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What are good principles for naming an algorithm?
My previous publication was about improving a known method A and I called my algorithm XYZ-methodA, where XYZ is a catchy word and methodA is the known method. Now I apply my general theory to method B, so I am thinking of naming my second algorithm XYZ-methodB. This second algorithm uses a sub-routine, that I also developed. I am thinking of giving it also some name like XYZ-methodC. However, this sub-routine is not that related to my general theory anymore, but is just used by XYZ-methodB to accomplish my goals.
Is this a good naming approach for methodB and methodC? Is it a good idea to use XYZ and put it everywhere like bumper sticker, indicating it is from me and increasing recognizability? That was kind of the idea.
What are good principles in naming my algorithms in general?
Naming them after myself is apparently not a good idea. But what is a good idea?

How about following how they name cars... and the consequences such as « Nova » and the spanish market etc So, use names that are relevant - : « method B quick loop » etc..

Similar and the duplicate is worth reading : https://academia.stackexchange.com/q/108033/72855

@SolarMike: I don't understand your first comment. What do you mean with the cars? Can you elaborate?

I'm going to vote for "Algorithm 1" and "Algorithm 2".  Let other people name the algorithms if they think they deserve names.

The bumper sticker idea is quite smart, provided it is indeed the same general approach being applied. Otherwise it becomes gimmicky. Also, IMO, it would be better if XYZ has some functional meaning besides just being catchy, but I understand this is not always easy.
For instance, suppose A and B are heap sort and bubble sort respectively. Suppose your general approach has something to do with hashing, and makes the sort faster. A name like Hashed heap sort and Hashed bubble sort would make more sense and have better recall value/correct association than say, Snappy heap sort and snappy bubble sort. This may be an oversimplified example, but the point about functionality is worth remembering.
Ultimately, the line between gimmicky and legacy is not predefined, and it's not in your hands. Since you've already published XYZ-method A, you could see how the response to that nomenclature has been (are other authors using that name? Do your collegaues and co-workers call it by that name? Do other people see it catching on?). If the response is positive, and the above points are met, you could go for XYZ-method B. Else consider learning from this experience and make a fresh start with a new name.

Yes, the same basic idea is behind the different algorithms. 2) The catchy name has a meaning besides being catchy. I originally had an analogy - although to be honest, since I don't have space to explain it, I am not 100% sure, readers get it :-/. 3) I should clarify: The paper is accepted, but the conference is still to be held, so I don't know reactions yet. The current paper is due today, so... ;-).

Going by that information, I would say try it out! With two names out, you get twice the feedback.

That would inflate my bumper sticker idea though ;-). In any case: Here I am searching more for a name for method C than method B. I don't have good idea though.


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How good of a conference can I realistically submit my first paper to? How can I figure out which conferences I'm good enough to submit to?
I'm working on finishing up my thesis in wireless security and I'd like to publish the results of my work in a conference, obviously the best conference that I can realistically get published in.
However I'm having a hard time figuring out what the criteria might be for this. I see conference rankings around, but how can you actually figure out where on that ranking you should fit? How can I learn how to evaluate these kinds of things?

This is what your advisor is for!

It is not a matter of "I'm good enough" but whether the paper is good enough.

@PatriciaShanahan Isn't it, unfortunately, the case that there can be some politicking that occurs in academia though? Such as preference towards school X, etc?

Asking your advisor, as suggested by @NateEldredge, is a good first step and many advisors will be able to help you.  In some cases, though, your advisor may be unfamiliar, may just not publish much any more (that was the case for my advisor), or may not be able to effectively help for other reasons.
If this is the case, then I would suggest two other methods for figuring out where to send your papers:

Look at the papers that have been published in previous years, and see how their scope and quality compares to yours.
Aim high, and see what kind of feedback you get back from the reviewers. The worst that happens is that they reject your paper.

You learn to evaluate these kind of things by experience.  You read the papers published in the conferences, form your own opinion of their quality, see how they impact the field over time, see how they are viewed by others, and revise your opinions.  Eventually you get a general sense of how "good" a paper should be in order to be published in this conference, and you compare it with your evaluation of your own paper's quality.
You bootstrap the process by drawing on your advisor's experience.
So: Ask your advisor.

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Using masters lab colleagues as references for PhD application?
I'm thinking about applying to a PhD program in computer science this coming December and I'm wondering a couple things about getting letters of recommendation.
For some background, I have a BS and a thesis MS in computer science, and I've been working in industry for a while now, but not that long.
I did a lot of work with my fellow graduate students while getting my masters and I think that, other than my advisor, they are in the best position to write a letter of recommendation for me. They have all graduated with PhDs and are now working as professors themselves. However I'm not sure if having my former fellow students write letters of recommendation would seem appropriate to a graduate committee. What do you all think?

When I started reading, I already thought about how to answer "no", because I was thinking of other students writing recommendations. If, however, they themselves are already professors, they should have some academic reputation with which they can vouch for you. Thus, I would suggest the following steps:
1) Ask them what they think about it and let them send the letters to you first.
2) Ask other people, e.g. your advisor from back then, contacts in the field, maybe even a contact in a graduate committee you know but don't plan on applying to.
3) Get "enough" recommendations to not depend on your former colleagues to much, so that you have the desired number of letters (some PhD programs post such numbers online) and these are but add-ons. As you have been working, and this working time was long enough for your fellow students to get a position as a professor, you might need to explain why you apply for a PhD just now, why you didn't so before and why you don't just stay in the industry. As this is rather important, I put an extra number for it:
4) Get recommendations from your current industry job to show that you are not (only^^) applying for a PhD because you want out of the company or lost your job, but rather because you want to learn, study, better yourself. One or two superiors at your current work place, stating that they advise on you getting a PhD (as you show the necessary skills, etc.) might be just as convincing as your former advisor. If possible, take supervisors who themselves hold PhDs and make sure that they sign as something like "Mr XXX, senior YYY at ZZZ, PhD in ... from ..." to show that they are able to judge your capability and the usefulness for you to get a PhD.
So long story short, I would if possible get letters from your advisor and from your current job. The former colleagues could be a nice addition to that, but I would not put the main focus on them if possible.

Note that some programs (I know many examples in the US) might prefer that you do not know the contents of the recommendation letters.

I get three letters, exactly three. My advisor will certainly be one of the three, but I'm on the fence about getting someone from the management chain to write one. I think my manager certainly would, but no one in my management chain has a PhD. Some of my colleagues have PhDs, but I would think that if I'm getting a letter from work that it should be from a manager or someone higher up than me.

Depending upon your other possible reference letters, one such letter from a former PhD student - now professor may be a good option.
The strongest reference letters, in the eyes of a PhD admission committee, will be from someone who can personally attest to your research ability with specific examples. The length of time they have been doing research/working in the field is important as it improves their credibility and allows them to make comparative statements between you and the bulk of people they have worked with or advised. Having a well established professor saying you are among the top 5% of students they have performed research with is very powerful.
As you mentioned, your MS advisor is in the best position to give you a reference letter, and indeed his/her recommendation is critical. If you have any undergraduate research experience or involvement with outside collaborations during your MS degree, they may offer additional opportunities for recommendation letters. If your industry experience involved any research, or if your letter writer can credibly state your suitability (and is perhaps even pushing you to get your PhD as Bemte mentions), that may be another good option.
If your only other options are letters from professors you have taken classes with (when your letter will only be based on grades/class participation) or letters from work (when it will only be based on work ethic/personality), do consider a letter from a former PhD student - now professor. If you were essentially advised by this student, in a sub-project or offshoot of their thesis, it would be considerably better. Be sure, however, that you at least worked together on the same project. Be aware that generally they will only be able to discuss the same work as your MS advisor, which will further reduce the letter's impact. Do not include more than one.

I worked on a side-project with the PhD student I have in mind, so the project was not my MS thesis and I'm the second author on a paper of theirs on the project. So that's good to hear!
I have a small follow-up question, what would make a stronger third recommendation letter, a letter from my current industry manager where research is not a part of my job at all or a letter from a professor from undergrad that I TA-ed for?

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Acknowledgments in peer-reviewed journal publications
I have a submitted a paper to a peer-reviewed top journal. It is in the second review round and as far as it seems, it will be accepted. I am considering to write an "acknowledgments" section (after the conclusion) in which I thank those researchers with whom I corresponded and whose work I cite. It would be five researchers of four teams. The correspondences were just 1-2 e-mails in each case, so I think it is not required of me to acknowledge those correspondences, but it might be nice to do so.
However, for this question, I would like to disregard the "nice-ness" and ethical aspects and focus on the "self-marketing" aspect: How does it make me look if I mention those five researchers? Does it look more like I am a good collaborator with a pro-active attitude, who gets in touch with people without being shy? Or does it make me look like I am someone who is not able to get stuff done himself, asking other to do his work for him?
Or missing something else that I should consider?

