text:
How do academics control their own biases?
As an academic, you are in the business of producing research. I know it might sound odd to call it a "business", but frankly, you get paid to do it, and most of you wouldn't do it if you didn't get paid, hence it is a business and you're selling a product (your research) to your clients (the rest of society) and you get paid a price for that product (grants and aid and donations and other types of support from governments and other institutions).
This means that there is a danger that your research output is driven by a self-serving bias. After all, the 'better' research you produce (as in, research that draws a lot of attention), the more of it you will sell and the more money you will make.
How do academics controls themselves for this bias, that may be occurring consciously or subconsciously?
One might say that peer-reviewing solves this exact problem, but I fear that all peer-reviewing accomplishes is moving the goalpost. Okay, so now the bias of the lone researcher is being controlled, but who controls the biases of the peers? After all, this bias is an industry-wide phenomenon. Your peers, the ones that review your research, have the exact same bias as you do, and are also interested in seeing your research be validated if it brings more attention to your field, a field which is obviously shared between you and your peers.
Hence the bias affects you all at the same time. Who is controlling that? Is there a 3rd party? If not, how do academics, as a group, control themselves?
Obviously, this question is more pertinent for less fact-based fields, so not for example mathematics, where if a wrong theorem is approved, it would be catastrophic and probably discovered soon enough, to the shame of all people involved. But for more experimental fields such as physics, medicine, etc., how do academics ensure that there isn't a cartel of researchers some where all (sub)consciously agreeing to promote research that advances their careers?

Are you talking about the bias of trying to do research which other people will be interested in? That sounds like a pretty good "bias" to me...

Catastrophic is a bit strong, even for math. In fact, lots of math papers contain errors that haven't affected the reputations of the authors.  It seems odd, but it is true. I originally worked in a subfield that had the reputation of every published proof having an error. They were by some very highly regarded people. Many of the proofs were cleaned up later by others. And the missing piece between the known world and a theorem often provided insight in itself. So, a bit of nuance is needed, even in math. We aren't as good at logical reasoning as we think we are.

Everything is in the end vetted by the community and by time.
Many researchers were fooled by their biases (including Galilei or Millikan who did systematic errors in their studies) and the biases were slowly uncovered by time. This is normal. Of course, a good researcher, as Feynman says, needs to take care not to fool themselves, and good researchers work hard to do so. In the end, however, it is time and the scientific community that filters out the wheat from the chaff.
One key thing to maximize your objectivity is to avoid p-hacking. Be aware what your hypothesis is before you run the experiment. Be aware of what parameters you extract from the experiment and how to factor them into your evaluation of the theoretical vs. experimental model.
Try to have at least two maximally independent ways of getting to a critical result. Understand the assumptions that got you a result.
Taking care of these various things will minimize the probability (it will never entirely go away) that you fool yourself and increase your confidence that you have done a proper job at doing good science.

The question seems to be about choosing the topic/ type of research so as to pander to grant agencies, rather than falsifying or having experimental biases. I'll focus specifically on the first.
Yes, grants and financial support do sustain research and most of us must tailor our work to have synergy with the funder. But rarely do researchers limit themselves to that focussed research. The usual tendency is to do this directed work (ie the bias in the question) so that other interesting ideas can be supported and pursued in parallel. The origin of dynamic programming and its nomenclature is a notable example of this. So while some research output is indeed directed by the interest of funding agencies, it would be wrong to conclude that all research is driven by this.
Note that the topic directed research could be biased, not its outcomes, unless there is something unethical or inadequately rigorous happening.

This is a good question, and arguably I would say research is not without bias. There are many biases that exist, and there are several fields that have actually become too bias and suffer from this cartel mentality, but that is an opinion.
One thing that you can personally do to combat your own bias is to practice being mindful about how you engage with your research and that of others. It’s very hard to remove bias from research because humans are inherently bias. This why there are fields of study dedicated to survey research and making surveys less bias.
You just need to practice good scholarship and encourage/promote it within others. That’s about all you can do to reduce bias in others aside from changing them as people.

The answer is about one specific type of bias and this seems to answer about biases in general.


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Is the new ACM 2012 taxonomy usable/in use?
I've wasted about an hour trying to figure out how I'm supposed to categorise an ACM article using the new 2012 taxonomy here, and how I'm supposed to represent those categories in my article.
On the plus side, the 2012 taxonomy has some perfectly apt categories for my paper (unlike the previous 1998 version).
On the minus side, the instructions are abysmal with respect to how it should be used, it seems to be completely incompatible with the standard TeX macros provided with standard sig-* templates, and not only do the TeX macros provided by this interactive system not work (\begin{CCSXML} and \ccsdesc), they don't even seem to even exist (at least Google turns up little if anything).
Is anyone actually using this new 2012 taxonomy and if so, is there any good guide on how to use it with a standard LaTeX sig-* template?
(Otherwise I think I'll just go back to the 1998 version ... as weird and archaic and seemingly useless as it is, at least it's a straightforward way to fill in those pointlessly mandatory category fields. Grrr.)

+1 Because I also wasted an hour on this a month ago. I ended up using the old taxonomy, though the new one was more appropriate :( Hopefully someone will know the answer!

how I'm supposed to categorise an ACM article using the new 2012 taxonomy — I don't think you are.

@JeffE, I'm not sure I follow. From the homepage: "It replaces the traditional 1998 version of the ACM Computing Classification System (CCS), which has served as the de facto standard classification system for the computing field. [...] ACM will a provide [sic.] tools to facilitate the application of 2012 CCS categories to forthcoming papers and a process to ensure that the CCS stays current and relevant."

@cabad, good to know I'm not the only one at least. I thought that I was doing something stupid or missing something obvious since presumably the ACM would have clear guidelines but it seems to be a non-trivial question as to what this 2012 taxonomy is for and how to use it. :)

The bounty will expire in 4 hours if anyone wants to post a reasonable shot at an answer :).

+1 to this.  I can't believe this is still an outstanding issue, nearly 2 years later.  By the time they start using the taxonomy, it might be as out of date as the 1998 one! ;)

If you're using sig-alternate.cls, this sample TeX file seems to have been silently updated in May 2015 to give an example of how to do this. Here's a precis:

Download sig-alternate-05-2015.cls into your local TeX tree (or temporarily into the same directory as your project)
Edit the first line of your LaTeX source to use it:
\documentclass{sig-alternate-05-2015}

Further down your LaTeX source, within the document enviroment (usually after your abstract), paste in the code that the 2012 ACM Computing Classification System gives you once you have chosen your categories, for example:
\begin{CCSXML}
<ccs2012>
...
</ccs2012>
\end{CCSXML}

\ccsdesc{Computer systems organization~Robotics}
\ccsdesc[100]{Networks~Network reliability}

Follow this with the line to print out your classification section:
\printccsdesc

And finally, add your own keywords:
\keywords{ACM proceedings; \LaTeX; text tagging}

I say this was added 'silently', because internally, the sample.tex file still says it was last updated April 2013, and it says This file should be compiled with V2.5 of "sig-alternate.cls" May 2012, whereas it actually compiles with "sig-alternate-05-2015.cls", which claims internally to have last been updated in Aug 2013, despite the date in its filename! No wonder everyone is confused.
Thanks to ayman's answer above, which has become broken, but pointed me in the right direction. (Could someone edit the broken link in ayman's answer to the sig-alternative.cls file from December 2014? --- I'm a newbie caught in the reputation catch-22 where I can't comment answers).

Thanks Bob. I guess this answer might change itself in future (esp. with all these updates and explicit dating of files), but I will accept since it's just a question of finding the most recent template from http://www.acm.org/publications/article-templates ... the rest of the procedure looks fixed. (Finally we have answers to this question!)

I've tried to follow these points, but I get the following error:
LaTeX Error: File acmcopyright.sty not found.
It's a pity that our time is wasted just like that by ACM's sloppiness.

@pms, you just need to add the acmcopyright.sty file to the directory that your paper is in. A recent version of this file seems to be here: https://www.acm.org/publications/article-templates/acmcopyright.sty/view.

Note that to get the copyright boilerplate that appeared with the previous style file on the first page of your document by default, you must also add a setcopyright command before the start of your document, e.g. \setcopyright{acmlicensed}.

