text:
What are the disadvantages of opening the source of your own science tools
I am currently finishing my PhD thesis and, as a great deal of the job was to create tools and protocoles, I am considering putting the different scripts I wrote on open source directories (such as SourceForge or GitHub).
The advantage I see for opening them is:

They will be available for everyone and can be reused by the scientific
community
They could be improved (and corrected) by others
It ensure my authorship for the different scripts (I can prove I put them there)

However, I was wondering if there is any drawback of doing so (for
  future publication, version maintenance, and so on).

I have to precise that not all the work was published yet. My field is biological science.

See also: Why don't research papers that mention custom software release the source code? at programmers.SE.

A bit related: What are risks or disadvantages in uploading to figshare or related services?.

Take a look at Top Ten Reasons to Not Share Your Code
(and why you should anyway).

The issues I have personally encountered working on this - my source code is a mixture of open source and closed source projects, depending on many factors:

You have to maintain your code. This might not be something some people care about, but for me, I dislike the idea of putting out code that doesn't run at least relatively smoothly. Which means while the custom workflow where data bounces between a Python script, a C++ program and then an R script for analysis might work for me, produce good and reproducible results and generally carry science forward, it sure as hell isn't going to see the light of day. Things need to be put into functions in case people end up using your code like a library, general messiness cleaned up, etc. That's...well...it's work.
Documentation. As with the above, I really dislike the idea of releasing something without documentation.
Lack of feedback mechanism/opportunity cost. This one is a big one for me because they are what make 1 & 2 so difficult - it's really hard to tell if someone is using my code. It feels a bit like shouting into an empty room, it has little to no impact on my career, and certainly people aren't using it to the extent that it would appear as a line-item on my CV. So I put in a lot of work that could have gone to another paper etc. purely for ideological reasons.
Sanitizing code. Releasing code into the open and not putting in things that might get you scooped means going over your code to not put in a glowing neon sign that says "Future Directions Here". You can't really have a code base that is the combination of three projects, one being written, one being tinkered with and one really only in the musing stage and open source that code without taking a risk.
Beyond that, for me, is the potential presence of private health data. So my "released" code needs to be scrubbed of any reference to anything that might be confidential, and along those same lines, now needs dummy data that will work and is validated to go along with the code because the data the code was actually written for cannot just get dumped on GitHub or whatever.

All of this is because you asked for cons. Despite this, I try to put up as much of my stuff as is possible.

Surely 1 and 2 are desirable even you are not releasing the code. Otherwise you will come back to the code a few months later with no idea how to run it.

@FaheemMitha It's a matter of degree. What's necessary for me to know what I was thinking, and for someone else to is pretty different. Similarly, I don't so much care about pretty, platform agnostic code when it's just me.

Maybe you could use C.R.A.P.L. when releasing your code @Fomite

Some disadvantages could be:

People may expect you to maintain the code. If you don't maintain it, the code may be rendered useless at some point.
You might feel forced to document the code. This is actually an advantage, but many people would not realise that ;)
You might have to work on cleaning up the code. Exactly the same point as above applies, if you ever want to re-use your code this is actually an advantage.
If people start using your code (this is not impossible), they could e-mail you and start asking questions. This takes your time. On the other hand, it also provides you the opportunity to be co-author (so hey! don't document, so people are forced to ask your help ;-)

More points are raised in the very similar question that was asked at Programmers.SE less than a month ago:
Why don't research papers that mention custom software release the source code?

I agree with cheeseman for the point 2-4. For me that points might fall into the benefit of opening the code.

I agree with both cheeseman and William. I just meant they might be perceived as disadvantages, whereas in reality, being forced to write proper code is actually an advantage (as I said in the answer)

My experience is that you do have to maintain the software, and people do ask support questions. But hey, that means: my software is successful (and if the support questions are too complex, I point them to the fact that I run a consulting business so they could buy my professional help ;-) )

Here are some objections I've heard. It's up to you to decide how relevant it is to you. This post isn't to say that I endorse all or any of them: it's just to list some of the potential disadvantages.
You might be giving away your most promising source of future funding: the exploiting and extending of those tools and protocols.
The tools and protocols are potentially your future career. You've put an awful lot of work into them. Only now, can you start getting value out of them. Giving them away, means giving away all your hard work, for others to leap ahead of you, and free-load off your development work.
You will get the aggro of users demanding more documentation, and the constant nagging of questions. And because they got the tools and protocols for free, their expectations may be even higher, and they'll feel even more entitled to more of your time, than if they'd paid for it.
Weird, I know, but from experience, many users have lower expectations of paid tools than of free tools, because with paid tools, there are well-defined boundaries of what the user gets for their money. As learnt from experience, and from behavioural economics experiments, people tend to value something more, if they've paid for it.

On the other hand, if there are papers describing those tools, you might get more citations if people use and/or extend your tools.

I can add that in practice, usually nobody is interested in my code ;)

As I commented here, it is hard to imagine someone else taking the hairball that is typical scientific research code and extending it, or even using it, without authorial assistance

(+-0) I completely agree that code and protocols are important for the future career (+1). But I beg to disagree strongly with the conclusion that you are giving away a source of future funding (-1). This can only happen if the PhD student is the owner of all the code in question, which is very often not the case. Please see my detailed answer.