The text I am considering is

We thank [...] for the fruitful correspondence by answering the questions we had regarding their respective work. We thank [...] for the provision of their respective code.

The reason I am writing the acknowledgement only now is because now the page limit is not an issue anymore, while it was for the first submission.

It does not hurt to say thank you, even for the most minor thing.  So and so inspired X.  I've seen authors acknowledge their pets.

Your motivation for acknowledgement should be that people deserve acknowledgement for their contributions to your paper. If you have any other motives, you're doing it wrong.
Don't acknowledge people just so that you look like a team player. It might end up looking like you're trying to prop up your work by attaching other peoples' names to it; they may rightfully be offended if you do so (as @Snijderfrey recommends, you can avoid this by asking permission to include someone in the acknowledgements; see also Is it necessary to ask permission before including someone in the acknowledgements of a research paper?). Don't use acknowledgments when citations are appropriate instead, or it'll look like you don't understand what a citation is. You never need an acknowledgment for something you read in a published work: cite instead.
Don't fail to acknowledge people just so you look independent. It might seem to the people who've helped you that you don't appreciate them and they may not want to help in the future, or it may look like you're taking credit for work that isn't yours.
Thankfully, there's a fairly broad set of norms regarding acknowledgement so you do not need to obsess over each paper and each person with who is acknowledged (and there are lots of resources here to help you decide).
In papers I've been involved with the acknowledgement section was always included with the manuscript sent for peer review. I would not assume that page limits/word counts/etc do not apply to additional sections unless the journal specifically says so, in which case it's puzzling to me that they'd count the words/length in an original submission. (of course, every submission system is different and there may be convenience reasons that they do this/recommend waiting to add the section later)

Your motivation for acknowledgement should be that people deserve acknowledgement for their contributions to your paper. and Don't fail to acknowledge people just so you look independent. Sure, here, I have a case where both would be fine - I don't think I have to acknowledge everyone I talk to, but here I could give some love if I want, I guess. You never need an acknowledgment for something you read in a published work: cite instead. Obviously, but I covered that in my post. I would not assume... the first submission was soft page limited, the subsequent once not.

@Make42 I'll restate my first sentences: "Your motivation for acknowledgement should be that people deserve acknowledgement for their contributions to your paper. If you have any other motives, you're doing it wrong."

They did not contribute to my "contribution" - otherwise they probably should be authors - but they contributed indirectly by helping understand their work.

"...like you're trying to prop up your work by attaching other peoples' names to it; they may rightfully be offended if you do so." True, and this can be avoided if you ask the respective people before including them in the acknowledgements. I think that would be good practice anyway.

@Make42 Not all contributions to a manuscript justify authorship. I would not ordinarily acknowledge someone for merely helping me to understand their work, that should be part of their publishing process not yours, though there may be exceptions where the help is directly related to the manuscript at hand (for example, help in reproducing a technique from a paper used in the current one).

@Snijderfrey: Regarding the reproduction: They provided the code I did the rest. There wasn't any hand-holding on their part... so, is this to be acknowledged or not?

@Make42 StackExchange isn't a discussion forum; Snijderfrey was commenting on a specific part of this answer, it's not appropriate to redirect a new unrelated question to them.

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Is it necessary to add experiment to my designed framework for a journal
I'm working a framework X and trying to publish it in IEEE Communication Magazine. But, due to its limitation on the number of text and figures, I wonder it is necessary to add any experiment or proof-of-concept system there?
Thanks.

It depends a lot on the journal, the research area, and the research topic that you are working on. For some fields of computer science, reviewers will immediately reject most submissions that do not include some artifact or implementation with a convincing experimental evaluation. For other fields, this is totally optional (but even then, it may help).
I'm not familiar with the IEEE Communications Magazine or the field of communications in general. However, you can easily find out (and this goes for any other journal as well!) You should do the following:

Look at other papers that have been accepted in the journal in the past, especially related to your topic. How many of them had an experimental evaluation? All of them, some of them, or only a few?
Ask an expert in your research field, such as your adviser or any professor you have access to. They will likely know whether this particular journal expects an evaluation, and they should also be able to offer other specific advice about to your planned submission.
Finally, consider whether your particular research contribution requires or would benefit from an experimental evaluation. Are your main claims sufficiently justified without an evaluation? Even if the journal does not expect it, the evaluation may be necessary to make your paper convincing. Similarly, even if the journal does expect it usually, if your contribution is clearly of excellent value without any evaluation, you may be accepted without it.

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Sub-referencing work from the referenced work
Sorry for the tricky title. I am working on a (IEEE) conference paper and in the related work section I have sentence that goes like this:
In [X], the authors derive YYY metric from the Gov. Institution Name's Obscure Parameters Database. Should I put a reference after the "Obscure Parameters Database"? My understanding is that whoever is interested - will be able to find it wither by looking up the [X] work or by searching the Internet for the database (it is open to the public). Am I correct?

Don't just assume that anyone interested can find the database by looking up {X} or searching the Internet. Find the database yourself and then cite it directly, with an appropriate URL.

The only exception to citing the original referenced work would be in some circumstance where you cannot access the actual original with moderate effort (including purchasing the article from a journal) or reasonably expect your readership to do so. For example, if the original document was a historical record in an archive somewhere, it could be appropriate to cite an article about that record that reproduces it in part.

Cite the database, and in citing it and/or in context, provide a way for your audience to know which version or part of the database was used. Ideally, you should provide sufficient details for your audience to know how the authors of work [X] produced their metric.


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Is it plagiarism to copy an ethics statement on animal research?
There are only so many ways you can say "This research was conducted in strict accordance with the guidelines of XX." I'd had the fear of plagiarism burned into me since high school (I think the rule then was 7 words or more verbatim were disallowed), but is it acceptable in science publishing to have substantial overlap with previously published ethics statements?
A slight variant is when you are describing a technique that has been concisely described by your lab dozens of times already, although this is slightly easier to think of variants than the above. But some amount of "copying" in these situations, whether inadvertently or on purpose, does not seem in the spirit of plagiarism.
How do publishers/the scientific community see it?

Committing plagiarism by copying an ethics statement has to be the most ironic form of academic misconduct possible!

Well, there is a gut reaction against it, but see the excellent answer below. For clarification, the "ethics statement" is a standard line for animal research: "These studies were carried out in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health, and all procedures were approved by X organization at X institution."

Both plagiarism and self-plagiarism are about violations of the expectation of originality. In the main text of a publication, there is an expectation of originality, and thus these concerns apply.
In the "metadata" of a publication, like acknowledgements, statements on ethics and conflicts of interest, etc., the expectation of originality is much weaker, and the primary concern is accuracy.  Thus, "boilerplate" text providing little or no narrative content can be freely reused (e.g., "This represents the conclusions of the authors and not of the funding agency or US government.").
In the unusual case where such a section does have study-specific narrative content (e.g., describing a novel approach to developing an ethics plan), then it would not be OK to copy it. Instead, you would want to discuss the relationship in the main text or methods section (which is a grey area for reuse, as sometimes it is "boilerplate" and other times narratively unique), and make a simple statement in your own words linking to that discussion in the ethics section.

Heck, your institution may even have a specific standard line that they expect you to use for an officially approved study...


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Can you still do a postdoc if you definitely don't want to become a professor? Will your advisor think less of you for doing so?
I'm a senior grad student struggling with existential angst. I'm fed up with my advisor, to the point of fantasizing about quitting my PhD. I likely don't want to become a professor. But at the same time, I still love my field of study (in the biosciences), I like research, and I have a postdoc lined up starting next year at a great institution working on a project that I am really excited about. Also, due to conflicts with my advisor, I am really worried I won't be able to graduate in time to take this postdoc job. My questions are:

Is it still worth doing a postdoc? Another way of asking is: have other people set out to do postdocs with the clear intention of not becoming a professor?  I don't mind the low pay and I'm excited about the topic, so my guess is yes... but I'm worried it might hurt my chances of getting a job in industry or elsewhere afterwards (not sure what I do want to do instead though).
Would it be a terrible idea to TELL my current advisor that I don't want a career in academia in the long run, but still want to do a postdoc? I feel that it might help with the current impossible standards he/she is holding me to, and hence speed up graduation. But, I'm worried that both my current and postdoc advisor will assume it means I won't take science as seriously, and hence won't do a good job as a postdoc.

You should also consider the funding side of things.  I took a postdoc job over a professor position because the field I am in is very expensive and the money structure is awkward.  I can easily get an academic job as a professor at this point with a good line on funding thanks to the postdoc.  (however, I'm having a good time, so we'll see when that happens)

If you don't become a professor what do you want to do? I work in a government lab and most of our PhDs have post docs before they get hired. Sometimes industry R&D positions require post docs as well.