Is it usable with sigplanconf.cls?

I get 404 not found for the sig-alternate-05-2015.cls download.

So it seems some rather recent documentation and code has been posted to the ACM site.
http://www.acm.org/publications/article-templates
Has all the needed code in the cls file to generate the CCS macros (so actually use that more recent sig-alternative.cls file from December 2014). And the document:
https://www.acm.org/binaries/content/assets/publications/article-templates/ccs-howto-v6-12jan2015.pdf
Discusses how to include it in LaTeX and in Word.  The SIGCHI template is being updated soon to reflect these changes as well.
For LaTeX, this document omits the code that is needed to generate visible output--it is \printccsdesc.

I get 404 not found for the HOWTO PDF.

Thanks, I updated the URL.

The only piece of official information I've been able to find regarding the status of the taxonomy is this notice at the bottom of ACM Computing Classification System toc [Retrieved 2014-07-24]:

Tools to help authors apply the 2012 CCS categories and concepts are being built. A new set of instructions will be issued in early 2013. Until then, authors please continue using the 1998 categories, following these instructions on how to classify your work: How to Classify Works Using ACM's Computing Classification System.

So it seems that the tools mentioned were long overdue already a little over a half a year ago when this question was asked. Not much of an answer, but as at the time writing Google turns up this question as one of the top results when searching for the 2012 CCS taxonomy, so I'm documenting what I was able to find out here.
The ACM Digital Library has shows both the 1998 and 2012 terms on the Citation Pages of all indexed articles, but this seems to be the result of the old scheme being mapped to the new one. I haven't seen any of the additional categories in the new taxonomy showing up.

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What is the "right" rate at which my papers should get accepted (to computer science conferences)?
In general, when submitting to first tier conferences there is a smaller chance of acceptance but also a better reward.
At one extreme, one may only submit his work to third tier conferences and get nearly all of them accepted at the first shot. Alas, especially for younger researchers, the visibility of these will be very limited and the author might not get recognition for the work at all.
On the other hand, submitting only to first-tier conferences bares a higher risk, especially for PhD candidate looking for a post-doc/position, as it may take several iterations till the paper is accepted and published.
So where should one aim to be in general? Obviously, better papers belong in higher tier conferences, but there may be a goal rate in which your papers should get accepted. If the average number of submissions before accepted is 2/paper (but not all of them are first-tier venues), should one aim higher? If it takes 3-4 submissions but papers end up in first tier venues, should we attempt less competitive venues and publish quicker?

Context: I'm a CS PhD student. My supervisor usually insist on sticking to top-tier conferences even if a paper was rejected 2-3 times. I wonder if it is better to lower the bar after a rejection or two to get my results published faster. From another student here I've heard that they usually get papers accepted in the first attempt, but most of her publications are not in a top ranked conference. What is the right balance here?

You should aim on doing quality work. Especially for PhD student, this is the most important. If you get really good results, even if for one reason or another they can't make it to TOP vanues, the quality is going to be reflected on your thesis and on the letters of recommendation. Tjis is one of the best periods of your life to do really cool research. TOP venues will veentually come.

@PsySp - obviously, it is better to do top-quality work. The question is where should I submit it to.

If you, and your advisor, believe your work is TOP-tier material, then submit there. In the worst case the work will be rejected but with some hopefully helful feedback. Then, based on that you can go on some less prestigious venue. That is good thing for (T)CS: there are many conferences all year around to submit your work.

OK, so say we submit to top tier conference and get rejected with so-so reviews. What then? Go to a lower ranked conference or wait till the next major one?

It depends on the context: if their reaction is "meh" then obviously the chances to get on a TOP conferences are being decreased dramatically and you can go on 2nd tier. If their reaction is "ok, cool =, but more work needs to be done", then do the extra work and resubmit!

@PolinaD, perhaps you can add more context or maybe an example to clarify the question a little.

I'm sure that this varies a lot by specific discipline, but my perception is that top tier publications really "count," while second tier publications generally don't count for nearly as much during evaluations (i.e. job placement, tenure review). I don't really think there is an equivalence- it's not the case that reviewers will consider two or three second tier publications to be worth one top tier publication, so it's always worth submitting good work to a top conference.
I think the distinction between top, 2nd, and 3rd tier conferences is a little misleading.
I think of top tier conferences as places that publish research that is well done, comprehensive, and broadly applicable. As a result, everyone in the discipline will at least glance at these papers. They also happen to be good papers, because only well done papers can be broadly applicable. The reverse doesn't hold though: merely being a good paper is not enough to be accepted at one of these venues.
Work sent to second tier conferences tends to be much more specific with a much narrower audience. The conferences themselves tend to be very subject-oriented, so people really interested in that specific sub-discipline can disseminate, but the results and the work aren't deep enough that the work would be interesting to someone not familiar with the specific field.
Putting that all together, consider a hiring committee that has to decide between someone with 10 top tier publications and another with 20 second tier publications. The first person has demonstrated that they can produce broadly applicable and interesting work. The second person has demonstrated that they can produce a greater volume of narrow, less general work. When it comes to academics, that first person is going to win every single time.

To a first approximation, promotion depends on top-tier publications and nothing else. If career concerns are important (and they always are) keep submitting to top-tier venues (as long as you believe the work is good), even if it takes several iterations to get in.
There's so much variability in what gets accepted that it's best not to take the outcome of any single set of reviews too seriously.  If you start to see a consensus among reviewers as to why they recommend rejection, then of course you will need to address that.  But otherwise, don't lose hope and keep submitting.
Context: I'm a social scientist.

I do not quite agree with "keep submitting". If your work is rejected more than 1 times, this means that there is a very good reason for that. Moreover, these venues have memory. You do not want people to say öh, not again this".

I'd generally disagree with that.  There have been re-review studies for CS conferences to see whether papers that were accepted would be accepted a second time by a different review team.  I do not remember the exact rate of agreement but it was surprisingly low.

So much depends on the taste of the specific reviewers.

@sessej - if you could share a link to such study it'll be great!

@PolinaD sure -- here's one: http://blog.mrtz.org/2014/12/15/the-nips-experiment.html .

@PsySp btw -- I didn't mean keep submitting to the SAME conference -- just to other top-tier outlets.

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Will I be paid a percentage of the fee that readers pay to download my article?
I am a fresh PhD student and I have a question regarding the scientific publication process.
Let's say that I have submitted a paper to a certain journal in Springer, Elsevier etc... and it has been published.
The editor will charge 31.95$ to anyone who would eventually download my article.
How much do I get from it (as the article's writer) ?

You are mistaken to assume that there are real people out there that actually buy individual articles for 31.95$ a piece.

@xLeitix Not so fast! ACM (the Association for Computing Machinery, the professional society for computer science) makes a significant fraction of its publication revenue from non-subscriber downloads of conference and journal papers from their Digital Library, at $15 per paper.

@JeffE Is there data on this? Who's the demograpics that actually does this? (and, most importantly, why?)

The only way I've ever directly made money from an article is through publication bonuses from my university.

Not exactly an answer to your question, but in Germany you can get a small one-time revenue (roughly 0.001 € per word, IIRC) from the Verwertungsgesellschaft Wort, which come from a tax on printers, photocopiers and the like. (And yes, this holds for articles published in foreign journals.)

This is the cost and profit related to the publishing process (typesetting, proofreading, archival, printing, distribution, etc.) to which you did not participate. The money you get for that paper is your salary/stipend while you were creating the contents.

You get exactly diddly squat.

@xLeitix you are mistaken to assume that out there there are people who are always affiliated to institutions which can actually pay for subscriptions to every journal. :-)

@Aubrey I am fully aware of this, but with so many papers being freely available on arXiv, ResearchGate, department web pages, and the possibility to just mail an author, paying 20-ish bucks for a single article seems like a horrible move for almost everybody in almost every case.

@CapeCode: My impression is that at least in some fields, typesetting and proofreading are entirely and exclusively done by the authors and possibly the editors of the proceedings, not the publisher.

@O.R.Mapper I'm aware of some fields where it is the case, but I think it's more an exception that the norm. Especially for subscription-based journals.

