some goofball trying to use them to get a visa.  So be sure to include your academic history (degrees and dates, honors if any) and the details of the program in which you are currently enrolled.  Definitely give your supervisor's name.
The course will be interesting and relevant to you.  Mention your areas of scientific interest (they should be at least tangentially related to the topic of the course).  List any relevant research projects, past or present, even if they are fairly minor.  Definitely include any published papers or conference presentations.
You have sufficient background to learn something from the course, and not get completely lost (getting a little bit lost is normal).  Briefly mention your GPAs and scholarships.  If it seems appropriate, list classes you have taken or books you have read that would prepare you for this course.


text:
My adviser keeps changing his mind about my papers. What should I do?
How do you overcome advisers constantly moving the football / changing their minds?
I write papers after recommendations from my advisers and every time I end up redoing the entire analysis or asking an entirely different question. I feel like Charlie Brown and Lucy keeps moving the football. Here are three examples:

I spent the entire third year of my PhD working on a paper with my committee chair using a specific type of model he specializes in to answer my research question. After completing the paper and submitting it to my department for review, my adviser comes back and says to scrap it. I pushed back a bit and asked what should be changed, but nothing could change his mind. He wanted a two-page outlining the new research question and modeling strategy. So I scrapped it and now the paper sits in a folder in my Dropbox.
I spent my summer working on another paper with my committee chair as part of my dissertation. I finalize my results and draft a paper for my proposal defense. My committee approves my proposal, but in a meeting afterwards my chair suggests I redo the research question and thus incorporate a new modeling strategy. The paper has gone through several revisions, is complete, and ready to be sent out for peer review. However, here I am again reworking the analysis with a completely different modeling strategy and question.
And finally, another paper I have been working on has had results for over a year, but is now undergoing a major revision to rework the modeling strategy, again. I am now on the 4th major revision of this paper having redone the entire analysis each time. I was literally writing up the results/discussion section of the paper when I received an email suggesting we rework the model.

On top of these three examples, I have two working papers that need minor revisions and are at a point where they could be sent out for peer review. I have published several papers as lead author and constantly review papers for other academic journals in my field, so while my experience is limited I know my research can be published.
I feel like my advisers keep moving the football and I can't get my dissertation completed. I was on track to graduate in the spring, but none of the papers for my dissertation are complete and it appears I will need another year. But my experience thus far has lead me to believe Lucy will continue to move the football, so I'm considering dropping out and finishing ABD.
How can I deal with this constant momentum shift of my papers with advisers?

This isn't directly relevant, but I'm wondering if your adviser gave you any reasons for all these constant do-overs. You haven't said so explicitly one way of the other. Is he dissatisfied with the existing work and thinks it can be done better? Or something else?

submitting it to my department for review — What?? Why does the department (or your advisor) need to review your research before you submit it for publication?

@JeffE Third year paper is submitted to the department for review. It is not necessary for publication, but necessary for pass/fail during third year.

I experienced a bit of what you're describing near the end of my PhD. I got a lot of good advice from colleagues that had completed their doctorates. Here's how I dealt with it.
Remember that it's your PhD, and you are (mostly) in charge. At this point,  you should have a pretty good idea of what's really required for a PhD. (If not, skim more dissertations from similar research projects.)
There will always be more that could be done to further the research. There's always another technique you could try, another analysis to do. Your goal should be to do what's required to finish the PhD, no more. (Of course, you want to do quality work, but if you've made it this far, I doubt you'd settle for less.) You can always continue the research as a postdoc, or let someone else continue it. That's what the "future directions" section is for in your thesis.
Your advisors are focussed on the research itself, and the logical next steps, rather than on wrapping up your PhD. That doesn't mean they're bad people, or deliberately trying to frustrate you. They're just human.
Sit down and figure out what you think needs to be done before you are ready to finish the experiments, finalise your thesis, and defend it. Then meet with your advisors and get their feedback. If they suggest doing more experiments or analysis, beyond what you think is necessary, you might say something like "I agree that's a good future direction, but I think that could be done post-PhD." Your goal is not to convince them that X doesn't need to be done, it's to discuss whether X needs to be done before the PhD can be awarded. Negotiate things from that point-of-view, and I think you'll find it easier to reach agreement.