1) If you are truly interested in the work, then yes, it can be worth doing. A post doc could also be a path to a long term non-professor role in academia, though those positions are quite rare and are definitely undercompensated. You should probably be aware, though, that your time as a post doc isn't likely to count much as "experience" in the non-academic fields unless the work is very closely related to an industry.
2) I have certainly heard stories of students that were pushed through by their advisors/departments at their request after not expressing interest in academia, so maybe this could help you - personally I think that's silly and isn't how PhDs should work at all, but reality doesn't always match the ideal. Have you done enough to earn a PhD in your department? It isn't clear what exactly your conflicts are with your advisor, and whether you are being held back when you should be allowed to graduate or if you have not been productive enough to have earned the degree.
It's also hard to give you advice on this because your current situation with your advisor suggests there isn't a lot of confidence that your advisor has your best interests at heart. That said, at least in the US where I have experience, the reality is that most PhDs in the biological sciences will not get professor jobs, regardless of their desires: the math simply isn't in favor of it when each professor graduates multiple students and yet universities aren't growing exponentially. A good advisor should understand that reality and take some interest in preparing students for whatever they want their post-PhD career to be like. In that context, I wouldn't really be interested in having a PhD or postdoc advisor who could not accept that reality, and from the advisor's standpoint I would expect the same level of productivity out of graduate students and post docs regardless of their career goals, except for being honest with them about the caliber of work that is required for those goals.

You love your field and you love research. Your post suggests that you don't view your advisor as a good professional role model, which is turning you off to academia. However, professors' personalities vary wildly. If you like research, like your field, are excited about the post-doc but dislike your current advisor, it seems that giving it all up now may be premature. You might start the post-doc and it reignites your interest in becoming a professor.
No, I wouldn't tell the post-doc colleagues or your current advisor about your disinterest in becoming a professor if you are deciding to go through the post-doc. In many/most fields, post-doc positions are designed to train you for academia, so some may see mentoring you as a waste of their time, unless you are in a field where post-docs normally go into industry (not sure which fields that do that, though). My suggestion...getting a post-doc is hard. They are competitive. If you still love other aspects of what you're doing, stick it out through the post-doc and make your decision after a year. Some people just get tired (or disgruntled with) their advisors after a year or two. It's normal. Hope this helps!

I disagree somewhat about the waste of time (for the advisor), at least in the field of biosciences: post docs are more advanced than graduate students so typically take less mentoring effort (and really don't cost much more: a research assistant might make a lot less but their tuition also comes out of their advisor's budget). Also the OP already has a post doc lined up. Again, this is a lot different in the biosciences vs other fields. Fellowships for post docs are definitely competitive, but not as much research associate positions.

Bryan, I definitely agree with you about how post-docs are high skilled and need less mentoring. What I meant was that they are often (not always) designed to further train academics, so some advisors may prefer to provide extra support to those going into academia. Sorry for the confusion. I edited my response to clarify it (though you still may disagree with what I wrote).

I like the softer statement, +1.

Maybe I was conjuring memories of snarky advisers from long ago when I wrote the first version. LOL!

If you look at the numbers, plenty of postdocs who do want to be professors don't get what they want.  So it's not unreasonable to spend some some as a postdoc before leaving academia.
Postdoc life is very different to the late stages of a PhD and is almost invariably in the form of short contracts.  If the employment uncertainty doesn't put you off, if you can get a postdoc position easily, and if it's doing something you enjoy, you're in a good position.  You can use the time to get publications and build contacts in the field, while taking stock of whether you want to continue in academia.  That's a lot of ifs.

This is a complex, two-part question, so before I take a whack at it, let me first say: if you love research, and you love your field, and are good at what you do, I expect you should be a benefit to a research group whether or not you are planning on becoming a professor.

Is it worth doing a postdoc? Take the opportunity cost seriously! If you could already get an industry position doing research you like, doing a postdoc lets you gain skills, do a different topic for a while - at the cost of much lower pay and delaying your industry start for a few years. (And moving!) Industries vary, so talk with someone whose job you'd like to see how they view postdocs. I certainly have not heard anything about liking former postdocs less - as long as you are still OK starting at an entry level!
Should you tell your current or future advisor? I would definitely not tell your future advisor immediately until you have a better sense for how they treat postdocs in general, or see how current postdocs who leave for industry are handled. I am not sure if telling your current advisor will help matters. This will depend a lot on why you and your advisor are clashing. Conflict at the late stages of the PhD is pretty common - even with good advisors - as you and your advisor start to develop different priorities and tastes about science. Unless your advisor has been explicitly saying something like "it is critical that you do X to get a faculty job/for your future career," I wouldn't expect telling them you're going to industry to help. Side note: even if they say this, don't necessarily trust them, especially if X is "publish this paper in a glamour journal." This is important for a trainee aiming for academia... but also very important for the professor. Even if the professor has the best intentions for mentoring people, their interests and your interests are better-aligned when the trainee is aiming at academia!

About whether to tell your advisor about your intention not to go into academia: In general I'd say yes, this is a good thing to do. Knowing what a student's or postdoc's actual aims are helps an advisor provide good advice, and helps tailor projects to things that would be useful. A recent Ph.D. student of mine was not keen on trying for an academic career, looked for a postdoc position with ties to industry, and was very straightforward about this; it turned out very well. In addition, advisors do worry a lot about the difficulty of placing people in academic tracks, and it can take pressure off to know that a student or postdoc doesn't want that path.
However, I don't know if this general advice applies in your case, since it sounds like your relationship with your Ph.D. advisor is not a good one. If you haven't already discussed your future plans with your future postdoc advisor -- something that should be done prior to accepting a postdoc position, by the way -- you really should. It would be weird to do this without also talking to your Ph.D. advisor, but that's what I would recommend.
This gets, however to the more important question: #1. What is your goal in doing a postdoc? It's fine not to have the goal of being a professor. It's good, however, have some goal. It's great that there's a particular project that you're fond of, but to me this is insufficient. There are lots of wonderful topics in science and technology; perhaps you could find one that both excites you and that sets you on a rewarding longer-term path. Or, think of particular aspects of the postdoc you've lined up -- experimental techniques, potential collaborations, etc. -- that set you up for something beyond. Congratulations, by the way, on being close to finishing, and on getting a postdoc position. Both are real achievements! Since you're passionate about your postdoctoral research topic, I'm sure you'll be valued by your future group, by the way.

In bioinformatics, I've known several people who did academic-focused postdocs who then went on to industry careers--some in biologically focused fields such as drug development, others in "data science" positions for Google and the like that had nothing to do with biology, but certainly made use of their analytical skills.  You don't say specifically what field you're in, so I don't know how much this observation applies, but it seems to me that having good research experience on your CV is never a bad thing.


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Standard practice when merging papers on arxiv
I and another author have decided to merge our manuscripts into one paper.
Both of us have already put preprints on arxiv. How should we handle the merging on arxiv? Is there a standard practice?
I can think of three options:

 Create a new submission for the merged paper.
 Upload the merged paper as a revision of both of the original preprints.
 Withdraw one of the original preprints and upload the merged paper as a revision to the other.

I worry that option 1 might look like we are spamming arxiv by uploading three papers when we really should only have uploaded one. Option 2 is undesirable because then there are two versions of the exact same paper on arxiv. Option 3 is asymmetric.
Has anyone had a similar experience?

I think I've seen both 1 and 3, never 2.  Whether asymmetry for 3 concern depends on the relationship between the manuscripts (e.g., if one is a sequel to the other, this "asymmetry" is fine).  What you want to avoid with 3 is having people miss some of your results because they've only looked at one of your preprints but not the other.

Option 1 should be fine if you add appropriate comments and withdraw old papers.
Here is how we did it recently:

http://arxiv.org/abs/1503.04963 (merger)
http://arxiv.org/abs/1412.2109 (withdrawn)
http://arxiv.org/abs/1412.2667 (withdrawn)

In the merged paper, it is important to add a comment; otherwise you will probably trigger https://arxiv.org/help/overlap


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Contacting Professors and Letters of Recommendation
Last week I emailed a professor from my undergrad whom I was close with to say hi and inform her that my undergraduate thesis had been published. I am currently in a master's program and asked her if she would be willing to write me a letter of recommendation for upcoming PhD applications for next Fall (and it is worth noting that she wrote me a letter of recommendation for the program I am currently in). She has yet to reply and having a letter from her would really strengthen my application. Is it in poor taste to resend her an email, or should I move on? Like I said, I would really like to have her letter as part of my applications.