@xLeitix I agree with you, of course, and I really hope that everyone who wants access of an article never has to pay that amount of money for a PDF. But I'm not sure that that never happens. We need to work in order to make a new, better system, in which we'd never has this problem again.

How much do I get from it (as the article's writer) ?

Nothing.
Moreover, through subscription fees, your university is very possibly paying a substantial amount of money for access to your work.

And quite probably most (if not all) of the downloads are from users with institutional access to the article as well.

Although some journals will kindly allow you to download your own articles for free. Check out Science's rightslink, e.g.

@dbw I never had could imagine such benevolence! There is certainly hope for the sharing scientific community.

Just thank the journal editors that they don't charge you the "downloading fee" every time the article is accessed. I really mean it and intend to do it the next time I hear from somebody that he couldn't get my paper because it was behind a paywall though I do not believe that it'll bring the journal editors back to their senses. As to "you've been already paid for your work" and "high typesetting expenses", this is just a ridiculous nonsense invented by the publishers to keep the science community at bay and milk it easily...

You normally get nothing.
Unlike a book, where you retain the rights as author to some of the proceeds from the sales of the textbook, unless you have some very special arrangement in place with the publisher, the publisher normally keeps all of the proceeds from subscription fees.
(Note in part that very few copies of articles are sold through the publisher. That's one of the reasons why they're so expensive. In general, most people who want such an article do so through interlibrary loan agreements or by directly contacting authors.)

This doesn't make much sense, does it? I mean, from the intellectual property perspective, I don't see much difference between authoring a book and a research paper. So, why different sets of rights are used?

You will not receive any royalties from an academic publisher (for an article---books are different).  You may even need to pay to have the article published, although in many fields, the best journals are free to publish in.
You will, of course, get the benefits of exposure and possibly opportunities to network with other researchers.  But there are no financial benefits from publishing scholarly articles.

there are no financial benefits from publishing scholarly articles that's not entirely true. There are large sums of money at stake (grants, appointments, etc.) that depend on how much and where you published.

Cf. my answer to the "How much do Springer-Verlag authors make per book sold?" question:

If the Work is sold electronically as part of a Springer e-book package, Author will receive an equitable share of royalties from the income generated by Springer from the e-book package. The share formula for each individual title within the e-book package will be determined by Springer no later than April for the preceding calendar year. This amount will be paid in addition to the royalty described above and shown separately on the annual royalty statement.

The same stipulation might hold for articles, too.

This refers to how Springer calculates royalties for e-books that are downloaded via a subscription rather than sold individually (and thus don't have a clear sales price).  It doesn't apply to journal papers, because Springer doesn't pay any royalties for them, regardless of whether they are purchased individually or through a subscription.


text:
What are the consequences of refusing to grant honorary authorship to a superior?
Recently, I learned about honorary authorships in papers and publications - e.g. the head of an institute or person who secured the financial grants.
If you are in an inferior position, like a PhD student or not being the head of an institute, and you do not believe in giving credit via authorship to anyone who was not significantly involved in the studies directly; (by the way, according to some scientific boards, not even securing grants or offering the lab counts as such), can you successfully deny adding an honorary authorship for your supervisor or other superior without having to bear negative consequences for your work and later supervision?
After all, honorary authorship has a bad influence on life balance of scientists if seen on a large scale.

"or person who secured the financial grants": Given the difficulty of securing financial grants, I wouldn't underestimate this role.

Strongly related question: What should PhD students do when they are told to add authors who did not contribute to the paper (e.g., head of school, international funders)?

@Massimo Ortolano: Of course not, but according to the honorary authorship article on Wiki, many universities do not see securing grants as having contributed significantly to design, execution, analysis, and paper writing of some research...what again is considered the requirement to count as author in good science, as it seems to be stated in several scientific board guidelines.

What are "respective moral standards" and what have they got to do with  the question? It's hard to understand, because you are asking about cheating a supervisor out of authorship.

Most of the time, just add the authors. This was advice I had from a good mentor. Sure, they may not have done the requisite work, but if they think they and there's some policy that they should be added, make them happy. In the end, it's a practical choice of making friends/enemies with the higher ups.

But this simply making happy policy has huge consequences in the large picture and accumulated over a lot of universities: stress increases and life balance goes down the river...which would not have to be at all. It's simply because some scientists want to be like Einstein or celebrated like Hollywood stars as having done huge discoveries for mankind. Of course, in the end, we're all humans, but we could at least strive for better situations, which do not come it thinking is not altered and no action occur.

It depends on how much of an unethical jerk the person who wants honorary co-authorship is.  Obviously.

This sort of scenario is an example of the potential for self-immolation that serves no purpose... since unless everyone else in your situation did he same. "Standing on principle" in the face of over-whelming force is dangerous, etc., ...

@paulgarrett: "Standing on principle" is incredibly valuable sometimes - case in point, the VT research group that helped uncover the Flint, MI crisis. That said - I agree, this is a matter of picking your battles. In the grand scheme of things, adding a supervisor's name to a paper - assuming they provided something, even if it's funding (which presumably meant they also had a role in the project's conception) - is a battle not worth waging. There are wars to be fought elsewhere of far more importance.

Standing on principle: good point that it might be bad in an inferior position and when facing reality. But why is it so hard for superior scientists to be honest and admit that the significant work was all done by their humpalumpas? I couldn't live with lying to have made a scientific breakthrough or merely some usual scientific work when I was not as involved in the process as others were. I'd always know that it's the work of others and not mine.

I once had an entertaining afternoon at a panel discussion on journal name integrity pointing out that the folks at the panel were all openly talking about violating one another's principles. Ultimately, it's still a field and area of handshakes and agreements, and what one person considers reasonable, another will not. And sometimes favors will win out

Related questions:
http://academia.stackexchange.com/questions/51185/my-advisor-escalated-things-after-not-getting-a-coauthorship-he-did-not-deserve
http://academia.stackexchange.com/questions/20076/what-should-i-do-if-my-advisor-insists-on-being-first-author-in-violation-of-my
http://academia.stackexchange.com/questions/26670/authorship-issues-in-numerical-mathematics

More closely related questions:
http://academia.stackexchange.com/questions/644/when-should-a-supervisor-be-an-author/
http://academia.stackexchange.com/q/12030/81

I'm surprised this is still an issue - though I guess not as surprised as I'd hoped to be. It's rather sad that there are still people out there who demand to be credited for work they haven't done.
Some journals have clear guidance for what merits authorship. For example, pretty much all medical journals sign up to guidance from the International Committee of Medical Journal Editors (http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html#two) which requires

Substantial contributions to the conception or design of the work; or
the acquisition, analysis, or interpretation of data for the work AND

Drafting the work or revising it critically for important
intellectual content AND
Final approval of the version to be
published AND
Agreement to be accountable for all aspects of the
work in ensuring that questions related to the accuracy or integrity
of any part of the work are appropriately investigated and resolved.

(So in the example above, getting the grant money would probably count as contributions to conception or design, so warrant authorship as long as the putative author then didn't abandon the project but could meet the other three criteria; but providing space for the work e.g. in a lab or recruiting participants, on it's own wouldn't be enough)
Most journals then require a statement of what the authors did to meet these requirements which is published with the article - so in order for someone who doesn't warrant authorship to claim it they, and their 'co-authors' have to lie in print.
So in the unlikely event my head of department, or anyone else, insisted on being added as an author when I thought they didn't warrant it, I'd ask them to justify the request using the ICMJE criteria.
Of course - thats the easy bit.
If you're working in an area which doesn't work like this, you have to think about keeping on board with the community. If someone senior really thinks they deserve authorship on your paper, and you don't, you have to decide whether you're going to keep them happy.
I'd suggest you may need to find someone else to persuade them they should't be named. That may be someone superior to them in your institution, or you may need to discuss with the editor of the journal you're submitting to - who can then ask for justification of contributions should they see fit.
Fundamentally though it seems that attitudes like this may suggest something rotten in the culture of either a department, or possibly a discipline. And culture change like this will take years.

And if you're a last-year PhD student trying to get the final few publications out, paying the journal fees depends on an advisor who's primary strength was always networking and not so much research content, who now finds you "sufficiently independent" to do only basic grammar checks in manuscript revisions, and ignores your e-mail about "how should I phrase your contribution please, the journal requires it?" -- that's exactly what you do. Or, at least, what I did; kept it as vague as possible, but ultimately invented his contributions in print beyond 'space/money'. Feels bad, would do again.