One of my colleagues went through a similar problem when he was in graduate school: his primary advisor kept moving the goalposts on him as he was trying to finish all his papers and graduate.
There are no easy solutions here. The best thing I would do is use the fact that you have all of this work done waiting and ready to go out. It sounds like you already have enough material for a dissertation. Therefore, I would suggest that you compile everything you have done so far, and present it to your committee. Let them know that "this is what I have done that's waiting for peer review," and ask if everyone can come to the agreement that it's ready to go out. If not, then ask, as mhwombat suggests, exactly what needs to be done. Then stick to it. (It seems your advisor has a severe case of "perfectionitis"—good for him in the long term, bad for you in the here and now.)

good for him in the long term — [citation needed]

I’m finding that many PhD advisors make better critics, perfectionists, and game players than mentors. Mentoring requires a certain high level of character and humility. Some mentors make it all about themselves and less about the person they’re guiding and the research. Moving the goalposts is not acceptable of an advisor. Yet,I’ve heard many of my peers who’ve completed their PhD say it’s a game. Also, some advisors act as gatekeepers and will not the people they’re guiding move forward without making the goal through the moving goalposts. That’s frightening! It shouldn’t feel like being hazed. It’s your PhD, your research, not the advisor’s. Decide what you want and negotiate from your perspective. The project will always have the possibility of being better. Know when and where to finish. You can always improve the project postdoc. Tomorrow is another day.


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Can I publish a report from a personal project?
During the course of my post-graduation, a friend and I worked on a personal project in pattern recognition. I honestly am not hesitant to admit that although the technique has a decent result on a publicly available dataset, it is not publication worthy in any journal or conference of note (or so I feel), nor do I (my friend is unavailable now) have enough time or background knowledge in the field to keep working on it till it is.
Can it be published as some kind of academic report or something on a site like arxiv or academia.edu or something? I'm interested predominantly because I'm wondering if this online availability would lend more credence to it being mentioned in my cv - as opposed to merely mentioning it and not having any transcript available.
PS: The method was something we came up with. It was not implemented from somewhere else.

please clarify what you mean by "publish" in your second paragraph. I can't answer for arxiv, but putting it in your academia.edu page will mean it is accessible to the world -- but it won't count as a peer-reviewed publication and may not count for much in other senses of the world "published"

@virmaior Well in the context of the line in question, I use "published" to mean simply putting it up for access on a site like arxiv or academia (with a tag perhaps saying academic report). Yes I realize it won't be peer reviewed and I should state that I'm not expecting it to mean much more than a clearly written account of my experiments and results.

If you want it to be worth something on your CV, you should invest the time to make it publication-worthy and publish it

I understand your point. I know that myself to be honest but nonetheless I will keep your suggestion in mind in case I find time to work on it though I admit it's unlikely. Thanks.

I don't think you can publish it in a way that you can derive credit from.  But if you want it to be public so someone else can take the ball and run with it, then publish it on the web (with your collaborator's permission).

@aparente001  I understand. Thanks.
PS: If you put that in an answer I'll accept it.

There are two different questions in here, one about personal projects and another about whether it's worth publishing a non-peer-review tech report.
For the first: there is no need for "official" blessing on any scientific work; I've published personal side projects just as happily as projects in my "proper" line of work.  These can end up being quite significant: one of my bits of side-dabbling, published in a minor workshop, kicked off my entire current line of synthetic biology research.
That surprising consequence also leads us toward the answer to the second: significance is where people find it.  If you've put work into something, and written it up in a non-embarrassing way, there's no reason not to put it up online in an archival format, whether arXiv, tech report, or some other low-impact format.  Symposia and workshops can be a lot of fun too, since they often accept things that are interesting but not expected to necessarily be high impact.
If a piece of work is non-embarrassing, what's the worst that can happen if you put it online?  Nobody cites it.  But you never know... your coauthor might end up building something more significant out of it later (happened to one of my side-publications), or it might get noticed by people who happen to be dealing with a similar problem (happened to another of mine), and collect a few citations or even unexpectedly many.
In short: there is never a reason to throw good work in the trash.  Put it online, and let the universe decide whether it's neutral or positive.

Non-embarrassing is the thought that has floated in my mind many times I guess. Thanks - I'll see what I can do.