Last week I emailed a professor And you worry about no reply yet? Have you exchanged e-mails with her in recent years? How often? What if she is busy recently? Wait at least another two weeks, then resend her another e-mail. If still no reply, then come back here, tell us the details and ask us what could be the possible reasons.

I have exchanged emails with her for the past year or so and she has always responds promptly based on experience. I am not planning on resending anything now and was planning on waiting, I just do not want to come off as annoying.

Unless your request is urgent, you should wait two weeks from the date of the original email for your follow-up.
The subject line is easy, it will be the same as the original, but prefaced by "Re: " (which is automatically supplied by most email programs).
Alternatively, if there is any other topic you are interested in corresponding with her about, you could write to her about that, and at the end ask her if she's okay with writing the LOR.
In either case, you can make clear in this new email what the deadline for the LOR is, but explain that you'd like to line up your references before, for example, the end of October, if possible.

You should absolutely follow up with her. At this point you have no idea why your email did not get answered. She could be at a conference. She could have missed it completely. Or she could have meant to write you back and simply forgot. I'm in my last year of grad school and none of these things are particularly uncommon for professors. Do not waste time wondering about why she did not write you back, simply reach out to her again. Your letter should say something like this: "Hi Professor So and So, I'm following up with you regarding the letter of recommendation for my graduate school applications..." When this has happened to me I almost always get an immediate response with a flood of apologies for the late reply.

What do you use as a subject for such an email and should I wait a bit longer?

I guess it depends on the deadline of your application, but I would give her at least a full week to answer. The subject can be Follow Up RE: Recommendation Letter or something to that effect.

Oh they aren't due until December, but I just like to give plenty of notice even though she has done it once before.


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How to incorporate a fellowship into a CV
I am updating my CV for graduate school applications and I have an awards/honors section and I am unsure how to incorporate a fellowship I received. With the way I have things formatted, every entry looks something like:

Name of award               Date when I received award and institution name if relevant
Description of the award

In every other instance, the description doesn't refer back to me in any way but I am having a hard time doing this with this fellowship. The best that I have been able to come up with is along the lines of

Summer Research Fellowship               Summer 2016, Blah Blah Blah University
I was one of four graduate students from Blah Blah Blah University's Mathematics Department to receive a fellowship during the Summer of 2016. I worked under Dr. Something, researching stuff that contributed towards my thesis.

Does this seem alright? Also, the research I did this summer is a part of my thesis, however my thesis is not complete yet and will not be until the spring. The way its written now makes it seem like my thesis is written (at least to me), so is there a better way to state this and make it seem more ongoing?


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Can I keep using my old academic affiliation for publishing?
I have recently completed my Ph.D. and would be joining the industry in an analytics profile where publishing is not mandatory. I want to keep on publishing to ensure my return to academia if I feel like it someday. Can I keep sending papers to journals and conferences using my old academic affiliation?

What does the institution/group you claim to be affiliated with think? Do they still see you as "someone associated with their team"?

It seems dishonest to indicate an affiliation that does not exist.

Do the answers here address your question?  The short answer is that your affiliation needs to accurately reflect the most current affiliation that supported the research.  A job in industry will likely not leave you much time to do research that's completely independent of that job and the company's resources, so they should be your default affiliation.

@DanFox: What does it mean for an affiliation to "exist"? Isn't both sides verbally agreeing to work together enough?

@O.R.Mapper: It means one has a mutually recognized relation with the institution in which it is understood that one's research activity forms part of that relation. This can be contractual, honorary, etc. What would be dishonest is to represent that one works at XYZ when one visited XYZ 4 years ago. Some people represent themselves as affiliated with a certain institution because that affiliation gives credibility they might not otherwise have.

When you are really not affiliated to the institution anymore, you should not put it on your publications. Certainly not, when the work you are publishing has not been initiated during your stay at the institution.
Many institutions have the possibility to offer you a 'zero hours' contract. In this scheme you remain affiliated to the institution, and can use their facilities (e.g., email address, etc), but do not receive any monetary compensation.
If you agree to such an arrangement with your previous institution, you obviously can still use the affiliation on your publications.

To add to the facilities argument, having access to journal articles is a major benefit if you are doing research. And if the OP is actually publishing good stuff, many universities/departments will be happy to accrue the reputational benefits.

Perhaps the last phrase is more correctly worded, that "if your previous institution agrees to such an arrangement with you, then in part of that arrangement, you generally are allowed to use the institutional affiliation. There may be reasons (e.g., the person has a history of retracted publications or is trying to publish about a perpetual motion machine) that a university might prefer to vet an adjunct.

I have a colleague in urban studies who continues to publish research even though she is not currently in academia and runs a non-profit. She lists the non-profit she directs as her affiliation on publications. In her case, it appears impressive that she is a "practitioner-scholar." I don't know what your exact discipline is, but if your current job is okay with you publishing your work while employed there,  why not list your employer? That doesn't affect the quality of your work. You can also credit your former indtitution in the suthor's note or author's bio, if there is one. Hope this helps!

It considerably depends whether the research you are publishing/presenting was done at your former institution or not.
Case 1: the research was done at your former institution
Your former institution supported your research (office, computer, lab, ...). The number of publications is an important metric for research institutions when they are evaluated. If you did your research at that institution, it is fair to list it as the affiliation of you or of one of the co-authors. Thus, the publication is counted as this institution's publication.
However, your former institution (head of department or similar) needs to be informed about the publication and should be asked in advance, whether it is desired to indicate the institution as your affiliation.
Case 2: the research was done after you left your former institution
In the second case, your former institution should not be mentioned because there is not connection between your current research and that institution.
However, if you are still using resources of that institution (e.g. a high performance computing cluster), you should discuss it with the responsible person there.


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Is being the second author out of two authors for papers from my PhD thesis going to affect my future job prospects?
I have completed my PhD recently and will be looking for academic jobs. During my Phd thesis work I published two papers with my thesis advisor and have put him as a first author. It was out of reverence for the guide and I have never discussed this openly with him. Both of these papers have two authors with me as second author. My question is that since I am not the first author, will that create a major issue for me while applying for academic jobs? My field of research is in computer science.

What sort of computer science? If theoretical, then the author lists should be alphabetical anyway.

Unless your advisor actually did more work than you on those papers, they should have objected to your offer of first authorship.

There are a lot of variables here. I'm in the US and personally never considered the order of authors significant, assuming generally that all were contributors. But in other places and with other persons it may be different. Do people assume that the first (or last) author is the "real author" and everyone else gets a free ride? I hope that isn't so. But I can't guarantee it.
Many people, it seems, include their dissertation advisor on papers arising from that work. I doubt that it is necessary and others are recommended to ask the advisor before they send the paper for publication. Many would suggest they not be included, but other advisors would have other advice. You might be able to avoid the OP's dilemma.
For purposes of job applications it will be useful, of course, if these are not the only papers you have in publication. If you have a few more, on which you are the sole author you will likely be in a good place.
However, your job prospects depend on more than your CV. Focus on that. If someone is hiring and gets a lot of applications, the first thing they do, typically, is to sort the candidates into two piles. The big pile is people who won't be considered. You want to get yourself into the small pile, but that will depend on more than the publications on your CV, including what you say about yourself in the opening (cover) letter. It will depend on your experience as well and how suitable your background is for the advertised job.
If you can make up a complete application package that gets you into the small pile, then your concern won't matter at all, since you will probably get an interview for the job and, if necessary, explain that this work was your dissertation work, done by you, with appropriate assistance. Your respect for your advisor led you to list him/her first. I don't think you can successfully explain that other than in person, however. It isn't the sort of thing that should be in the CV.
However, it might be possible to add a parenthetical note to the listings of the articles that this paper was based on your dissertation. Don't say more, however, and be careful even about that. I suggest it as a possibility, but don't necessarily recommend it.
But, again, your goal is to get an interview in which you can show the interviewers how suitable you are for the position.
And write a lot of papers as sole author if possible.

In my experience on hiring and tenure commitees, in subfields where author order matters, it really does matter. People don’t necessarily assume that second and later authors got a free ride, but they do assume that they contributed less to the paper. Especially for joint student-advisor publications, listing the advisor first is a strong signal that the advisor deserves more credit, because “everyone knows{ that savvy advisors game the system by listing their students first (improving their chances of getting a job) even when the advisor did the work.

@JeffE, totally outside my experience, but scary as can be. Student beware.


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Should I cite a paper that I haven't read if I use a theorem in it?
In my Master's thesis I use a theorem that is recent enough that I could find the article where it is proved, but I've actually learned the theorem and its proof in two books by other authors. Is it necessary to cite the original article, knowing that I haven't actually read it?

Why not citing all three?you offer the reader a trackback of the theorem. If you are citing in a MSc thesis you can cite also the books, but for journal papers the referee would have some objections when citing textbooks.