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Data publication basics - where, why, how, and when should I publish my unpublished data?
Many researchers have unpublished data. Some of this data may never be published as a manuscript. But I would like to make scholarly contributions of data that I have no intent on publishing, e.g. by publishing a "data paper"
The term "data paper" may be too new to be familiar, so here is a description from the Ecological Archives website:

Data Papers are compilations and syntheses of data sets and associated
  metadata deemed to be of significant interest to the ESA membership
  and the scholarly community. Data papers are peer reviewed and are
  announced in abstract form in the appropriate print journal as a Data
  Paper. Data papers differ from review or synthesis papers published in
  other ESA journals in that data papers normally will not test or
  refine ecological theory. Data Papers can facilitate the rapid
  advancement of ecological knowledge and theory at the same time that
  they disseminate information. In addition, Ecological Archives
  provides a reward mechanism (in the form of peer-reviewed, citable
  objects) for the substantial effort required to compile and adequately
  document large data sets of ecological interest

This brings up the following questions:
What makes a good data repository?
Which data repositories provide a doi: for raw data?
Should published data be separate from articles on a CV?

When you say data, do you mean rows and columns of numbers (which is the obvious assumption) or is it all DATA pertinent to research such as equations, figures?

@dna Perhaps data papers can include descriptive statistics but not more than that.

@david do you mean something like DataOne?

@David: You need to provide a more complete description of what you're looking to publish. Is it just raw unformatted data; is it post-processed data of the type that fits an existing archive? What resources do you have available to you at your institution? Is there something field-specific already available?

@aeismail it is post-processed data but not necessarily  a standardized format. The specific field is earth science, and might be appropriate for Earth System Science, Ecological Archives, or, as suggested by abe, DataOne.

It is sad that non-reproducible results can be published at all (happes a lot in computer science).

There are a few things that I would consider when choosing a data repository:

Does it let you release your data under a license you're happy with?

Applying too restrictive a license can prevent anyone from doing anything useful with the data, so think about what you're prepared to allow. In particular, remember that most of the research done in academia could be considered "commercial" from a legal perspective. On the other hand, you may wish to choose a license that ensures you get credit for your work. You may or may not agree with them, but reading the Panton Principles will give you some idea of the issues here. Also take a look at this list of licenses written with data in mind

How easy will your data be to find?

People will only use your data if they can find it. I recommend Googling (other search engines are available) for some datasets you know of in your field and see if they come up — those repositories which are indexed by the major search engines will put you at a big advantage when it comes to attracting citations.

What repositories are well known in your field?

Your institution may have a repository which you can easily deposit in, but it won't be the first place colleagues in your field will think of to look. If there are well-established repositories I would prefer those, or make sure your data is indexed by a well-established aggregator (I know ANDS runs a national aggregator in Australia).

What does your institution allow?

In many cases, your institution will own (or otherwise have a claim to) the data you generate as part of your research, so check what your local policies are and if need be ask your supervisor, head of department, legal team, etc. This will particularly affect your choice of license.

The other parts of your question can probably be answered better by others here (or maybe it should be split into several?)

Figshare provides online hosting and a permalink to your dataset, though it does not provide a DOI. I've been posting some figures there, but not data, and I quite like the service. They allow the option of keeping the data private as well, so you can use to store the data and later release it when you're done.

Update: I think Figshare now provides DOIs http://figshare.com/faqs/#q2

If you have a website with free preprints of your work (which you probably should have), put your data (and code) there. Alternatively, I know people who use GitHub (or similar) for the purpose of (distributed) storage. This has the charm of persistence and an immediate potential of collaboration.
For a (hopefully) persistent approach to citability, DataCite looks legit. In particular, they issue DOIs and are funded by libraries and research facilities from around the globe.

I think the best place for data is in a subject-focused data repository, but in the absence of that, there are repositories such as Dryad.
Biomed Central just announced a partnership with a site called LabArchives to host data of BMC authors, including DOIs for the data and the re-use promoting CC0 license, but I don't have any experience with the site.

Sounds like it might be appropriate for Pangaea: http://www.pangaea.de/submit/


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Is it commonplace for a recruiter to ask to see an unpublished PhD thesis?
I would have thought the document and overall findings are to be a closely guarded secret until defense or publication, so you can imagine my horror that a hiring professor would ask if he can have a pdf of my dissertation. This is in the context of a job application, whilst he decides whether or not to invite me for an interview.  I have already sent them the other standard documentation that was requested in the advert.  Is his request as unorthodox as it seems to me?

Are your findings a closely guarded secret? You tell us!

Since your dissertation is supposed to built on already published results, with some exception, like industry sponsored research, it is pretty unlikely that every single page of your dissertation is highly guarded secret. Also, I can imagine good reasons to ask for a PhD thesis, e.g. if you hint expertise in your CV that otherwise not clear from your publication record.

Just to clarify, to me, the word "recruiter" suggested a recruiter from industry.  I don't think people usually use that word for potential academic employers.  (Though I think my answer would be fairly similar if an industry recruiter were involved.)

Yes, it is a strange request, because your thesis is already available from your web page, and probably arXiv as well.  Right?  (Ha ha only serious.)

Recruiter for which type of job? Unpublished in the sense that it's not been published yet? Have you completed your PhD or not?

@JeffE: Well, I think most people do wait to put their thesis on their web page or arXiv until it's actually finished.  In this case it sounds like the asker is still writing it and has not yet defended.

The thesis has not yet been submitted to the faculty. It exists as a series of documents on my lap top. It is a work in progress. Thanks for all your responses. Things seem to be working out on the job search (touch wood).

@TheWonderer Then please modify your question and replace "unpublished" with "unfinished", and "recruiter" with "potential postdoc supervisor".

In a word, yes.  It is very common for academic employers to want to know about a candidate's research in progress, and they often ask for research plans, unpublished manuscripts, reports on ongoing projects, etc.  From the employer's point of view, they want to know as much as possible about what the candidate is doing, so as to evaluate the promise of their research program and their productivity.  This is especially true for junior candidates who do not already have a large body of published work.  So a request for a draft of a PhD thesis would not be out of line.
When a candidate shares such material as part of their application, the hiring professor or committee has an ethical obligation to hold it in confidence.  They should not circulate it beyond those people within the department who are involved in the hiring decision.  Also, it would be ethically inappropriate for anyone with access to this material to exploit it for the gain of their own research program (e.g. by trying to solve the candidate's thesis problem before they do, or giving it to one of their own students).  As the candidate, you have the right to expect that this will not happen.
Of course, as a matter of practice, if you want the job, you don't have much choice but to give them what they ask.  But I wouldn't see such a request as unusual or unreasonable, and I don't think you need worry about them using it unfairly.  If you are still worried, you could send them the thesis along with a note saying "since this is work in progress, I would ask that you keep it in confidence".
Also, I would say it's an exaggeration to say a thesis should be a "closely guarded secret" or to react with "horror" to a request to share it.  It's generally prudent not to share unpublished work indiscriminately, but it's not as if it were missile launch codes.  If there is something to be gained by sharing it with someone (e.g. useful input from an expert, a potential collaborator, a job) then often that's a good idea.  It seems to be pretty common for people starting out in academia to overestimate the risks of people stealing their work: yes, there are horror stories, but in the long run, you usually have more to lose from excessive secrecy than from reasonable openness.  Paranoia is generally not a helpful trait for an academic.

"has an ethical obligation to hold it in confidence" - exactly, and if the OP doesn't trust in that, there should be no problem adding a note stating just that into your document - e.g. a footnote, or a greyed out watermark, on each page, saying something like "unpublished version - do not cite, do not circulate". (Of course, this shouldn't sound/look like specific distrust towards your prospective employer, but rather like a standard note that was routinely inserted to the document for the very purpose of handing out preliminary versions to collaborators.)

"It seems to be pretty common for people starting out in academia to overestimate the risks of people stealing their work" +100

+1: I found terrifying when researchers (and not only young researchers) hide their current projects as if you were really going to start a whole new project just to scoop them. I regularly present unpublished research sometimes even in its "embryonic stage" and I find that it is much more helpful to do this rather than hiding in your corner and not telling anyone. Also, it is a very good way to start collaborations and to have people become interested in your research.