Too long for a comment:
@EnergyNumbers wrote:

You might be giving away your most promising source of future funding: the exploiting and extending of those tools and protocols.

Assuming that opening the source is accompanied by a corresponding license, making the code publicly available under a FOSS license may actually do the exact opposite:
It might ensure that you can exploit and extend those tools even after you leave your current institution, thus securing a promising advantage for future funding/employment negotiations.

As a PhD student employed for doing the corresponding research by some university or research institute, you usually do not own the code you wrote. Instead, your employer has the copyright (depending on your legislation, you still may have the authorship rights, but the economic rights are your employer's).
Other people may have been involved in the development, so they have intellectual rights to the code as well.

In this situation, a FOSS license can give legal certainty that you can go on using and developing the code after you leave your current university (which is not unlikely to happen after a PhD is finished).
Of course, the license must be granted by the holders of the copyright (university, co-authors' universities, etc.). This will not happen unless you
a) bring the matter to the attention of your university (supervisor, IP office, etc.)
b) you convince them that the FOSS license is good for them as well*
However going for such a FOSS license is IMHO advantageous for both you and your university:

for you, because you can throw this piece of software into negotiations for your next job and go on using it.
for your current university, as they have a much better chance that the code is maintained so they can go on using it. It is a huge difference between e.g. people in your current group using your code and your group finding someone else to take over the maintenance of the code.

I wrote might: because you'd have this advantage without FOSS license if you are the actual copyright holder of the code.
That would be the case, if you were not paid for doing the research (but e.g. only for being teaching assistant), or you were paid by a scholarship and didn't sign a contract that transfers the copyright of the work you do during you PhD to your university, you actually own your code. So you already have all rights to deal with your code in future as you like, and granting a FOSS license to the public doesn't change this.
* In my experience, IP offices tend to see $$ as soon as you start telling them that you developed a software, but have no idea about the costs of selling the software (infrastucture and ensuring maintenance) that you can in practice avoid with FOSS licenses.

How can you grant a licence over the university's software? If you were able to grant any licence, you could just grant yourself perpetual irrevocable rights.

@EnergyNumbers: good point. I clarified that of course the university has to grant the license, but in practice the PhD student is the one who makes them do this.

"In this situation, a FOSS license can give legal certainty that you can go on using and developing the code after you leave your current university (which is not unlikely to happen after a PhD is finished)." The "not unlikely to happen" refers to leaving the university, I presume?

@FaheemMitha: yes


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Software/App for electronic research notebooks
I want to keep a research notebook for my computational "experiments". Basically, I should at least be able to write text and attach images like plots. Other nice features to have would be

linking to past experiments/pages
latex equations
uploading papers, or other urls
being able to transfer data
dating and version control
open-source tool

I am already familiar with trello and tiddlywiki. Trello is good for attaching stuff and organising tasks, but I need a notebook where I attach a plot, write stuff around it, attach another below it. It doesn't have a paper or canvas. Tiddlywiki is a little painful for attaching pics and equations, the file bloats, it seems I am keeping a blog.
What is a good, free electronic notebook tool for research/lab work?

I just saw http://springpadit.com, but I don't know how good it is. Anybody used it?

Hello, highBandWidth: Welcome to Academia.SE. As a moderator, I have to agree with Nunoxic that the question is similar to the Nonlinear Note Taking. Please indicate in which sense the question is different, or it may be better to merge or close the question.

If anything, this question is better than the nonlinear note taking one as it is more detailed with specific desired requirements.  Please keep it open.

@aeismail, the reason I asked this question was that Nonlinear Note Taking is too focused on trees and mind-map structures. Lab notebooks (the physical kind used in wet-labs etc.) are not really the same as mind maps.

@highBandWidth: Okay. Thanks for the clarification. I can agree with that assessment.

A little bit of necroposting (adding a comment as I don't have any reputation on academia site). After huge research of available tools and even after deciding to create my own software, which could satisfy me, I've found zimWiki, which has almost everything you want and I wanted too. It allows inheritance of pages, linking, attaching items (including tex, graphviz and other plugins), stores pages as Markdown txt file with folder of included files, so you can easily use it with git to have version control, or to share it any page.

People really like https://obsidian.md/  I haven't gotten into it yet, but it seemed promising

For the last month, I have been using Gitit for this purpose.  That link goes to a live demo where you can try it out.  It satisfies all your requirements:

It's a wiki, so you can easily make links between pages.
It's built on pandoc, which understands TeX and uses MathJax to render it (it technically renders a subset of TeX, but it's a pretty substantial subset)
It's actually a Git repository, so you can upload anything you want to it.  Or just put your figures out on the web (via figshare or a public Dropbox link) and link to them.
Same as 3.
Again, it's Git.
It is open source: https://github.com/jgm/gitit

As a bonus, you can put it out publicly on the web if you want (or just run it locally on your machine).  I run it on an internal server at my University and my students and post-docs use it to.  Thus it's a convenient way to share information as well.

Is there a guide on how to publish my gitit wiki on the web? Or at least, how can I backup my gitit wiki on the cloud instead of storing everything on my local machine?

@Heisenberg You can back it up on any site that hosts git repositories (e.g. Github, Bitbucket).

I just figured out that the wikidata folder is just a regular git folder. Do you know if there is a guide regarding hosting gitit online? The README mentions Apache hosting but I'm not sure how to set one up.