Why don't you read the article so then you can cite it after having read it? You don't need to give it a thorough read - just enough so that you can cite it while responsibly knowing what you're pointing your readers to.

It depends how well-known and wide-spread the result is. If by now it is a very well-known  result and the publication already happened quite some time ago, it may not be necessary to quote the original paper.
In doubt I'd quote the article and the books, or at least one of the books. A possible formulation could be:

The result below is due to Paul [reference to article]; we recall it in the form given in a monograph by Miller [reference to book].

I do not think it is necessary to have read the original paper to be entitled to write this. If it is not too much work to track it down, it could still make sense to at least take a peek at the article you quote.

Though if you cite a paper, you should try to at least look at it, just to verify that it contains what you think it does (you do not need to read it in detail).

I like the double citation, it also makes it a tad more reliable: not only it passed peer review, the book authors also trusted it.

@Kimball yes, which is about what I said in the last sentence. Yet, in the context set up in OP that the result in question is included in at least two books by (it seems) two different authors, I would still maintain it is not a necessity. Also note that my proposed formulation makes explicit that "the form" of the result is taken from the book (not the article). Say, somebody credit's van der Waerden's theorem to van der Waerden, do they have to track down that 1927 volume of  Nieuw Archief voor Wiskunde to check if the paper "Beweis einer Baudetschen Vermutung" really contains that result?

@Davidmh It's also very helpful in the case that the original form of a theorm isn't the most commonly present version anymore.  Often times, the original author still gets the most credit, even though later authors have figured out how to make the topic much more comprehensible.

@Kimball I agree, although in some cases this may be prohibitive or even impossible to do.

quid: in that case I don't see the point of citing van der Waerden--just say it's due to van der Waerden.  (and I wanted to more strongly emphasize that you should, @Ryan when possible, have seen each paper you cite.)

@Kimball so how do you know it is due to van der Waerden? (The relevance of such a reference for example could be 3 in vectornaut's answer. In the very specific case this may not be that relevant, but one could come up with related examples where it is.)

When I cite a theorem, I typically have three goals.

To point the reader to a precise statement and proof of the result.

To accomplish this goal, I cite the clearest source I know of, or the one best-suited to the way I'm using the theorem. In my experience, the clearest source is often not the original one. As people use a result, they often notice places where the statement or proof can be clarified. As a result, the presentation of a theorem often improves with age, even if its mathematical content remains the same.

To point the reader to a trusted statement and proof of the result.

I must admit that I've cited many theorems whose proofs I don't fully understand—especially considering that, to really understand a proof, you also need to understand the results it depends on, and the results those results depend on... If you have read and understood a proof of the theorem you want, though, I might encourage you to cite that proof, on the principle that the best proof is a trusted proof. As a bonus, since clear proofs are by definition easier to read than confusing ones (in most circumstances, at least), this tends to support goal 1.

To give the prover credit for the result, if necessary.

In some cases, the attribution of a theorem is already carried in its name, so there's no need to use a citation to give credit. In other cases, however, the history of a theorem can be hard to track down, so it's nice to cite a proof by the people the theorem is attributed to. Unfortunately, this often conflicts with goal 1, since the first way something was done is rarely the best way it can be done. A nice solution, if available, is to cite a later, cleaned-up proof written by the result's original authors. Another solution is to cite the clearest reference up front, but add an attribution citation later in the sentence, or in a footnote.

I think this is a very nice answer, in the way that it separates out the various purposes of citation, and acknowledges the tension between goals 1 and 3

Somewhat on a tangent, but writing my thesis, I really enjoyed tracking down 100+ year old papers (and one even from the 18th century) to give a citation to something, that can be considered common knowledge by now (Drude-Lorentz model), just so it would be easier for the reader to track down these hard-to-find papers. Not sure, whether that falls into category 1, 2, or 3.

@LLlAMnYP, same here! While referencing my thesis, I got to look up some cool and surprisingly hard-to-find papers related to the Erlangen program, and I had fun tracking down the history of a folklore version of the uniform ergodic theorem in an attempt at goal 3. I think the citations you describe could serve either goal 1 or goal 3, depending on what the "common knowledge" consists of. If the common knowledge is that a certain fact is true, but the original paper is the only reference with a precise statement or a complete proof, that's goal 1.

You should read the original paper and then cite it.
Citations exist for many reasons.

You should cite articles to show that you've done your due-diligence in learning the background information. Like the infamous Van Halen brown M&Ms, this is a quick way for your readers and reviewers to check that you actually know what you're talking about.
You cite other articles to allow readers to find the relevant background material. Research papers create a web of information and providing signs pointing to the important previous work is important for those not immersed in your paper's field.
Finally, you cite other work to give recognition and "props" to those who have done important work in the past. This is especially important to any work that you're actively building off of.

All three reasons I mention above are relevant to your question. This is your Master's thesis. You need to show that you've down the background reading, give an overview for future readers, and cover the important previous work.  Sure you can cover secondary sources, but primary sources are better.  If you're already familiar with the theorem and its proof, skimming the original paper shouldn't take much time and citing it is the more correct thing to do. Doubly so for a thesis.

Reading the original paper seems unnecessary (possibly a waste of time), particularly if you already know a proof of the result you're using.


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Graduate coursework not taken for a degree- still relevant for graduate admissions?
I have recently graduated with a Bachelor's degree in the United States and have taken a job as a research assistant at a large private research institution. Part of my employer's package involves free tuition for full time employees for up to 6 hours per semester, including graduate courses. I was considering taking advantage of this opportunity, and my PI and I have agreed that 3 hours per semester (1 class) would be a good compromise between wanting to work and gaining knowledge as an investment in my abilities as a research assistant. This is an exciting opportunity because my undergraduate alma mater was a relatively small institution with no niche coursework. My cumulative training up to this point has included being lucky to catch course offerings and being the beneficiary of summer REUs..so the opportunity to take niche coursework is highly lucrative for me. My question is as follows:
If I take 3 graduate courses (summer included), when I apply to graduate school down the line in about a year or two, should I report these courses and do they make any difference? Secondly, how do I put these courses under the education tab in my CV/resume?

At least in the United States, applications for graduate admissions typically instruct you to include transcripts from all undergraduate and graduate study. So there isn't really a choice of whether to report these courses or not.

The coursework is helpful, especially if you do well in them. It will show that you have understand and have experience with these concepts. The work is not as important as your research, but will be of some benefit. That being said, whether you can transfer them as academic credit towards your graduate degree will really depend upon the school.
As to your CV, simply add a section under education mentioning that you took courses at your new institute. You can list the courses under that and submit a transcript for them when you apply to graduate school.


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If a PhD student is working slowly on a project, is it bad form to give the project to another student?
I think my advisor may have done this to me.  Initially he hired a master's student to "help me" with the project and he told me I would be supervising him.  But now he wants the master's student to work on core parts of the project, and he says that since I will be busy this summer, the master's student might be the primary person working on the project.
I am thinking of quitting the project because it looks like I am being replaced.  Am I overreacting here?

Talk to your advisor about how you're feeling. For all you know, he may think you're not that interested in the project and thought he was doing you a favor by getting someone else to work on it...

If you are not more productive on that project as that masters student, then why is it so? If the student can achieve the project goals without you, but you needed their help (i.e., couldn't do it in the expected time on your own), then why should you supervise him and not the other way around? No offence intended, I don't know the details, but it's worth to take a look at the situation from that perspective with the fact that you know better and see how it looks.

Agree with the comment above.  I hate it when a good idea of mine go to waste because a student cannot execute to bring the idea to fruition.  For poor students I make sure they get simple projects that I don't really care about so that I never have to hire someone to salvage it.

"Being replaced" is not a good reason to quit.  Quit if you cannot perform your responsibilities.  Otherwise try to perform them.

Don't quit
Being in a PhD is never as perfect as we want it to be. BUT if there is a problem of performance from your part, try to tell the supervisor about your feelings and how you can improve to get back on the roads.
If you quit, you'll be seen as a "coward", or worst, as someone your supervisor should not have given the opportunity to do a PhD.