@O.R.Mapper -Great idea

@xLeitix Those chances are much higher for an unaccomplished researcher. The story that scares me the most was when some guy republished Perelman's proof of Poincare conjecture as his own and got away with it, until the international academic community stepped in to defend Perelman's intellectual property years later. The chances are if an average young scientist's ideas are not worthy of the Field's medal, no one is going to bother to step in for him if he is scooped by a more accomplished or talented researcher.

@ArthurTarasov : It sounds to me that you have garbled the story about Perelman. Perelman's preprints were extremely terse, and there were three separate multi-year efforts by experts to go through the preprints, correcting errors and supplying all the missing details. The question is, was Perelman's proof "complete" and should he get 100% of the credit? One group was Cao and Zhu, whose paper originally contained wording that was perceived as giving themselves too much credit and not giving Perelman enough credit. Also they included some material from another expert without attribution.

(continued) The academic community quickly responded with outrage, and in the published version of Cao and Zhu's paper, they changed the wording accordingly. Anyway, even the most extreme opponent of Cao and Zhu would not say that they "republished Perelman's proof as their own," nor did they "get away with it" for years. For someone to try to "republish Perelman's proof as his own" would be like trying to steal the Mona Lisa and sell it to a pawn shop, hoping nobody notices.

It might depend on the field, but it strikes me as pretty normal to ask for the PhD thesis in the context of an academic job application.
Your PhD thesis shows the quality of your research.  Your PhD thesis shows the quality of your ability to communicate your research.  Both are essential skills in (academic) research.  Unless you already have many published papers — and it appears that you do not (or else why would it be secret?) — then your PhD thesis is the only document that can serve as evidence that you do possess those skills.
If you are worried about results leaking, you can ask for the manuscript to be treated confidentially.  If you are worried about the recruiter stealing and abusing your results, you might want to reconsider if you want to work there in the first place.

As others have said, it's not unusual.
However, to answer those talking about paranoia; at my Uni, we used to have seminars where we discussed with other PhD students different aspects of our thesis. This was done with the explicit agreement that these discussion will remain in strict confidentiality, and we will not use each other's work. However, there were no written, signed documents to ensure this.
So after one such sessions where I was explaining a central point of my thesis, one of the fellow students, who was researching an entirely different subject, was quite interested and stayed on to discuss at length my thesis. I was flattered by the attention - only to find, a few months later, that he published a book containing, basically, all of my PhD thesis. I had to completely change my thesis, and although my tutor commented on the fact that the book contained what looked like my work, there was nothing I could do. The guy who stole my work is now a lecturer at the same University.

Did you confront the thief? Did you have any way to prove your authorship (eg., via publications, preprints, witnesses,...)?

I would prefer if horror stories came with context, so people know when to be scared.  What is missing from your story is (i) how anyone can publish an academic book in "a few months," (ii) why the faculty in your department -- especially your thesis advisor and the other student's thesis advisor -- did not resolve this issue and (iii) why in the world a university would hire a former student who was accused of stealing another student's work.  You only mention a "tutor," so I'm not sure where in the world this distressing story is set.

Pete, I haven't been here a while, apologies for the late reply. To answer your questions: (i) I don't know how he did it, but yes, the book was published about 10 months after our discussion. (ii) The faculty downplayed the whole incident and didn't want any fuss. I was a foreign student, the guy is a local Brit, the reputation of the institution mattered more than what happens to a 'bloody foreigner'. (iii) See point ii. Everything was kept quiet, and someone with a published work looked great on paper. A guy with the ruthlessness to do that will presumably have a great career in academia.

I know at least one country where it's a general requirement that you send two copies of your thesis for any application for an academic position (in a particular field). Very few recruiters have the time and inclination to actually read it but that's still a requirement. Theses are also all archived (on microfiches!) and can be ordered from any university library in the country.
It's all a bit silly now because online repositories are much more practical than either copying thousands of pages or reading microfiches on a bulky machine but it underlines the fact that in principle a PhD thesis is a public document and one that (academic) recruiters might want to see.
Also, a (completed) PhD thesis is a form of publication, even if you haven't put it out in the form of a book. Depending on the field, it's not as well regarded as journal papers but it would certainly establish your priority claim in the extremely unlikely even that someone would try to publish something based on it.

Thesis archives, whether on paper, microfiche, or electronic form, contain completed and submitted theses, which are safe to divulge. The OP has, apparently, yet to defend their thesis, so the situation is rather different. If the requirement you mention in your first paragraph also holds for theses in preparation then you should really point to specific resources that state that.

@episanty That's not entirely clear to me, from the question. Either way, the requirement underlines that it is not unusual to request an applicant's thesis.

After recent experiences of my ideas stolen and authorship credit being stolen from me, I have become one of those people who overestimate risk. It is better to be safe than sorry. To help: seek advice reg. this situation with a trusted adviser/ graduate's guide/ free legal services of uni. This can also help to prepare a professional approach.
Do you have an option to ask the recruiter to sign a form / letter / email communication that the unpublished thesis will be treated as confidential, and clarifying the extent of confidentiality. This cannot be an uncommon request, if you cite examples and state your worry in an upfront manner.

Digital document signatures have the ability to authenticate possession with a timestamp... digitally sign the document, get it countersigned by a trusted timestamp authority, and then if the recruiter does try to steal it or make it public, do the world a favor by ending the thief's career before anyone else gets taken.  You don't have to get their signature on any document to have rights, the author automatically holds exclusive copyright.  A footer like OR Mapper suggested is quite enough to exercise that right.

I personally found that the much-feared phenomenon of stealing ideas is quite rare, but it does happen. More likely are scoops where someone with better visibility gets out with a very similar idea; and it does not help much to be earlier, the second discoverer may well attract most attention. Remember Stigler's law: "discoveries are never named after their discoverer". It's the general risk of being a scientist; therefore, enjoy the process of discovery and don't worry too much about due credit - if you deserve it, you won't get it - in fact, if you get it, that's when you should worry ;-)


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How does PhD admissions committee look at my old gre score after starting my Masters
I am currently an international Masters student studying at a US university and I'm in the process of applying to several computer science PhD programs in North America. I didn't have the chance to retake the GRE exam to increase my score. I'm wondering how the PhD admissions committee takes into consideration my 3-year-old GRE score... will they give it less weight given that I've already started my Masters, or will they treat it exactly as if I have just took the GRE exam?

What was your score? If it's baseline for acceptance I would retake. If it's strong I wouldn't pay attention to it.

I do not have experience from the perspective of a committee, but I believe that the general way to look at it is that the GRE scores, no matter how old they are, are simply another part of your application package, regardless of timing.
There is no difference in consideration for undergraduates if their GRE is new or from their freshman year; I would imagine that there is no difference that you took your test before your Master's.

Sorry but as soon as I read your statement "I do not have experience from the perspective of a committee" I stopped processing/believing what you wrote afterwords.


text:
What does it mean if a professor does not answer your email in time?
I recently joined a research group as a postdoc. I wrote the professor an email to ask quick but important questions including asking him when when he wanted me to start. It's been over a week and I haven't received get an answer. Other emails I've sent previously have also gone unanswered for long periods as well.
With that background, my question is: do professors sometimes (intentionally or otherwise) not respond to emails in a timely manner?

Have you seen Is it acceptable to ignore emails in academia? This seems to be a duplicate question.

I get that professors are busy, as a student that also works on campus using three different emails, I really get it. But a professor usually hands out their preferred way of contact and when they’re in their office. As well, because our emails at universitys are our main source of communication it should be checked daily. I myself happening to be dealing with a professor that only looks at emails and doesn’t usually respond. Which is maddening when you need a response for matters like needing a paper extension or you need to bring your child to class.

I wrote him an email to ask quick but important questions, like, when do you want me to start. I didn't get an answer even after a week. And similar things happened before as well.

Some professors are notoriously bad in answering emails. This does not necessarily mean anything. Don't fret about it.

So I want to ask that as a professor, sometimes will you (on purpose) to NOT answer emails in time?