For uploading papers and annotating them, I use mendeley.
To organize my citations, I use citeulike which is nifty for it bibtex entry generation. I also use Jabref locally on my computer to manage my papers.
I am into numerical  simulations as well and I generally add my results to latex documents (figures and all) as I eventually need it in a latex format for my dissertation! Plus this way, I save time!
Have you tried google notebook? I haven't used it in at least 3 years so I don't quite know how good it is now.
Good luck!

Google notebook is down: Google recently stopped development on Notebook, which means it's no longer open to sign-ups by new users or being improved.

Org-mode
I use Org-mode to organize and track my research.  It is an Emacs major
mode that seems to hit most of your requirements.  The .org files are
plain text which should guard against bloat and lets you access them anywhere, even when you do not
have Emacs or Org-mode available.

linking to past experiments/pages

Org-mode has linking capability to any type of file, as well as to
specific locations in a document.

latex equations

Org-mode has support not only for LaTeX equations but for a number of
programming languages via org-babel.  You can include the code blocks
inside your .org file.

uploading papers, or other URLs.

Because it is only a text file, this sort of behavior can be
accomplished through the linking mechanism.  The links
can be to other documents/papers on your machine or URLs.  Visiting a
URL in Org-mode will open your browser to the requested link.

being able to transfer data.

I am unsure what you are looking for here.  Org-mode has a nice
built-in table editor with automatic column width adjustment and some
spreadsheet behavior.  If you do not want the actual data in the .org
file, you can always link to do the data. If you are looking to import
data into the file directly, Org-mode has a function org-table-import that
will parse TAB or whitespace separated data into an Org table.

dating and version control

I use Org-mode to track my time spent on various research items.  You
can set the headings in Org-mode to behave like multi-state TODO lists
and assign time to them.  Most headings start as TODO, switch to
STARTED when I clock in on them, and then I can update them to DONE
when I am finished.  It can also generate reports based on your tracked time.  For example, I use a built-in report for the last week to help generate weekly research updates.
I handle my version control and distribution
through Dropbox, but since the files are plain text any version
control system you are comfortable with should work fine.

open-source tool

Org-mode is open source.
Org-mode also can be set to display inline images, so even though the
actual .org file stays in plain text for VCS, when you open the file
in Org-mode you can view the images, and comment on them accordingly.
While the .org files themselves are plain text, Org-mode has a number
of export options, including LaTeX, PDF, HTML, DocBook, OpenDocument
and others.  So if you want to turn your research notebook into
something more visually appealing than a plain text file, there are
many options.  I would recommend this paper for a good description of what Org-mode can do in a research environment.
The downside is that it is a mode for Emacs. If you are not already
using Emacs it has a steep learning curve and can require extensive
customization to get things running exactly the way you want.
Org-mode and AUCTeX (the Emacs LaTeX mode) are the reasons I spent the
time to learn to work with Emacs and I have not been disappointed.
However, if you are looking to get something up and running quickly
(and are not already familiar with Emacs) it may not be your best
option.

Check out GitHub hosted blogs using what's called "jekyll":
-http://jekyllrb.com/
-https://github.com/mojombo/jekyll (see the wiki tab for example sites)
-Easy way to start: use jekyll bootstrap or octopress
Jekyll is just a bunch of code that makes it easy to have stuff that you have on blogs/lab notebooks: tags, pagination, etc.
Some cool things are that its free, open source, versioned, handles images/papers/etc, can integrate comments (I use Disqus).
It does require a bit of a learning curve over other blog platforms, but its well worth it.

The good thing about jekyll is that you can add files and they can go into version control along with your text/notes. The bad(?) thing is that unlike a lab notebook, you can't drag and drop images and visually mark/annotate stuff.

I personally use VoodooPad, which is basically a personal wiki, in conjunction with LaTeXiT for latex equations. I've found it to work very well; you can store many things in it, including papers. It's all text-based so you can back up using Git or whatever you like. They have a free version. Not open source.
I'm surprised nobody's mentioned Evernote. They claim you can put anything at all in it, and from what I've seen, that's true. Backup to Evernote cloud. Free, not open source.

It sounds like you're looking for something like http://figshare.com
It's part of Digital Science, which is part of the same family of companies as Nature Publishing, but I know the guy who runs it and I think he's really sharp & going about things the right way.

figshare seems a like a place to host individual files, whether images, pdfs or datasets. Do people actually use it to keep daily records and the like?

source: Stack Exchange

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What is a "full-time teaching faculty" (and does advising count)?
Ed Tufte offers a discount to his seminars for "full-time teaching faculty" (as well as full-time students).
Does "full-time teaching" exclude full-time faculty who spend part time doing research? Does advising count as teaching?

Update
I contacted the organizer and they clarified that "full-time teaching" excludes most "research" faculty; it is intended for faculty whose primary job is to teach, not research faculty who also teach.

You'd have to ask him to know for sure, but I would expect "full-time teaching faculty" to refer to full-time faculty whose duties include a substantial amount of teaching.  It would exclude adjunct professors and other part-time faculty, and would also exclude faculty who never or rarely teach.  I expect that very few college or university faculty positions literally involve teaching "full-time".