Are you affiliated academically or with some research organization? If so, one possible option is to investigate whether you would like to issue your results as a technical report. (See also this discussion on this very site on why technical reports exist.)
Some examples:

The US government issues regularly scientific and technical reports
Universities/departments frequently do too: ETHZ, Cambridge, MIT.
So do private companies with R&D budgets: HP, Google.

If permitted by your sponsors, such reports can also be posted to arXiv together with the internal technical report number.

Though to be honest, with online publication as easy as it is, there is no real need to go through the above except if you want it to "look more official" somehow.

If it involves a lot of code, you can put it as a repository in GitHub or Bitbucket. It won't count as a publication, but it will be available for others to see and possibly re-use or work upon. In some fields, bioinformatics for example, it is perfectly ok to list one's github repositories in the CV, serving to showcase your skills to future employers.

I don't think you can publish it in a way that you can derive credit from. But if you want it to be public so someone else can take the ball and run with it, then publish it on the web (with your collaborator's permission).


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Is it possible to switch between Ph.D. departments at the same university?
I recently asked about the ethicality of staying in a Ph.D. program (first-year) while attempting to transfer to a different university that I had declined previously. Unfortunately, the funding was cut short for said program and I did not get off the wait list for funding.
The main reason I wanted to transfer was due to the fact that I wanted to focus on a more applied math program as opposed to the current program I am in that focuses on bioinformatics/biology. Since the transfer/funding did not work out, I was curious if I could possibly transfer from the Ph.D. I am currently in to the math Ph.D. program. They are both under the same college of sciences.  I did my undergrad in both math and cell/molecular biology and I believed I could incorporate enough math but if possible I’d like to just get the applied math Ph.D. and apply it to biology instead of the other way around.
My two options are either to stay in my program and recruit many math committee members or to outright move to the math department. I don’t particularly want to ask my own department yet because I don’t want to be looked down upon or lose any funding because I do want to stay here and will happily finish (eventually) by incorporating more math based individuals.
I was wondering if this has been done before or if anyone has any advice on how to go about this? Obviously I’d like my funding to carry over and I believe since they’re in the same college of sciences it may be doable. I’m worried that I’ll be criticized or judged for wanting to do this or lose my funding. Since my first option of going to the other program at a different university didn’t workout and I didn’t hear about it till a week ago, I was unable to really follow this second option.

Whether it can be done or not depends entirely on the regulations of your particular institution. What is much more likely to say is that you will probably not be able to carry your funding over from your old department to your new one. Funding very rarely can be transferred, since it is usually attached to some project or department, rather than any individual.

The only time I have seen funding carry is when it was attached to a project and the PI was jointly appointed by the two departments.

The funding I’m offered is in the form of a GTA teaching labs. Most of my funding actually comes from the biology department and a minority of it comes from my actual department. I’m not sure how they manage that but I assume it has to do with my department being much smaller.

Realistically, in the cases I have seen, the student had a champion in the new department who was able to push the change through. It will also help if your current advisor is supportive.

@Dawn Since I’m just now finishing up my first year I haven’t really decided on who my advisor will be for the rest of my stay here. I have one that is technically my advisor but he’s the individual I chose when applying to do my first lab rotation (I must do 3 before deciding exactly who I want )

First thing, unless you got a funding from an outside source to the university, it is VERY UNLIKELY your funding will be carried over (for example, math funding is usually by TAing/teaching as everyone takes math classes, I guess biology funding comes in the form of lab work).
Second, it is very likely that this late in the year, admissions in math are already done deal (and they tend to have limited spots as usually math admissions are fully funded with TAships). I would suggest looking into adjacent fields which are more bio-friendly and less competitive than math, say statistics (bio-stats? experiment design?) or CS (systems biology?).
Now it is evident from your post and the previous one that you are unhappy with your field of study and position, and it effects you and your work.
Instead of complementing too much, the only honorable/reasonable way to solve that (and maybe move to other program in math, in this university or another), is to terminate the bio program, on good terms (schedule a meeting with director of graduate studies, shake his hand, thank him for the opportunity, say this program is not a good fit for you and ask him if he can assist moving to math, maybe he's BFF with someone from the math admissions committee, it is clear this step is terminal from the biology perspective, but at least you keep your credibility and won't get bad recommendations from the bio staff), right now, you're wasting time (yours and the bio staff) and money.
Your first option is not very viable one. Most math professors (even the applied one) are not usually drawn to bio (rather than CS/Physics), and they are busy people, I highly doubt that you would be able to convince them to participate in a bureaucratic thing (committee) for a student not from their department. Moreover, as in biology you're tied to a lab, rather than being a more-or-less independent researcher as in math, eventually your research would need to align with the intentions of your advisor, namely a bio guy, and this would give even less of an incentive to the math people to support you.
Good luck whatever you do.