Please inform us on how it turns around, do not hesitate to edit your question :)


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Is this level of publication politics normal in academia?
I'm currently finishing up a master's thesis in computer science/applied mathematics and have for the last few years been sure of my goals: to pursue a PhD.
The decision to do a PhD or not should largely be a function of your research potential. There's a lot of questions of the "am I good enough for a PhD" sort, but my concerns are of the opposite flavor. I'm fairly convinced that I would make an able researcher, based on discussions with several members of faculty and my output record thus far.
Lately, I've gotten a taste of academia's backside. There's the general record padding done by a fraction of faculty: publishing/coauthoring stuff they KNOW have no novel content, blatant reciprocal out-of-context citations and stuff like that. This strategizing almost seems to spill over into the problem selection process as well - a good problem is one that has potential for publication quantity first and foremost.
Not all professors do it, so I guess I could live with it. What's worse is the attitude from what is supposed to be peers. PhD students who I've proposed ideas to pitching them as their own to their supervisors. Others acting threatened and stand-offish, leading to awkward social situations. There's much less free exchange of ideas and much more politics than I thought.
It seems like such a cynical culture at times. Most of the professors are great, but I don't know if I'd want to enter academia if this is a typical situation between peers. So my question is: is this really typical? Am I being unreasonable in expecting less politics between peers? Is it possible to work in this sort of atmosphere without becoming part of it?

Short answer: it really depends on where you are, and who is around. From my observation, in mathematics, as a rule of thumb, the abuse of science that you describe becomes less common (but does not disappear) the higher up in the "prestige hierarchy" one goes. Humans remains human though, and politics takes different forms :-)  Academic jobs generally have more autonomy than most "usual" jobs, which makes it easier to cope with politics which is present in both kinds of jobs.

You will need a job unless you hit a lottery jackpot tomorrow. If not in Academia, then it will be industry or government. Would you believe there is no politics in those places?

I only know of such culture in materials science where every small measurements are published.  I also know of a famous editor who wants me to cite a significant portion of his published works before accepting my paper.  I am sure to him it's the norm.

Novel content is seriously harmful to science to over-emphasize. Solid research that supports others' more novel claims is good research.

"Publish or perish" and "impostor syndrome" pressures can lead many young researchers down such a path.  Habit keeps the older ones there.

When it comes to a workplace, politics is inevitable. There are always bias in opinions, bureaucratic criteria that are bendable to some, possible hierarchical influence. These are all common in almost any workplace (at least AFAIK). Academia is no different in this case. There are people who prefer quantity over quality and some others the other way around.
At times, the level at which you could be a part of this depends. You may be able to avoid in being a part of this to some extent, but you may have to witness this nonetheless.

There is this well known quote saying something like:

Academic politics are so vicious and bitter because the stakes are so low.

Don't know who said it, I heard it in an episode of The Mentalist.
I tend to disagree, while the stakes might be low from Humanity's standpoint, at the individual level the stakes are very high: the perspective of cosy government jobs, well-paid academic positions (in many countries, professors enjoy salaries and job security that people in other branches would only dream of), etc. will bring the worst out of the best people.
The answer to your question is yes, it's common. It's increasingly common as the number of people working in academia exploded in the previous decades. But it's basically a two-gears system: there's academia of the serious, hard working and brilliant people who get the funding they deserve because of the excellent output they generate, and there's the academia of the "me too" crowd where much of what you described happens: people who try very hard to have an output that looks like the one of brilliant academics.
Here's a quote from 1963 cited in recent comment published in Nature:

Scientific eminence [is] concentrated in a very small percentage of researchers, and that the number of leading scientists [grows] much more slowly than the number of merely good ones, and that [yields to] “an even greater preponderance of manpower able to write scientific papers, but not able to write distinguished ones”

In any system where funding is attributed on subjective criteria, or bad objective ones, politics will be preponderant. In that I disagree with several other comments that say academia is no different than a commercial business. Of course it is.

"because the stakes are so low" https://en.wikipedia.org/wiki/Sayre's_law

I am very curious as to where a full professor makes between $150K and $250K a year.  This article https://en.wikipedia.org/wiki/Professors_in_the_United_States has some information on salary information.  Among all academic fields the highest median salary for full professors is listed as $136,634.  The same article lists the common range as "high 70's to low 100's; mid 100's at elite universities".  With regard to "two gears": where do the brilliant, serious hard-working people who leave academia because they can't get jobs fit in to your metaphor?

I did a bit more research (starting in July I will be a full professor, so I am very interested in full professor salaries; I'm not upset or anything like that).  Of the 114 colleges and universities in Massachusetts (your profile says you live in Boston), the median 2012-2013 faculty salary lies above $150K at eight of them.  The top four: 4. Boston College $159K, 3. Babson $173K, 2. MIT $179K, 1. Harvard $203K.

+1 for a number of reasons, but most importantly for pointing out that it's not the same in academia and industry: academia is far worse. After my Ph.D., I worked at a number of high-powered finance outfits on or near Wall Street which, by common, easy prejudice is supposed to be all cutthroat. However, it was, by and large, a collegial group effort, while in my Ph. D. I had my ideas pitched as someone else's, and knew of breathtaking politics. I only disagree that successful researchers are less likely to be egotistical: all of the above are tenured at top 5 places now (one a Nobel prospect).

@PeteL.Clark the people you mention do not fit in any of the two groups because they're not in academia anymore. I think this is a different issue. The salaries I mention are in Switzerland, where I currently reside.

Thanks for the explanation.  I think your answer as is is somewhat misleading, because (i) Switzerland has no "full professors" and (ii) faculty there are not paid in dollars, and though if you converted the exchange rate for Swiss ordinary professors into dollars you would get your figures, that ignores a lot of other effects: from what I understand, cost of living in Switzerland is very high.  According to https://www.myscience.ch/living/salary/salary_in_switzerland, the median salary for university graduates in Switzerland is well over 100K CHF.  The corresponding US figure is about $45K.

@PeteL.Clark agreed that these figures represent an exception. I removed that bit.

So my question is: is this really typical?

Whether or not this is typical depends on the field and depends on the environment. The local environment is probably the most important - the department and the university.

Am I being unreasonable in expecting less politics between peers?

I would argue that yes, you are being unreasonable.

Is it possible to work in this sort of atmosphere without becoming part of it?

Yes, it is possible.
Ultimately, one can argue that the fundamental mechanisms of academia are not unique from any other workplace. Thus, it is a business  - the inputs and outputs are just different. Also, people are involved, so politics will naturally occur. Here, though, politics kind of blends with the mechanisms of collegiality - is it due to politics that you were written into the grant, or is it because you can contribute to the project? Or is it both?
Despite these similarities, there is one striking difference between academia and other fields - a meritocracy does exist and eventually the literature will weed out the crap. This just doesn't occur on the timescale of careers usually.
The key is to do the science that aligns with your passion. This will help you keep your head above it all.
And its also important to keep in mind that you don't need to be in a top-tier position (where cut-throat politics usually occur) to do good science. Good science can happen anywhere. Fast and expensive science usually only happens at top tier places, but that doesn't mean its good.

What's worse is the attitude from what is supposed to be peers. PhD
  students who I've proposed ideas to pitching them as their own to
  their supervisors. Others acting threatened and stand-offish, leading
  to awkward social situations. There's much less free exchange of ideas
  and much more politics than I thought.

It sounds like you just got into a bad situation.  For instance, maybe your advisor assigned you to a project that actually "belongs" to one of his PhD students, and the student wants to maintain ownership of his project.  Unless your work is clearly separated from the PhD student's work (i.e. you are assigned your own independent subproblem), it's possible that the PhD student could be in danger of losing first authorship, or losing control of his project.  Sometimes advisors make these decisions without getting permission from the students, and the PhD student might not actually want an extra person helping with the project, especially if your role on the project is not clearly defined.
Before you start a new project, it's useful to get a sense of where you stand with everyone on the team, and where people stand with each other in general.  Not saying this is your fault, but you may have inadvertently crossed professional boundaries, just by being on the team.  You probably want to avoid being on those sorts of teams if possible.

This seems like really weird advice... Why wouldn't you want help on the project? And how would a master's student go about getting a sense on how "he stands" with the rest of the group before the project has started? Isn't it common practice for master's students to work on similar problems to PhD students? This seems like absolutely awful advice to be honest.

@asdfguy Well, people want their project to be theirs, and they react badly when a newcomer tries to take over for them, and essentially steals their project (this is known as "scooping" someone).  They have worked hard on their project and they don't want some master's student to render their efforts useless.

@asdfguy Getting a sense of where you stand can be difficult, but you may be able to do it by talking to the grad students involved with the project before agreeing to work on the project.  You can gauge things like how excited they are at the prospect of working with you.

I don't think any of the PhD students are working on anything remotely connected to what I'm working on so that's hopefully not what's going on in my case, but I still find it troubling that people could see it as the master's students responsibility to make sure he isn't crossing any professional boundaries. If a PhD student feels slighted and passive-aggressively takes it out on the master's student instead of taking it up with him/her directly, how could anyone ever think that the master's student is the one behaving badly?

You probably want to avoid being on those sorts of teams if possible. — I'm not sure how feasible it would be for most master's students to avoid teams the way you describe. I think your post makes a good point, though, that a master's student could be stepping on toes without even realizing it.