I don't think there is a single definition. The website refers to

Full-time students not currently working, and full-time teaching
  faculty only

I think in this case, it means people who do not have jobs outside the university, but it may exclude people who have a portion of their salary paid by grants (e.g., post docs). The best thing to do is to ask.

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What should a progress report contain?
What are the key components of a progress report? There are no official guidelines from the funding agency; all I have is a set of project objectives listed in the original proposal and a target length: three pages.
I am at the stage of putting together a draft for the PI, and I would like to due my due-diligence (get some basic guidelines here) before asking the PI for further input.
Here are some of my questions:

What sections should it include?
Are there any essential "key concepts" to include?
Is it acceptable to cut and paste from the proposal?
Should I include figures and graphs from unpublished findings?
How would the writing style compare / contrast to a proposal? To a research paper?

Finally, is there a good resource that provides a comprehensive (if brief) overview of writing progress reports? I have a few books on scientific writing, but none specifically adress progress reports.

Have you asked your PI for copies of old progress reports. The answers you get here will be "correct", but they may not be what your PI is looking for.

Good engineering practice suggests:

An executive overview: a couple of sentences (3 lines) which states either "The objectives for the period have been reached." or "The objectives have not been reached, because ..."; then "No obstacle in the way to the next objectives." Or "Possible obstacle are ....; contingency plan is ....".
A summary: what were the objectives for the period; then for each objective what has been done towards that objective. A little reuse of figures/graphs here is acceptable.
a main results section, as space allows: here you select one or two "main achievements" from the previous reporting period, and you give more details about that, with possibly references to external reports / draft papers / additional materials that the report reviewer can go analyse if they are interested.
an optional  obstacles & contingency section: if the executive summary lists problems, here you details what these problems are (either the obstacles in the previous period, or the foreseen obstacles in the next period, or both). Also detail your planned contingency actions.
a report of effort spent: here you detail where your budget (and man-hours of work) was allocated to each objective/task.

Also, don't make it too long. It's extremely important that the reviewers of your project can get an overall impression of the progress in a very short time. (they will typically have many projects to evaluate in a short time)

I would also add: deviations from the work plan and explain why these deviations were made. Also note any planned future deviations. These are generally approved if reasonable, and it's best to make them explicit.


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How to handle not having my PhD advisor as a reference?
I received my PhD in 2009 and my adviser will not provide a good recommendation for me. This is mostly because we have fundamentally different approaches to science, and in retrospect I see that I could have avoided a breakdown in our relationship if I had been more deferential.
At this point, I leave his name off of my list of references, but I suspect that a diligent potential employer might call him anyway. I would be willing to discuss any concerns that were brought up in such a call - indeed I think that doing so will help me to find a good fit in a new position - but I do not know if I should, or how to state this fact in my job applications.
I am currently finishing my post doc, and one recommendation has been to take another post-doc so that I at least have two supportive references from postdoc advisers - and that the additional publications will place less weight on recommendations. Still, others have told me that not having a good reference from my adviser is a kiss of death.
How can I most effectively handle this situation?

Long term, what is your career goal? Are you aiming for a tenure-track academic position, considering industry?

@Amy I am mostly interested in doing research in industry, a government agency / national lab, or an NGO.

Do note that industry positions are much less likely to contact your references, for a number of reasons. This is more of a problem for your academic future than your industry one.

@CharlesMorisset one senior scientist on my committee has served as a valuable reference, but my current work is outside within the scope of his expertise.

@eykanal "Do note that industry positions are much less likely to contact your references" - that has not been true in my experience, at all

@Amy - This has very much been my experience, but I'm fairly inexperienced here. This is something which interests me a lot... would you mind discussing this in chat?

Is there another committee member who you did have a good relationship with?  A recommendation from him or her could help a lot.

I've personally seen a few careers survive this exact problem (caveat: I don't necessarily see the ones that don't), but it isn't easy.
The best way to surmount this problem is to be referred into a job in an industry/government/NGO lab - and have someone within the organization pulling for you. If you're doing an academic post-doc right now, that's fine, but you need to start connecting to people who work in the kinds of places you want to work. If you do another post-doc, do one for a company or a government lab. If you've got someone who can pull you into the fold at a company or lab, you've got no issue at all.
Here's my advice if you are sending out cold-call applications:
The issue won't come up in the application stage (don't mention anything negative about your experience in your cover letter, or your application will get trashed). The trick will be how to handle yourself during the interview stage.
You say here:

"in retrospect I see that I could have avoided a breakdown in our
  relationship if I had been more deferential."

You're going to need a much better story than that. Because you are going to have to explain it at some point (probably when someone asks why you haven't listed your old PI as a reference), and that line will throw up red flags about your ability to handle being managed. You'll have to be prepared to talk about it in some detail, but focus everything on what you learned from it. How do you handle conflict better now? Have recent examples ready of your excellent interpersonal skills.
Avoid talking about this problem for more than a few minutes in an interview, but don't hide the fact that you've have this issue in the past. Employers will call your references, and chances are good that it will come up. Even if one of your references mentions it with you in the best possible light, if it's the first time the employer has heard of it they will feel like you've withheld information. While companies will generally not call someone you haven't listed as a reference, they will get in touch with everyone they know who may have also worked for your old boss, gotten a degree from your old department, collaborated with your old group. This may be an issue if your field of study is small. If you've changed your research focus somewhat since then, this is less likely to happen.
You can overcome this, but BE PREPARED. And once you get your first non-postdoc job, it'll all be downhill from there.

thank you for this is a very useful answer and encouragement. For the record, I never would consider using the quoted phrase in an interview. Here I used it to briefly paint the nature of our relationship. Indeed, I agree with many of my advisers observations, although we interpret these observations differently (e.g., either as a strength or a weakness). My current work demonstrates the strengths of my approach (without necessarily dismissing, and often embracing, his approach).