Since the time that has passed from that linked post to now, I’ve been able to actually enjoy the field I am in. I believe most of my unhappiness came from the classes I was taking and or the instructors. I’ve been able to take some courses this semester that have re-sparked my interest in the field I am currently in. I am after all in a computational biology program in which many of the faculty do incorporate mathematics (mainly biophysics, which happens to be one of the courses I just mentioned). I don’t think I am wasting their time nor mine. I’m not in a purely bio program.

However I do agree with most of what you said. I think my best bet is to continue the program and pursue what interests me thus far (biophysics etc) and see if I’m able to integrate some more math based individuals into my research/committee. I was assured by the head that he can get me in touch with individuals they have done work with from the math department.


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In APA style, How should rough financial numbers be written?
If I have approximately five million dollars, should it be written as such? Or is one of the following more appropriate?

5 million dollars
$5 million
$5,000,000

4.31e stipulates:

Use numerals to express numbers that represent time, dates, ages, scores and points on a scale, exact sums
  of money, and numerals as numerals.

(emphasis mine)
As this isn't an exact sum, I might be more inclined to spell it out.  This would also play along with the exception listed right below 4.31e:

Exception: Use words for approximations of numbers of days, months, and years
  (e.g., about three months ago).

Is there another option I'm not considering?  Is this addressed somewhere else in the guide?

Your question has two components: 1) Whether to write out the number as a numeral or in words, and 2) whether to indicate "dollars" in words or with a symbol.
I did not find a direct answer or example in the manual, but a discussion on the APA style blog may provide some guidance:
http://blog.apastyle.org/apastyle/2010/04/feel-like-a-number-part-3-the-earth-day-edition.html
To address issue one, look at the question in the comments sectiom (comment #7 from the top) where a student asks about the proper way to write about an approximate number of people. The author of the style post states that the correct answer is "Almost 3,000,000 people." She provides the explanation that because 3,000,000 is larger than 10, is should be written as a numeral. She does not comment on the issue of this being an approximate amount, but because the question is about an approximate number of people, it seems she interprets the exception to rule 4.31e as only pertaining to the units of time listed in the exception. Also, note that in the body of the blog post, the author refers to approximate units of time rather than approximate numbers in general.
To address issue two, look further in the comments section, at the bottom two comments on the page. Here, someone asks how to write about an amount of money that is less than $10. The author notes that in prose, she would recommend writing out the word "dollars," while in tables or with mathematical operators, it might be more appropriate to use the symbol (referring to rule 4.45 about describing statistics in text).
In sum, this discussion seems to indicate that "I have about 5,000,000 dollars" would be the correct form. The number would be written in numerical form because a) it is over 10 and b) it is not an approximate amount of time. The unit of money ("dollars") would be written in prose text and appear as a symbol on tables or when discussing mathematical operations.


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In APA style, what is the appropriate way to differentiate between two organization divisions that both have the word "and" in their names?
I am writing a paper in APA style.  I am attempting to list two organization divisions of a library:

Information Technology and Technical Services
Academic Outreach and Services

How do I write and/or style these in a sentence to clearly define the separation of terms without looking like a poorly written sentence?  I'm not entirely convinced using quotes or italics is correct, but I'm leaning towards italics vs. anything else.

The two major divisions, “Information Technology and Technical Services” and “Academic Outreach and Services,” ...

vs

The two major divisions, Information Technology and Technical Services and Academic Outreach and Services, ...

Normally I wouldn't quote the two, but I'm not sure how else to write it.  Italics would work as well, but I don't know if that's appropriate or not, as the APA style guide doesn't appear to have suggestions for anything corporate/organization-related (4.08, 4.21).  4.21 suggests using italics for clarifying words, so that seems somewhat more appropriate than quotes, but the given example doesn't give me much confidence (the example given is "the small group [meaning a designation, not group size]").