I wanted to pursue a career in academia because I thought it was cleaner than the corporate world. Somebody told me that academia is not free from politics either. I only learned much later how true this is.
Nothing is free from politics. It is exactly because of this that academia need people like you who are willing to stand up for what is right. Even Academia.SE is not free from politics. But at least you'll know that there are people here who care about what is right.

In academe you have more freedom than perhaps anywhere else to choose your intellectual partners. Not all professors engage in ugly behavior, and good work is a great strategy, and so many good intellectual partners are available as you move up. Some of your peers will certainly succeed through cheating and bullying, and they will be your neighbors.  Some disciplines are better at fighting this than others, and even within disciplines different tribes form around this dynamic: consider the subfields around you.  Bottom line: if you can live next to ugly behavior, even push back against it, without it hurting your own quest for understanding, you can likely be happy in an academic setting.   This is, in my own experience, more difficult in industry and government career paths, where your partners are more often picked for you.


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Relative importance of journal citations compared to classroom performance by academic field
With regard to tenure decisions how drastic are the different weight placed on journal articles compared to teaching ability in the classroom?
I know some in the STEM fields that seem narrowly focused on research prior to obtaining tenure and others in other academic fields that seem to spend very little time on research.
Is the relative weight of importance really as drastic as it appears? Or is it exaggerated by those who have a bias one way or the other?

The main differentiator is arguably not the field of study, but the school. Academics in a research university are likely evaluated largely by their research. For academics in a liberal arts college, teaching is a much more central aspect.

Note in some (non-STEM) fields, one isn't expected to publish articles, but rather books.  Sometimes the rule is basically: "one book for tenure, 2 for full professor."

You should be aware that the question and its title are rather different. In a department like mine, research and the resulting publications are very important.  Citations, on the other hand, are not particularly important. We care about what the experts in your field say about the quality of your research, not about how many people (expert or not) cite it.

It doesn't depend on the field as much as the position. Consider three faculty members, all epidemiologists (my field):

One works at a school specifically focused on Masters of Public Health degrees. Research is done at the school, but as the MPH is primarily coursework based, with a single small project at the end, most faculty have a heavy student load.
One works at a major research university in a 50% hard money position, which comes with a teaching load of one graduate level class per semester.
One works in a 100% soft money research institute that does not offer any classes, and whose students come from other departments.

Note all of these could be at the same university.
Their tenure evaluations will weight things very differently. The first will probably be judged primarily based on their teaching ability, while the last likely hasn't taught at all, and may have actively been discouraged from doing so.
Where field comes in is what kind of positions exist, and in what proportion. For example, in the liberal arts, there are a large number of positions that are teaching centric, while medical schools often have a vast number of faculty whose positions will never involve teaching.


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Can I include NIST data in my research software which lies on GitHub?
For some research software I have written, I needed some atomic data from NIST. I wanted to put that software onto GitHub (MIT license) but I am not sure if I am allowed to simply also upload the NIST dataset which I need. The NIST copyright page is not too helpful here, it only tells me how to cite the NIST dataset in a paper.
The source code has some comments in it clearly stating the origin of the data, same for a readme file. Would you consider that as enough?

In doubt, I'd contact NIST: at the bottom of this page there is a contact email.

How did you obtain the data?

@MassimoOrtolano good point, I just thought this might be an often encountered problem and a lot of researchers out there have dealt with it

@AzorAhai--hehim you can download a wide variety of datasets directly from their webpage.

@Alf If I (i've never made an account or gotten permission from NIST) could go and download the data right now, there should be no issue with you rehosting it.

Their copyright page seems fairly clear to me.  It even goes into what to do if you create derivative works based on it.  That said, best practice would be to include the download as part of the code.  Most platforms have the ability to retrieve a url, for example, if the data is available that way.  Also, note that Github is not really intended to store datasets, though it will work for that if the dataset is relatively small.  It can greatly slow down other work on the rep though.
If you're unable to include the download as part of the code, perhaps include a set of "data download instructions" in the readme.md file. That alone would be more than I'm used to seeing - many times when I've seen the code from published research, it's provided as if you already know how to get all the data yourself.

In my understanding that statement about derivative works only refers to the non-Standard Reference Data products, i.e. not if I include some Standard Reference Data - datasets - but maybe I'm misunderstanding something here. Anyways, plan was to include the dataset as a separate file (it is not large) and write clear instruction where this is from and how to obtain it.

You can have work under multiple licenses on a single repository
Typically each file would have its own copyright heading, and on your LICENSE or COPYRIGHT file you would state "Project Foobar. All files under src are copyright 2020 by Alf, available under MIT license (see file MIT-License.txt). Contents of dataset folder are made by NIST, published at https://www.nist.gov/alf's-dataset, and available under XYZ terms.".
Do note that in order to combine works under different licenses, they must be compatible. You would not be able to (legally) use, copy or distribute a work which is © by someone else that has all rights reserved, unless you get their permission to do so.

I'll probably do something along this line, after figuring out of course if the licenses are compatible.

Have you ever looked at NIST Refprop? I think they offer options to incorporate this purchase package into other software. I am not sure the specific properties you are looking for would be included though.

No, but if I understand correctly, I need to purchase the NIST Reference Fluid Thermodynamic and Transport Properties Database (REFPROP), and that is something I am not planning to do


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How to handle a situation where you are part of 2 competing projects?
I am part of 2 collaborations which are more or less competing (in a friendly way though). Since I am the only one direct connection of these two groups (apart from the topic of course) that has now put me into a somewhat strange situation:
Both collaborations are about to submit a paper to an important journal in our area. In one of papers I am actively involved in the writing process, in the other I am actively involved in correcting what has been written by a collaborator. Particularly in this journal, I have the feeling that the paper which is submitted later might be rejected as being no longer the first one - although both papers are using different approaches to get to a similar result. (Of course, I might be wrong and everything goes through smoothly).
My question now: being part of both collaborations, can I tell the other collaboration that their colleagues/competitors are about to submit a paper where I am also involved ? Or would that be ethically not OK ?

I think you've inadvertently allowed yourself to slip into a situation with serious conflict-of-interest aspects... As @Bryan Krause suggests, "side-by-side" publication would be a solution to this conflict. But, generally, as B. Krause notes, it was a bit of an error to allow yourself to get into such straits. Srsly. Even if people are friendly, you don't want to find yourself in such situations in the future.

To your question: Yes, and urgently. Such a situation might work if everybody is aware of it and OK with you sharing information. But if one paper gets rejected or later some problem is found that you obviously knew about, but didn't tell the other side, there'll be hell to pay.

Not sure if it applies to your field, but in some cases it is appropriate for researchers to publish simultaneously when they are working on something so similar at the same time (especially with a consistent finding but a different approach, like you suggest is the case here).
Some journals may consider the two papers side-by-side and publish them in sequence in the same issue, or they may be published in different journals. Typically there would be some acknowledgement in each paper of the presence of the other, or a third brief review/editorial possibly coauthored by some of the authors of each paper.
There's a great blog post that talks a bit about the process for simultaneous publications from the Vice President of Editorial at Cell Press (for those outside of biology, this covers some of the most respected journals in basic biology research): http://crosstalk.cell.com/blog/how-papers-from-different-groups-get-published-together
I'm not sure about the ethics overall, but it seems like the issue is being a part of both teams like this in the first place...you would have been aware of this way before the state of writing the actual papers. I think you certainly should have spoke up earlier in the process, at this point you may have already entered the "damage-control" phase, especially if the outcome ends up negative for either of the two groups (i.e., if they are unable to publish or end up publishing in a much lower journal).

nice idea with the side-by-side publication, I'll have to think about that.

just as an additional comment: there was actually no chance to speak up earlier. But I agree with you: as soon as one becomes aware of such a situation, one should try to sort it out.


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Is it OK to extract datasets from somebody's paper and work with it in your own papers?
Let's say David Smith has published a paper a while ago. In this paper there are some results plotted in a graph. I want to use this dataset in my own research and extend it with my own results. Unfortunately, it is not possible to contact David Smith. So I use some of tools mentioned for example in this question to extract the dataset from the plot (which, of course, might introduce some kind of small errors).
Do you consider it as OK if I now publish a paper which includes the old dataset from David Smith + my new data in a new plot? I would, of course, cite the old paper by David Smith. (I might deduce some results from the old+new data that a somewhat different that the original conclusion by David Smith.)

@Roland my doubts are about extracting the data with software-tools from their plots and do further research with it - instead of having the proper (real/raw) dataset and allowance from the original author.

@Roland I see, let my try to explain: I think my personal feeling is that using these tools to extract data feels a bit like just copying somebody's data + I might introduce errors by extracting the data which could lead to wrong conclusions about the original dataset (only on a first check, though, a through check would/should reveal that I made an error). But that issue is tackled by JayFromA's answer.