Re-reading it, my reaction to how you phrased your question does sound rather harsh. But believe me, it's only because I have heard people say truly ridiculous things in interviews that aren't too far off this! I think if you can tell a story like "Hey, he was wrong about a lot of stuff, but I've learned since then he WAS right about this one thing..." that's a good spin.

I don't understand why people don't expose their jerk advisor in public! I am going through a similar situation right now and I am going to expose him. It is our job to save hardworking PhD aspirants from these academic black-holes.

Here in Germany, this wouldn't be a problem, as the PhD adviser is normally excluded from providing references for hiring processes in academia, since it's assumed the advisor would support the student.
However, while there is reason to be concerned about your advisor not giving you a good letter of recommendation, all is not lost. Since this is not your previous position (you're coming from a postdoc), the PhD advisor's weight will not be as significant. It's still important, and you better have a very good "elevator speech" explanation why he might not support you. But the fact that you have a postdoctoral advisor means that you do have some credentials; if he can write a strong letter in support, it might further give credence to the idea that your there was just dysfunction between you and your PhD advisor.

"Here in Germany, this wouldn't be a problem, as the PhD adviser is normally excluded from the decision-making process in academia, since it's assumed the advisor would support the student" is wrong. Especially in the German academical system, it is exactly the opposite of what you stated.

@GennaroTedesco: A Doktorvater or Doktormutter cannot normally be used as a reference for a faculty hiring situation in Germany.

Well, that seems to be in discordance to most cases I have seen. Where have you taken such information from? :o

From the hiring processes I've participated in, both as the candidate and as a member of the committee itself.

There are some good answers here. I would like to add that this happened to me also. For a long time, I was also apprehensive and worried about prospective employers noticing that I don't list my advisor as reference, how to defend myself in interviews etc. but then I realized the best solution is to be upfront about it. When you are hiding something, people think you are guilty vs. when you are upfront about it - people tend to sympathize, plus most importantly you have no fear.

Falling out with your supervisor is bad, but it's not insurmountable so long as there are other people who like your work and will recommend you.  Remember: even if your former supervisor is the leader of their field, there will always be some people that disagree with them!
In the UK you can only list two references anyway, so your postdoctoral supervisor and another committee member other than your supervisor would probably be fine.
The main issue is actually the interview.  You need to be sure you have a good understanding of where any of your professional relationships have broken down and how you would address similar situations in the future.  This may be too scary, but one good person to discuss this with and get ideas from is your former supervisor!  Even if you know you will never use them as a reference, both of you will be in the same field for much of your remaining careers, so it's worth burying the hatchet if possible and finding a new, more adult relationship.  Students often think their supervisors feel more strongly about them than they do, since students have only one supervisor and obsess about that relationship, but supervisors have many students and other responsibilities and basically just need everything to go as smoothly as possible.
If communication really is no longer possible, it still isn't necessarily the end of your career, but if communication is possible that would be my advice.

Great advise! That was my first idea too. Are all the bridges really burnt?

I don't think any of my own bridges are burned, but I wasn't writing about me, I guess I'm not sure what your question is? I did switch supervisors during my PhD though.

I also had a falling out with my PhD supervisor but managed to secure a good postdoctoral position in spite of it (I'm told the letter of reference provided by my PhD supervisor was "very concise", but I was lucky that my skillset was rare and urgently needed by the group I joined).
When applying for positions at the end of my postdoc, I did not use my PhD supervisor as a referee, but instead used my postdoctoral advisor and two other senior academics with whom I had worked during my postdoc. My postdoctotal supervisor said that it might look odd not to have my PhD supervisor as a referee, but in fact, it wasn't a problem. It did help that my postdoc work was very collaborative, so there were several people who knew me and my work very well and were prepared to speak well of me. If your postdoc has been shoter (mine was a 3 year position) or if you have not been able to develop collaborations with other academics during your postdoc, it may well be that another postdoctoral position would help. If your PhD supervisor is well known and well regarded, it might also count against you if you did not get on (in my case, my PhD supervisor was obscure and was thought odd by most of those who knew him). Regardless of all these considerations, if I were you, I would apply to both faculty positions and attractive postdoctoral positions, and see how you go in practise.


text:
How can I provide a great external evaluaton of a faculty member's promotion and tenure case?
I recently received an email asking if I would be willing to evaluate a colleague's application for promotion and tenure. We are both at R1 universities in the US. According to the guidelines, I am qualified to serve as an external evaluator even though I am neither tenured nor in a tenure-track position. However, this means that I have limited familiarity with the process.
I am inclined to accept and support the case, but would like to know:

What is typically involved in such a review? How much reading and writing? Can I expect to do this in a single day?
What makes a great (great = valuable to the committee) evaluation?

Before spending the time on the review, you might want to make sure your colleague's institution is aware of the nature of your position.  There is often a requirement that external evaluators already have at least the rank for which the candidate is being considered (and have tenure for tenure cases).  It's possible that their asking you represents an oversight, and they'll throw out your letter once they realize that you are not tenure-track.