I'm not a professor, but, no, this is not how I would expect an adult person (in a management position, none the less) to behave. If the professor is indeed having second thoughts about you and decided to just not answer anymore, I would say you dodged a bullet there.
However, I really think that this is unlikely. Just send a polite reminder, or propose to have a quick chat e.g., over Skype, at a time of the professor's convenience.

Would you explain how to propose to have a quick chat ? By e-mail or by phone? Or some other means? If by e-mail, how would the OP know the e-mail won't be overlooked again?

I see no other way than to do it per mail. If he consistently ignores your mail, you should start worrying.

As a professor, I will second the quick chat suggestion.  Sometimes I will spend an hour writing an email that ends up less productive than a half-hour (or even less!) conversation.  Knowing that kind of email in advance makes me more likely to put off responding to the original email.  So I am likely to respond to the follow-up with "Sure, call me at x time and we'll sort it out."

If one is deliberately ignored, it's not the right place to work at, anyway.

Unlike other professionals, academic faculty have multiple competing tasks of wildly varying natures and deadlines. Broadly divided, we need to balance:

Teaching: Two to four courses a semester with dozens, scores, or hundreds of students; a handful of TFs; and occasional irate deans and parents. One or two or three independent readings with students outside of that. Letters of recommendation. Trying to find internships and grad programs for advisees. Handling postdoc requests. Working with academic review committees. Working with course of study committees. etc. etc.
Service: Serving on several unrelated college or university committees. Serving on the steering committees of affiliated programs at the university. Having the provost scout you out for a pet committee. Running a search committee. Doing grad admissions. And this is just university service. If you do service work on your national association, then there is considerable committee work there. Not to mention doing peer reviews of journal articles, book manuscripts, grant proposals, etc. etc.
Research: And if you can find time after all that, there is your own research. Trying to keep several articles in the pipeline, tracking down an editor to listen to your book proposal, getting around to writing the conference paper you promised, etc. etc.

The way some faculty handle the multitasking is by singletasking. They only do postdoc intake work on Friday mornings, for example. Others give up and have a mailbox from hell.
In other words, things can easily get lost. While a simple questions such as yours might seem to be simple, it might require the prof to have to e-mail the department chair (who is even more busy than the average prof) for an answer, which then gets lost again.
I'd give it a week and then politely ask again. Use the same e-mail title (or reply-all to your own e-mail) so as to bump the e-mail thread back up to the top of the prof's e-mail queue.  It's important to try to keep e-mail threads together as faculty have limited brain resources and we rely on our e-mail as our offline memory extension.

Since it has been a week, I think it would be acceptable to email them again just saying that you just want to make sure that they did get your email and that you would appreciate their opinion/response/whatever regarding your questions.
Professors receive tons of emails daily, and it isn't uncommon for them to miss important ones that get buried in their email.

I know the problem very well and had to wait very long for an answer. It should not be understood as an impoliteness. Professors get a lot of emails and answering every email can be a lot of work. If they just do not have time and read the email, then they forget often to respond later.  This issue is not specific to academia.
I would first of all not write email, but call him. Another email could also be overlooked.

I disagree with both points in this answer. First, if the  mail contained rather simple questions, the probability of an answer arriving after a week approaches 0. In a busy inbox, such mails are typically either answered quickly or not at all. Secondly, I would advise against calling out of the blue and wanting to discuss organisatorial matters right then. Send a polite reminder, and let the prof decide when to answer.

Visit or call.
For a while, I used e-mail as a rough to-do list - if there was something in my inbox, it was a task - once I sent a reply, the task was done (in my mind - acting as though a reply was guaranteed). Psychologically this worked well for me, as it let me off the hook. And, this may work well as a student, if you receive only a few dozen e-mails a week, of which many will be group e-mails.
But, as everybody has said, professors get a lot of e-mail.
So I came up with a new system. As early as I could, send the briefest possible e-mail, with a succinct subject, and add it to a list. Whenever I see my advisor, or whenever the list gets a bit long, or whenever a deadline is approaching, I corner my advisor and go through the list. In most cases I find that he's seen the e-mail(s) and didn't get a chance to respond, because he gets hundreds of important emails each week.

Timely manner differs for everyone.  Also, some professors do not regularly check their email, or they may have a specific email address they use aside from their college/university address.
I have found it is usually best to ask a professor which way they prefer to be contacted, than to just send and email and expect to hear back in the same amount of time that, say, my parents would write me back.


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I think my professor misunderstood something I said and may have taken offense; what should I do?
I am following a graduate mathematics course. While in class, I noticed that my classmates notes almost sliding off her inclined desk, and I whispered to her that gravity was a bitch. I think I saw the lecturer, a woman, react to this but I am not sure. I am now worried that our lecturer thinks I called her a bitch. I have the utmost respect for her and I'd hate for her to think otherwise. How can this be fixed?

Ouch! I very rarely use swearwords, for exactly that reason. Perhaps she'll overlook it if you behave polite, non-confrontatively, and neutral-nice to her, and with good and constructive participation in class so that she may understand she wasn't the target. Don't grovel. If you distinctly notice a difference in behaviour, you may come clear to her, but some things are better solved implicitly. I am not sure it is good advice, though, some misunderstandings are difficult to resolve.

Swearing is important for at least a few social and neurological reasons. It can even be used as endearment. Maybe you can explain this to her (possibly preceded by an explanation how you weren't, in fact, demeaning your colleague)?

@101010111100 Swearing is relinquishing control. Many things would be comfortable and important doing, and people nonetheless refrain doing (so I hope) in company or else the burden to bear this is on others. Unless you are in an obviously and unambiguously friendly context, swearing always puts the cost of understanding on others. I once had to do with a colleague with very outspoken opinions who also was using swearwords a lot. You never knew whether they were swearing at you, at your argument, at their own argument or just in general. Very unpleasant.

I'd say, forget about it (easier said than done, I know). Most likely, this is a non-issue.

I talked to her today and she didn't give any indication of being insulted- thank goodness.

I think the best course of action is to explain what happened and apologize to the instructor. After that it is up to her if she is willing to accept your explanation and apology. Natural you should avoid repeating this attempt at joking in a classroom setting and save it for more informal environments.

Apologize for what, exactly?

For swearing in class, for speaking during the lecture, for giving her the impression that they were gossiping in class. There are many reasons to apologize in this case, but the main one is that it is a good way to humbly seek to redress any misunderstanding with someone, no matter if there was no intentional harm.

None of these warrants an apology, they are not inherently wrong. Qui s'excuse, s'accuse, and all that. You can show some regret if you want, but anything more would be a lie.

+1: People are so sensitive about stroking their own egos that they forget that other people have egos, too - frankly, I found that a swift apology to clarify a misunderstanding can go a long way to avoid rancour and ill will that otherwise will drag on for months. It's more often than not the right decision.

It's generally not wise to use the word "bitch" around women. If you're certain that she noticed and was likely offended, you should apologize for being too...colloquial. It's generally not wise to use any questionable terms in mixed groups.


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Is it beneficial for a student to publish their research code and data?
There are at least four benefits of releasing the code and data produced during a thesis or research project (citing textually this laboratory):

Allows to reproduce figures in the revisions of a paper
Other people who want to do research in the field can start from the current state of the art, instead of spending months trying to figure out what was exactly done in a certain paper
Makes easier to compare the method to existing ones
Increases the impact of the research

This is really cool for someone trying to develop its own study as he/she can have access to world-quality material for free. However, I have observed that this is a practice followed by well-known universities, with federal financial support, and that usually host international students. Is this practice also recommended for universities with little or no federal financial support and no grants for students?
I am curious if a student from a university like the latter would improve his/her chances to work in academia by releasing his/her material in this reproducible research modality.

An article about a computational result is advertising, not scholarship. The actual scholarship is the full software environment, code and data, that produced the result. (Buckheit & Donoho, 1995)

Yes, you should publish your code and data.  Reproducibility is part of the definition of science: if the results of your experiments or computations cannot be replicated by different people in a different location, then you're not doing science.  Far from being a mere philosophic concern, reproducible research has been a key issue in prominent controversies like climategate and cancer research clinical trials.
The person most likely to benefit from your efforts to clean up and publish your code and data is your future self.  Why?