Since this is about style for the article text, not the citations, I removed the [tag:citation-style] tag and replaced it with [tag:writing] and [tag:writing-style].

@NateEldredge As an aside, it seems that the application of style manuals (e.g., APA, MLA) to non-citation related issues is not readily classified by the existing tagging system. Perhaps there is a need for a new tag.

I had initially tagged it as writing-style, but someone else changed that.  I agree with @JeromyAnglim that a new tag would be useful, as I was a little confused which tag(s) would be appropriate given the topic.

If following APA style you should not use quotation marks or italics for names of organisations.
You could use an in-line list to make it clear.
To apply this to your example:

There are two major divisions: (a)  Information Technology and Technical Services and (b) Academic Outreach and Services.


text:
How to know a community of researchers in order to be more successful in research and getting papers accepted?
Knowledge is what lies between heads of people in a community; This is an idea, I recently learned from a video tutorial on writing research papers in a youtube video. In this video, a professor presents such a model of knowledge which is different from what I already thought.
This suggests a measure of success in research is the amount of change she's able to effect in the space between heads. This video talks about community and people in power in that community. So we must know the community, its structure, who the people in power in the community are, and what knowledge is already in the space between heads.
The ideas proposed in this video seem tantalizing but I feel I haven't completely understood his thesis.  I will try to lay out what's hanging me up about this:
I want to understand what a "journal's community" is? since this professor says that will affect the acceptance of a submission.
In short, please help me understand the outlined aspects of this model of knowledge?
Note from question editor: if you have some ideas about how to improve this post further, with the goal of getting it reopened, please grab your red pen and help out.  Thanks.
We usually want to know something from a perspective. Here we want to know a community such that we as researchers can better understand how to communicate with the community through Papers. All of the aforementioned sub-questions are around this single thread.

Attend conferences in your area.

This question may be borderline on-topic. It is possible many people voted for off-topic instead of unclear. The SE system cannot show multiple close reasons, when there are 5 close votes, the system can display only one reason. That said, I don't exactly see what is unclear. Your suggestions on what to divulge at the bottom are indeed irrelevant, as you think. Please don't feel pressured to reveal your 'real name', pseudonyms are ok.

Meta discussion about this question

What is unclear in this question? Every question should be self-contained. Unless we watch the video, how could we know what he meant by "community"?

Voting to reopen.  Please see https://academia.meta.stackexchange.com/a/4095/32436

@user85361 - See what you think about my edits.  Thank you.

I interpreted Prof. McEnerney's comments as 'birds of feather flock together'.   Basically, if you don't behave like you belong, then you are considered an outsider and hence doesn't know the area.  Tell-tale signs include using the wrong technical terms or jargon, using non-standard methodologies, etc.  One rule of thumb is simply to look at articles in journals you want to target and compare your article with published articles. For example, if the community expects mathematical proofs or theoretical work, does your article contain such proofs or theories?

@Prof.SantaClaus, Thank you for your comment. Would you please explain it a little more

I have deleted the question which was the reason for some people thought the question is unclear. Please verify and vote to reopen. Thank you all. I just want a better understanding of a subject through discussions with members of this excellent Network of people. Thank you.

@TheGuy, Thank you, What if I can't?.

@user85361, Thank you for your edits. Check it now.

@Code, I have edited the question. Please check it now.

through discussions Please note that we are a Q&A site. We don't do discussions.

1) Communities usually revolve around research topics, rather than journals. There are smaller and broader communities. The smallest ones are about a very specialized topic that only three research groups in the world are knowledgable about. The broadest ones are about an entire overarching research field. Of course, there also are overlaps between communities.
2+3) In my field, the only correct answer would be: Go to meetings and conferences. This is the place where people go to exchange ideas, in talks and informal conversations.
4) This is a very broad question. There can be all kinds of relations between communities, personal ones (overlaps) and emotional ones (respect, envy, disregard).

I feel it is not a research topic that defines communities except the largest ones. Often I see journal and editorials of them which although they work on the same topic, I didn't even know them.

Of course we can use term community in a very broad sense such as research community. But this way we miss the point that what is our aim, in talking about community: Getting our papers accepted and change the mind of people in the community.

@user85361 You might have a wrong impression of the way that the term "community" is used in academia.

Often I see journal and editorials of them which although they work on the same topic, I didn't even know them. — Well, there’s your first problem.