@MarkMeckes I've also heard that some places ask for a junior letter, usually from someone the candidate has mentored. But definitely check.

@MarkMeckes thanks for pointing that out - I'll check with the dept head. A quick review of the institution's guidelines indicates that evaluations can be from scientists with equal or higher rank or equivalent experience; I received a  promotion last year that could be interpreted as equivalent to tenure.

"Equivalent to tenure" is open to interpretation, especially at an R1. It would be best to check with the person who asked you, whether the candidate or otherwise. Did the candidate mentor you? That might make a difference in an answer.

@Buffy the candidate did not mentor me. I've updated the question to indicate that I am qualified to serve as an evaluator - the suggestion to check is good and I will do so, but for the purposes of this forum I think that it will be useful to have an answer to this question since it is difficult to find guidance on Google.

For context: I’m in math. Take this advice with a grain of salt if you’re in a discipline with different norms.
A good (meaning useful) letter is typically around 2-3 pages long, although I have seen letters as short as 1 page (not very useful) and as long as 5 pages (useful, but not in proportion to its length and tedious to read).
At least 85-90% of the letter’s length will be devoted to discussing the candidate’s research. It’s appropriate to comment briefly about other aspects of their work such as teaching, service, organizational work, outreach etc, to the extent that you feel such feedback would be helpful, or to the extent you were explicitly asked to discuss those things. Unless you were explicitly asked about them, it’s also appropriate not to discuss anything other than research.
For letters I have written, I would estimate that I spent around 4-8 hours in total doing the review. That time is spread out over several days, which I feel is important to make sure the review is thoughtful and I have time to weigh my words carefully and make sure I am willing to commit to the end result. I am usually familiar with only a part of the candidate’s work, so I spend a good amount of time getting up to speed on their full body of work and trying to estimate its significance. But I think it probably wouldn’t make sense for me to agree to do a review if I felt like I needed more than a day’s work to get to a point where I can meaningfully comment on the significance of their work.
In the letter I usually include both some general comments and at least a few paragraphs on each of 2-3 specific results and papers I am more intimately familiar with. My suggestion is to aim for a good balance between the general and the specific - the people reading the letter need a bit of both.
It’s okay to use some technical language, but don’t overdo it - many of the readers will not be experts in the specific area the candidate is working on. For the benefit of those non-experts, it’s helpful to include language that manages to convey how important and influential the candidate’s work has been without getting into a technical discussion. To some extent you can achieve this by relying on “sociological” data such as how prestigious and well-regarded the journals the candidate publishes in (or conferences they lecture at, etc) are, but try not to put too much emphasis on such things or you will risk coming across as a shallow person who only cares about prestige, and your feedback may be discounted. (Also, as JeffE said in a comment, such sociological indicators of prestige can often be estimated by non-experts directly, so your discussing them is potentially not as helpful as a more expert/technical commentary. But to a limited extent, I think it is appropriate and potentially helpful to comment on prestige.)
Good luck! Writing this sort of letter is a big responsibility, but also a very valuable service. It speaks well of your reputation that you were asked to do it.

"risk coming across as a shallow person who only cares about prestige" The person reading the letter might care a lot about prestige - increasing prestige might be their job.

@AnonymousPhysicist “increasing prestige might be their job” No, no one has the job of increasing prestige. Perhaps you mean that their job is to increase the level of excellence of their department, which of course would lead to increased prestige, but that would be a side effect not the main goal. Anyway, I’m not sure I understand your point here. The person reading the letter could be any number of things (evil, stupid, misguided etc) but that’s not something that should concern OP, and doesn’t affect any of the suggestions I made in my answer.

There are typically three things evaluated for tenure: Research, Teaching, and Service. The importance of each depends on the institution, but at an R1 you can guess that Research as evidenced by quality publication is by far the most important. At small colleges it would likely be Teaching first, but not necessarily. But no candidate can afford to not have some evidence in each of the three areas. For some, a book (or three) might be evidence of Service, or of Teaching. Only a seminal book would probably count much in the research area.
In many ways the quality of a publication record is best measured by how much the individual has influenced other researchers in the field in question. How often have they been cited, for example, or how much work has been done to extend the work of this candidate. In other words, how central is this person to the current work of the field. For a mid-career academic, writing a lot of papers may be necessary, but not sufficient.
The kind of person who the institution really wants to tenure is the kind of person who they really don't want to lose. For an R1, think of the following in addition to the publication record. Does the candidate properly mentor grad students? Does he/she hold advanced seminars or run labs? Does he/she bring in exceptional visitors to lecture or talk? What have the advisees of this person gone on to accomplish? Does the person mentor junior faculty effectively?
In some fields, such as CS, in which conferences are important, is the candidate regularly represented? Does he/she participate in conference committees? That can be evidence of service, but also of having a central place in the research community.
At some institutions, grant funding outweighs a lot of other things. One wants to say "outweighs everything" but that seems a bit cynical. But if a prof can draw enough grant money to fund grad students it will be hard for the institution to let them go.
Another factor, not usually formally weighed in, is how collegial is the person. Is the other faculty happy to share the coffee room with them? Note that it is the more senior members of the faculty who are going to be making the decision at most places.
At many universities the candidate creates a dossier for examination by the tenure committee. The dossier may be used to a greater or lesser extent to guide the discussions. But the candidate gets to make their personal "case" for tenure. If you have an idea what they want to communicate and accomplish in the dossier, it might be helpful to both support that but also to supplement it. Sometimes it is hard for a person to say good things about themselves and others can do so more easily. I once mentored a candidate who couldn't bring himself to point out how great he was.
Some places will even formalize the mentoring process for a candidate. Ideally this starts a couple of years before the tenure decision when the person still has a chance to enhance their record in appropriate ways. I've mentored other people (for promotion, not tenure) who refused all advice and didn't advance.
The time to do such a recommendation can vary widely depending on how well you know the candidate and his/her position in the field. If you have a lot of personal knowledge and work in the same field it might go quickly, but I doubt that a day is sufficient. I would want a week, actually, but might do better in some situations. I put an important recommendation together (for an award, not tenure) in a few days. Part of that was just thinking about presentation, so wasn't full time work, but the ideas needed a bit of time to settle and mature.
It can also vary depending on just how important your recommendation is. If it is expected that your support is vital, then it naturally takes more work if you want to be helpful. But if you are just a minor commentator and others will bear the major weight, then it can be quicker.
But, I wouldn't do it unless I actually wanted to do it. Just repeating things you can easily find (Google) will be less than helpful. If you have no personal knowledge, you aren't the right person.