@Roland I see what you mean and I guess I was just a bit too, hmm, maybe cautious or shy but it principle everything published is something I can further use or work with I guess (with proper acknowledgement)

If you cite the original authors in your plots and when comparing results/conclusions (or simply everywhere you use their data/work) you should be fine.
Also make it clear that the data is "reverse engineered" from their graphs/plots and not the "original" data.

clearly stating that it is "reversed engineered" instead of saying "old data from Ref. [xx]", I like that idea, thanks!

Good answer. I would also like to mention that meta-analyses are doing exactly that, with lots of articles!


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Should I include visiting students in my CV
I am currently a Post-Doc in the field of physics. During the last years, a number of students from different universities (from across the world) were visiting me for short (1 week) or long (3 months) periods.
Since they came to specifically work with me, I was supervising them during that time and now I am wondering if I should include them somehow in my CV (e.g. in the section Teaching, listed as visiting students or something similar) ?

Sounds like a good idea to me, especially if the outcomes were positive.

Would you just name them in your CV in the respective section or what else would you write (e. g. specific tasks, help, collaboration)?

My idea was to name them in the respective section and then try to (very briefly) name the project.

Is this your collaboration project which was the reason for their stay/visit or is it 'just' their research/dissertation project? If you directly collaborated with them, I would put them in the CV and anem what you did (together). Otherwise, it might not be clear for a reader of your CV what this 'visiting student list' exactly means?!

@Stefan_W good point. It was actually "my" project (or projects where I had a leading positions) or simulation software I had written they were interested in. So I will incorporate that in the description, thanks (I would actually accept that as a valid answer).

Does "visiting students" mean "interns"? (If so, then this addresses @Stefan_W's issue "it might not be clear for a reader of your CV what this 'visiting student list' exactly means." )

@user2768 no - but good point, hadn't thought of "interns" - "visiting students" was referring to (mostly) PhD-students who were working on projects similar to one of mine and were looking for expertise/guidance

@Alf, although your institute has called them "visiting students," would another institute call them "interns"? Also, are the visiting students calling themselves interns? From what you've explained, they sound very much like interns. (Noting that the definition of an "intern" is very vague.)

@user2768 hmm, OK, I see, that seems to be a problem with the definition of "intern" as you said and strongly depends on the field.

Just to make it transparent for future readers that your question got a (preliminary) answer suggestion:
If you directly collaborated with them, I would put them in the cv and mention what you did (together). This helps the visiting student, because his/her name is mentioned in relation to you. It also helps you to keep track of your collaboration project and to show others (in future applications) what you did in the last years. As you said, being in contact and supervising students for a certain time can also be seen as a form of teaching. Perhaps, later you will publish with some of them papers and then, it is interesting to know that your co-author(s) might have been a former visiting student Otherwise, if you just mention their names in the CV, it might not be clear for a reader of your CV what this 'visiting student list' exactly means.


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Do you consider EPJ Web of Conference - papers as peer-reviewed papers?
I have published a few conference proceedings papers in the Journal EPJ Web of Conferences. All of them had some level of peer-review included, but not as rigorous as in a "normal" journal in my field. Although the peer-review process became more serious recently (in that journal), so far I had my corresponding papers listed as unrefereed publications.
I just needed to update my full CV and was wondering if I should include those paper in the refereed publications section, the interested reader will of course see that it is "just" a conference proceedings paper (albeit a somewhat refereed one).
I was wondering what your approach is here, do you consider such papers, i.e. "somewhat" refereed conference proceedings paper as "full" refereed publications?

Not specific to EPJ, but yes, conference paper review is different from most journal review due entirely to time constraints. And the proceedings published by EPJ have their own review processes, but are likely to be more time constrained than journal review.
Journal papers can take a long time to review, by several reviewers and  with several iterations of (hopefully) improvement. This isn't possible for conference proceedings due to the short time between the end of the call for papers and the conference itself.
So, for conference papers, one round of review with an accept/reject decision by the program committee is pretty typical.
In some fields (CS) conference proceedings are the main vehicle of new result dissemination. In others, conferences are much more informal.
But both sorts of papers are refereed by knowledgeable people in my experience.
If you want to split these for a CV as might be appropriate in Physics, consider "Journal Publications" and "Conference Proceedings" as the headings rather than making value judgements on the rigor of the two systems. Those in the field will likely know of the different review processes.

Note that there is a third option for conference paper review, called shepherding, used in the patterns community. In this system, a "shepherd" is assigned to a paper who works closely with the authors to improve the paper. The work can have several iterations over a short period, and the shepherd and authors are (obviously) known to each other. It has some of the advantages of journal review, though isn't blind, providing several feedback iterations. Shepherds are typically knowledgeable about the subject of the paper and the process itself.
Also note that special issue journal review also may have tight time constraints, similar to conference review.


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Where to upload conference posters and how to share them?
When presenting a scientific poster at a conference, I am often asked by colleagues if they can get a copy of the poster. Often, I have DIN A4 prints ready (quite hard to read...) and I am also happy to share them via email, if somebody is interested.
It would all be much easier if I could just upload the poster to some open repository where it is archived such that I just need to share a link.
Neither arXiv seems to be the right place for it, nor figshare. Is there some open repository for scientific posters which I missed so far?

I like to post them on figshare. Why not?

@DavidKetcheson so far, I only used figshare for data/results and videos (visualizing results). I've never seen someone use figshare for conference posters (you are the first one), but maybe I missed that...?

@Alf I also use figshare for posters. Now you know of two.

@Gimelist they are spreading!

I don't know of any open repository that hosts research posters. But, some conferences do upload a pdf copy of all accepted posters to their website so you can check the venue where you presented your work to see if they offer something similar.
Another option which I see all the time is uploading the poster to your personal website or the website associated with your research group or lab. These websites always have a publications link that usually includes a subsection for poster publications.

good point, a few conferences deposit indeed pdf copies of the posters on their website (an exception, though, in my community).  I like your second idea, talk my boss into providing a posters section on our website (so far, only peer-reviewed publications appear there)

I usually upload posters to my own website. Then I add a short link and a QR code to the bottom of the poster saying "Scan here for PDF of poster".

that has been exactly my approach so far. I would, however, prefer something more persistent and also something which I can recommend our new students to do (I can hardly expect them to have their own webspace)


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In an international collaboration, what can be used for a shared meetings log or electronic labbook?
I started to have more and more international collaborations recently resulting in more and more (video conference) meetings. While in some meetings, there is one guys summing up the result of the meeting and send it around to everybody via email, I do not think this is the optimal way as sometimes people share references or results and then they send it again via email to everybody.
My questions now is if you have any recommendations on what to use for a shared meetings log or a shared electronic notebook, where everybody can contribute to? Requirements would be

ability to type formulas
insert images
insert link
accessible for editing by everybody (maybe after some kind of registration)

Git repository managers (e.g. GitLab or GitHub) seem to meet your requirements. You can keep your logs either in a project's wiki page or in a markdown file (e.g. your project's readme).

@101010111100 hm, indeed, GitLab offers the possibility to manage user-restricted access (yes, GitHub does that, too, but it requires a premium account, if I am not wrong). One could also use GitLab to share pdfs (papers/references). I have never used a wiki page on one of those platforms, but I will definitely have a look into it!

This isn't really academia-specific; you can use basically any platform for writing and editing shared documents. Google Docs, whatever Microsoft's online office offering is, ShareLaTeX or Overleaf (if you prefer LaTeX), etc.

@ff524 The Microsoft online office offering is OneNote, and while it's a part of the office suite it's actually free. Quite handy for the people that don't want to pay, and for the vast majority of people in academia that have it already installed.

@VonBeche Actually I was referring to office.com which AFAIK has much more than just OneNote (all free).

@VonBeche Microsoft products are somewhat problematic: most of us (actually the vast majority) work on Linux at our institute. But, true, the web-option mentioned by user ff524 might be an option


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Transferring results of Google Scholar search to My Profile
Searching Google Scholar I find thousands of references, mostly to my poetry, but also to my articles and books.  Is there any way of transferring some of these articles, books, and poems to "My Profile" without typing each in separately? Thanks!


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How has your joint / secondary appointment in another department turned out?
I am curious about the experience of faculty who hold / have held appointments in multiple departments. Has it helped you researchwise? Any unexpected challenges?
I am thinking primarily about people in research-focused universities in science and engineering, but other perspectives are most welcome.

I'm not sure why this matters. Do you have a reason for asking? Context might help.

This is in essence a shopping question, which we don't particularly like on this forum. Try asking a more specific question.

Separately: My personal take is that dual appointments are a really bad idea for pre-tenure people and a moderately bad idea for associate professors. They are a good idea for people once they have all of their promotions out of the way.