Error is ubiquitous in scientific computing...I find that researchers quite generally forget what they have done and misrepresent their computations. (Donoho)

The first step toward working reproducibly is simply to put the code and data that is used in your published research out in the open.
You may adopt reproducible research practices for philosophical reasons, but you will soon find that they bring more direct benefits.  Because you write code and prepare data with the expectation that it will be seen by others, you'll find it much easier for yourself and your colleagues to build on past work.  New collaborations may form when others discover your work through openly released code and data.  And the code itself may be the main subject of publications in journals that have come to recognize the importance of scientific software.
More resources:

Top Ten Reasons to Not Share Your Code (and why you should anyway)
Publish your computer code: it is good enough

Thanks David. Could you please include in your answer some possibilities of PI protection? Patents can be expensive and there is a risk that they would never be used.

@JFonseca I don't know what "PI protection" refers to.  I'm also not familiar with patent law in any country; if you're planning to patent your work then you should probably get advice from someone who knows your country's patent laws.

Two selfish reasons to publish that relate to this answer: 1. It may increase how well known you and your code are; 2. If others use it, they may find bugs. That will initially be embarassing, but is better than continuing to use code and getting the wrong answers from it.

Well, my country follows the international standards defined by the WIPO, so patent's law should be similar to the ones stablished in the US. Now, I was curious about using reproducible research as a way to boost your chances to get funded, which seems something improbable unless you are already affiliated to an institution, like you seem to be. Afterall, there is no issues if government pays.

Well, my country follows the international standards defined by the WIPO, so patent's law should be similar to the ones stablished in the US. Now, I was curious about using reproducible research as a way to boost your chances to get funded, which seems something improbable if you are not affiliated to a public institution. I was hoping to see some evidence of the private sector or personally financed researchers releasing their code.

@JFonseca In the question you asked specifically about a university student.  Now you are raising a totally different question.  I think it's interesting, but you should ask it as a separate question.

Go it, thanks @DavidKetchenson. I created https://academia.stackexchange.com/questions/120497/incentives-for-independent-researchers-to-work-on-reproducible-research for that topic.

The core of scientific research is that we are open on how we came to a certain conclusion. That way we can move beyond "I am wearing a white lab-coat, so you must believe me", to "this is how I got my results, you can replicate them and see if they are robust, or you can try different approaches and we can discuss and learn how that affected the outcome". So making sure others can understand in detail how you got to your results is central to doing good research. Releasing code is an important step in that, regardless of the university you belong to.
So don't think of this as a service to others (it is nice if that also happens, but that is not the goal). It is about doing good research by documenting how you got to your results, and making that documentation available.

Thanks, @MarteenBuis, is there any standard way to determine by beforehand if a journal is fine with you if you decide to release your code on the Internet? I am asking because it may exist some conflict of interest if your code is also used to generate the figures included in the paper.

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


text:
Can I still publish a paper in a journal after it has already been assigned a DOI through Zenodo or ResearchGate?
Zenodo and ResearchGate can assign a DOI to an article. After publishing an article on Zenodo or ResearchGate with a DOI, if the article is good, will the article still be accepted for publication by peer-reviewed journals?  Assume that the journal in question allows green open access (i.e., posting of a preprint on a public site).

That depends what you mean by "publishing". Perhaps you could clarify exactly what problem you're facing that prompts this question?
(the answers to your second and third paragraphs are: (a) Yes, you can upload to all these places; and (b) whether it's the appropriate action depends on what you're trying to achieve)

Later, I want to send my article to a peer-review green journal for publication.

Is there anything against using arxiv or similar platforms? High-ranked journals are often okay with accepting papers that have been published as pre-print there. However, some journals are quite strictly against sharing work on platforms such as ResearchGate after peer-review/publication - it feels like they might decide against reviewing papers that have been uploaded to RG before submission as well.

The existence of a DOI is irrelevant to the question.

To "publish" something really just means "make it available to others". So, there are many ways to publish something: You can strive to get it accepted in the most prestigious journals of your field, or you can just put it on your website -- strictly speaking, both qualify as "publishing". Putting an article on Zenodo, ResearchGate, or arXiv is closer to the latter than the former; the fact that some of them can give you a DOI really just means that you make it easier for others to find and reference what you uploaded.
From a practical perspective, the difference between all of your options is how much vetting and endorsement the locations where you publish provide for your work. Academic journals review your article, and this provides a level of endorsement that lets others trust that what you published is useful and correct. On the other hand, putting an article on a web site or ResearchGate involves no vetting and, consequently, does not bestow on you the prestige that comes with the vetting. If you wanted to use your "publications" as part of a job application, it is this prestige you want, and consequently, putting your work on a website of your own will not be enough.

Thank you! Yes, the best way is to submit my manuscript to a peer-review journal. My question is that after putting an article on Zenodo and ResearchGate with DOI, the article will still be accepted by a peer-review green journal for publication if the article is good?

Strictly speaking, journals typically require you to assign copyright to them before publication, and that would prevent you from publishing the work in any other way. In practice, they often turn a blind eye to pre-publication on arXiv, researchgate, or your own website, even though strictly speaking you shouldn't.

You need to check with the individual journal(s) you are interested in eventually submitting to. In my experience, most have posted policies somewhere in their "instructions for authors" sections.
Most likely the presence of a DOI is completely irrelevant, but there isn't a general rule on what publishers will consider prior publication.

Thank you! Yes, I just found that Zenodo is a preprint server.


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How many math PhD spots are offered each year by the top 50 US programs?
I'm trying to estimate how many math PhD offers are awarded each year in the United States, say at the top 50 schools, if that constraint helps. (I'm interested in departments called "math," not "applied math.") For the top 50 schools, is it on the order of 500? More than that? I know programs vary greatly in size, so I'm looking only for a rough estimate of the total.
I know that the AMS releases data on the number of PhD's awarded each year, as well as the average completion rate for PhD students. But is there data showing how many PhD offers are extended each year, or at least how many students matriculate?
One reason I'm interested in this question is that I know that between 4000 and 5000 people take the GRE math subject test each year. I'm curious to what extent the top 500 scorers on this exam fill the spots at the top 50 schools, but that is a harder question to answer, because so few schools release data on their admitted students.

Those between 4000 and 5000 people taking the GRE math subject test each year may not go to top 50 US math schools. They may go to top 200 math graduate schools. They may go to math graduate schools outside the US. They may never go to math graduate school at all.

@scaaahu: yes, obviously. But most top 50 U.S. schools require the subject test, as far as I can tell. If they offer around 500 spots, I doubt they're taking a lot of people below the 90th percentile. (Not necessarily because their scores are high, but because those are the people who are most likely to have strong applications on the whole.)

I was once told that if they selected only the top Math GRE scorers, every program would be 99% Chinese.  I'm now in applied math and we don't require the subject test, so I don't know how accurate that is.

The total pool of PhD applicants accepted by the top 50 schools is more or less the set of people who end up going to the top 50 schools. Schools make a lot of offers that aren't accepted, but most of these people end up going to a different top 50 school.

At MIT, in pure math, if we used the GRE as the sole basis of admission, we'd probably only take people who scored 98% or higher. But we always admit a reasonable number of people who score below 90%, and occasionally admit people who score as low as 60%. Extrapolating, I'd guess that there are a lot of people who aren't in the top 500 GRE scorers who get offered one of the top 500 spots in U.S. math graduate schools.

@Peter Shor: Thanks for your comments. Can you tell me how many students MIT matriculates each year? Is it >20? Chicago's page says "15-20," for example.

All the information needed for this calculation is on our web page: around 110 students total, 2/3 in pure math, average time to completion of degree slightly less than 5 years. And very little attrition. So on the average 15 students per year in pure math (in practice, it fluctuates quite a bit around this mean).

@Peter Shor: Thanks. I did see those numbers, but there is no explicit information about attribution rate, so I wasn't sure by what factor to split the ~73 pure math students. Some schools come out and say directly "we admit around X students a year from a pool of Y applicants." To my mind that information is more valuable than the number of grad students enrolled.

@DavidKetcheson -- having been on our graduate committee for the past 3 years, I can say that if we only took the top scorers in the Quantitative GRE test, we'd have more Chinese, but not 99%. Maybe 50-60%. I can't speak to the Math GRE since we don't require that.