This answer is missing the most significant bit.  Especially at R1 institutions, promotions and tenure committees want an expert evaluation of the quality (depth, novelty, visibility, relevance, impact, etc.) of the candidate's research.
Not merely the amount of research, and not merely the prestige of the research venues —both of which the committee can judge for themselves—but the quality of the work itself—which is best judged by experts in the field.  This expert research evaluation is the main purpose of tenure letters.

I agree with JeffE. I don't think this sufficiently addresses the question.

@Buffy In addition to the comments above, I was also hoping to hear something about the level of commitment and content: How much time will it take? How many publications will I need to read? How much googling? How much text would I write?

@Abe, I can't judge the time commitment as I don't know how well you know the candidate's record. A day sounds very optimistic. Gather the data, think about the issues, think about what you want to say, write it, review it.

@Abe, That depends on a lot of things. Who asked you to do this? The candidate or another? Are you a major commenter or a supplemental one? It sounds like you don't know the candidate's record very well and you need to know enough to be honest. Again, it is a judgement call. The less you know, the more you need to know. I think the most important thing is that you have an understanding of the place of the candidate in the research spectrum. If you have no idea of that you might need to do a lot of work. What you know is better than what you've heard, of course.

@Abe, your questions seem to imply that this was imposed on you and is a burden. If so, you may not be the right person to do it.

@Buffy answers to your questions ...  dept. chair asked me; I am one of 6-8 external evaluators; I know the candidates work and use it in my own. The reason I would like details about the amount of work is so that I can evaluate the commitment before I agree to it. It seems that it could be an opportunity to contribute and learn similar to reviewing a paper or serving on a grant review panel. I just feel that I need to understand what is required to produce a quality review before accepting the invitation.

@Buffy ps Was my interest in quantifying the time commitment that came across as being a burden? Even then, how would seeing this as a burden (as opposed to service) indicate that I am not the right person to do it?

I suggest that you comment only on things you actually know about. If the candidate's work was important to your own say that and give some specificity to it - which work, how helpful. Don't try to comment on things you don't know first hand. If you see it as a burden rather than an opportunity then you aren't as likely do to a good enough job of it. It was the third comment in this (too long) stream that made it sound to me like you thought it just a job.

@Buffy I am a little confused by several of your questions to Abe. Does the candidate ever request their own P&T letters? I thought requesting letters was always the job of the chair of the P&T committee. Also, how is he supposed to know if he is a major or supplemental commenter?

@Dawn, It is possible for people to seek support on their own in some places. I tried to give a comprehensive answer for the process as a whole, not just for R1, given that these questions and answers are supposed to be general enough that a future visitor with slightly different concerns can benefit from them. I don't imply that he will know his position in the hierarchy of reviewers but might, and might be able to infer it from various clues. Sorry that my answer was so badly received.

@Dawn, I will guess that in a lot of places (most?), while the invitation to comment comes from the chair, the candidate provides a list of suggested reviewers to the tenure committee or department head. This is to avoid the problem of random commenters with no connection to the candidate's work. So, the candidate is in a position to know, even if the invitation, formally, came from another.

My understanding is that there is almost always two lists, one from the candidate and one from the apartment. The P and T committee would take some from each list to request the letters. Perhaps that is not the case in all places. The candidate would not know who has been asked and their relative importance to the committee.

@Buffy thanks for your updates - your answer now better addresses my question.

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


text:
Beginning PhD in related field without subject area expertise, will that be a problem?
I just finished an undergraduate degree in psychology, with a focus in biological sciences and pre-medicine courses. In looking at my options for graduate school, I've taken an interest in biomedical engineering; tissue engineering, medical devices, medical imaging, etc. My biology is pretty solid, but I'm not much of an engineer, aside from a few math courses. My question is, are students entering a PhD program typically very well-versed in the field, or is there a lot of "learning on the job"?