@Wolfgang: I decided not to mention Chinese students' scores on the GRE in my comments because I didn't want to compute these statistics, but my impression is that the Math GRE isn't any different from the Quantitative GRE in this respect.

If all you're interested is a ballpark number, then here is one way to estimate: At Texas A&M, the math department hires 20-25 graduate students every year. (We make about twice as many offers.) If this was representative, then the top 50 schools would hire 1000-1250 students each year.
Now, A&M is a big department (~85 tenure track faculty). Most departments will be smaller, but in the top 50, most will be at least half the size. So my best guess is that the top 50 programs together will hire ~750 students each year, plus or minus maybe 250.
(And, for comparison: Practically all of our hires have a Quantitative GRE score above 163. This coincides with about the 85th percentile.)

Thanks for these numbers. But I'm not talking about the general GRE, measured 120-170 on quant and verbal; I'd expect most top PhD math students to get a perfect score on the quant section of that. I'm referring to the GRE subject test in math.

I don't have any experience with that since we don't require our applicants to take it.


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Letters of recommendation: what information to give to a recommender
The head of our department is writing a letter of recommendation for me for MD-PhD (MSTP) programs. I have two graduate level classes with him. He is very busy and writes letters regularly for students. I want to make sure that he does not end up using a canned letter.
I will be sending him my C.V., Cover Letter, and letter of intention. What else should I provided? He knows me in a classroom setting--I have not done research in his lab.

remind him of your grades, class projects and the result of the project.  Professors usually forgot students names and performance (specially in the undergraduate level).

He knows me in a classroom setting — Unfortunately, that almost guarantees that he will write a canned "did well in class" letter.

@JeffE That's not necessarily true. I got a wonderful recommendation letter (basically sticking to David's advice) from a professor with whom I never did any research/projects together. It's all about context: I did some class projects for his classes which he only evaluated, and since he was one of the rare professors open to suggestions about his first-time subjects (he had a new subject and a subject with his completely new programme) we had a few informal after- or between-class talks about the student perception of his classes which he seemed to appreciate.

...we had a few informal after- or between-class talks... — So the professor knew you in more than a classroom setting, which meant he could actually say something substantial.  My point stands: A professor who knows you only in a classroom setting can only write about your performance in the classroom.

You won't find a better or more complete answer to this question than the one given here, by Professor David E. Keyes.  Here is the key paragraph:

Likely reference writers (for instance, well-known professors of core courses) are sought out by many well-qualified candidates. To ensure that such a writer is well primed to execute your reference efficiently, you should create a self-contained packet containing all the information the author will need to dispatch the reference in one sitting: (1) contact information for the recipient of the letter, (2) a description of the position and application closing date, (3) your own application essays and cover letter, (4) a resume, (5) relevant transcripts and scores, and (6) an explanation of the niche of the writer! It is very useful, as a reference writer, to receive a reminder along the following lines: "Professor Keyes, your letter will be the one that comments most authoritatively about my analytical ability, my promptness in completing projects, and my reasons for wanting to pursue X next fall. Remember that you gave me an A– in partial differential equations two years ago and it was your suggestion that led to my summer at Los Alamos with Y." You should provide this packet in both hard and soft copy. Writers of lots of references maintain files that may be hard or soft, or both, and you should make it easy for those writers to locate your files quickly for subsequent updating and future requests.
Some faculty write many dozens of letters of reference during peak months, and they may even ask candidates for sample text to be incorporated into letters, to ensure that they capture their niches. You should not be flustered at such a request, and should not be modest in complying. You should be aware, though, that your words will not pass directly into the delivered product; they will be used simply to get the author's juices flowing following the formulaic paragraphs of the letter.

When I agree to write a letter of recommendation for a student, I ask him/her for the information listed here, including most of what David mentioned, as well as a self-assessment of the student's strengths and weaknesses and a list of long-term career goals.

Send him information about the program and department you are applying to. Also ask him/her if they might know someone in the department you are applying to. It might be beneficial to name that contact person in the cover letter. Finally provide a deadline.

Give your letter-writer a packet containing:

A copy of your transcript (showing what courses you've taken and the grades you've gotten).
A copy of your personal statement or other essays that go with your applications.
A brag sheet, with reminders of things your letter writer might want to mention.  This might include significant acomplishments.  It should also include reminders of interactions you've had with the professor (e.g., you may remember that you suggested I study with wibbly wobbets do or don't wangle their wuckets; see my research paper, where I found that they do, but only on Tuesdays; or, you may remember that I solved two of the optional bonus problems in your class).
A list of places where you are applying, and the deadline for each.  Highlight the first deadline.


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My professor who doesn't let me use my phone to read the textbook online in while I'm in class. What should I do?
I'm currently taking a course where I acquired the textbook as an e-book. Physical copies were available too, but I find kindle-versions far more convenient as I can read it wherever, whenever, using the kindle app on my phone.
Then naturally during lectures, I'll have my phone out (on mute of course) so that I can access the book. This is no different to any other student in the hall who have their physical copy out. In fact, I am less disturbing, because when those other students need to look something up, you'll hear pages turning, while my finger is silently scrolling my phone.
And yet, my professor doesn't seem to realize the benefits of technology and bans usage of phones. I of course do not intend to follow this policy: I've paid money for my e-book and am not going to spend more money for another physical copy just to appease this tosser.
However, my question is specifically, what should I do? Should I just keep on using my phone as usual, or should I contact some authority figure immediately? I'm not really worried about what he can do (because there's not really anything he CAN do, he can't throw me out of class or anything), but I would still like to take optimal steps.

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

Are you sure the textbook is not in the university library?

It might be worth stopping by office hours or after class and just asking the professor how he would like you to proceed. "I would like to be able to use the textbook during class, but I only have a digital version and you don't allow phones in class. Is there a way I can be able to look at the textbook without having to purchase a new book?"

Sounds like an outreach to others to justify a lack of regard for the rules set in place by those who are given such authority [ie the professor] You want to talk about how it is not a distraction to have your phone out; if you are the only one with their phone out, it is likely a distraction. Furthermore, phones tend to be distractions overall in most settings these days; much more so if you other students are paying attention, and potentially "induced" to pull out their phones for non-study purposes. What should you do?  Comply with the reasonable rules that in no way infringe actual rights.

"I'll have my phone out (on mute of course) so that I can access the book. This is no different to any other student in the hall who have their physical copy out. In fact, I am less disturbing, ..." - As a student, I would find what you're doing more disturbing. I've been conditioned to tune out the sound of turning pages, but a phone screen (especially in a classroom where phones aren't allowed) now that's something that would distract me. You might not be like me, but enough students are.

As a general rule, faculty members have wide latitude to set the policies for technology use in their courses, as well as the consequences for violating such policies, if any. So long as the policies are not excessively punitive (e.g., failing a class because your phone accidentally rings once), it is unlikely that you will gain any relief from the university administration.
So this is one of those situations where both of you have the freedom to do what you wish, but that does not spare you from the potential consequences of your actions if the faculty member decides that they are inappropriate.


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Will having a recommendation letter from someone in a different subfield hurt my chances of admission to PhD programs?
I am applying to the graduate program in astronomy in US universities. In support of my application I have provided three recommendation letters.  Two are from my thesis advisors, while the remaining one is from my course instructor who works in condensed matter physics. He is well known in his field, but perhaps not in astronomy. I did very well in his course and he agreed to write a good (but not detailed) letter for me. Will this hurt my chances of admission?

Will this hurt my chances of admission? — Compared to what?  Compared to having only two rec letters, definitely not.  Compared to having a weak third letter from a third well-known astronomer, definitely not.  Compared to having a strong letter from a third well-known astronomer, possibly.

Obviously, the better your letters of recommendation are, the better they support your application package.   Impersonal, though supportive, letters may not hurt your package, but they don't help as much as fantastic letters from people who know you well.
So, not so much "hurt", but "not as much help as it could be", which some would say is equivalent to "hurt"

When you have to produce 3-4 recommendation letters, which is a lot for a PhD candidate, it is normal that some will be from slightly unrelated people (an instructor from a course that you liked, tutor, head of department, etc). It does not hurt you, since many (most?) other applicants besides you will have the same situation.