While shan23's answer is good, it is also somewhat incomplete. There are a few things to watch out for when you're coming in to a field from another department:

You will need to keep in mind the qualifying procedures for your new department. Will they expect you to pass exams in undergraduate coursework in the new discipline? If so, then you'll need to do a lot more "catch-up" work early on to make up for the potential shortfall.
Unless the new area is an interdisciplinary one—such as biomedical engineering—they're probably going to want to see some track record in the area. You're going to find it a lot easier to move into biomedical engineering from mechanical engineering than from economics.
You may find it helpful to try to find a position as a lab assistant or something similar to this in the new field before you try to start the graduate coursework. However, this is by no means required. (But it would help to prove the "dedication" aspect, which is what you'd need to convince a graduate school admissions committee about in order to have a successful application).

+1 for the idea in your second point. In BioEngineering, many students are able to successfully enter the field from a very wide range of backgrounds (comp sci, math, neurosci, bio, others), because it's such a diverse field. Students entering less interdisciplinary fields would have much more difficulty.

I had asked the same question related to CS in TCS.SE (found here) - from that, I'm summarizing the answers I got w.r.t your field:

Before grad school is a very early stage to change fields. Many people shift then. It's acceptable and expected. In your application, explain your changing fields (so the readers understand why the letter writers are not from psychology, why you took lots of biology courses, etc)
If you have research experience (especially if there's some angle towards biological subjects in them), it still counts for you, even if it's in a different field
If you have good grades, it still counts for you, even if they are for courses from a different field.
Admissions committees are generally looking for "strong" students where "strong" is largely defined via prior research experience. i.e. they especially want to know if you've had the experience of doing research, were successful at it and have a good idea if this is something you really want. The letters are important as experienced researchers' evaluation of your research ability and potential and grades give some indication of overall academic aptitude. Thus, if you have strong letters from your supervisors, it still counts for you, even if they are from a different field (strong = from a professor who knows you well and has great things to say about you).


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Advisor asking me to work on research not covered by my grant
I have a rather difficult quandary. I'm a first-year student, and I joined my lab group to work on a clinical psychiatry/neuroscience grant. I've been making slow progress towards familiarizing myself with the grant. However, my advisor (actually, one of my two-advisors... they both run the lab together) has been having me work on a separate project of his, completely unrelated to my work. From what I can tell, this project would take a few months to work out, and the result would be my co-authoring on a small paper with another graduate student in the lab.
My worry is, I receive a stipend from the university every month, and that stipend is paid for my the psych/neurosci grant. By working on the second project, I have the feeling that I'm "stealing" from the first grant. I was told by my advisor that this sort of time-sharing between grants is normal within the research world. My question is, is that true? If it is a problem, how should I deal with this?

@CharlesMorisset - re:interest, I'm not really, but do you think it matters? And with the "few months", I'm not that good at gauging time, but I'd imagine that this project plus coursework will keep me busy full-time. I'm not sure, though.

Time sharing between grants is extremely common - I've often been asked to work on projects unrelated to what I am formally being funded for.
As @CharlesMorisset mentioned, many grants are now written with a sufficiently robust idea of where they're going, how they'll get there and that they'll work that a considerable part of the research is already done. Additionally, since grants need fairly strong preliminary results sections these days, one is essentially forced to use current funding to do the research for "future" projects.
So I wouldn't feel bad about it for the reason you've mentioned. I would consider asking your advisor "why this project?" Do they just need a warm body to do the work? Would they like to give you a shot at an early, modest publication? Is there a particular skill they are hoping you'll develop working on this project?


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Is autism more prevalent amongst students in well-ranked universities?
I read on
https://www.wired.com/2016/10/president-obama-mit-joi-ito-interview (mirror):

And if we were able to eliminate autism and make everyone neuro-normal, I bet a whole slew of MIT kids would not be the way they are.

Is autism more prevalent amongst students in well-ranked universities (vs. all universities)?

That's probably a very hard question to answer, if for no other reason than those statistics are likely hard to come by. You'd have to look for some sort of national survey of universities' "Services for Students with Disabilities" offices. Maybe there's some form of reporting that is part of the Americans with Disabilities Act?

(I understand why the tags "health issues" and "disability" were added, though I wouldn't call it this way)

I agree that this may be a very difficult question to answer. With that said, surely the issue is going to be much less high vs. low ranked universities, and more about subject areas. I'd strongly suspect that students in the sciences are more like to have autism than those in the arts and humanities. Where an institution, as a whole, has a particular prevalence of autism it may say more about the balance of arts/humanities vs. science in their composition than about their prestige (of course prestige may in turn correlate with that composition)

For several reasons (including lack of diagnosis) it is a question hard to answer. However, there are several mental illnesses (eg. schizophrenia, bipolar disorder) that seem to be more common to professionals, and there are a lot of studies on the correlation between intelligence and autism, too.

There is research to suggest that the general belief (or stereotype) is accurate relative to subject area - specifically, some (but not all) areas of STEM (science, technology, engineering, mathematics) have a greater amount of autism prevalence than would be expected by pure chance. There is no research I can find that considers rank of University comparatively, but there is research that compares the prevalence of autism spectrum signs/symptoms/behaviors/classifications between various fields.
Science, Technology, Engineering, and Mathematics (STEM) Participation Among College Students with an Autism Spectrum Disorder

Findings suggest that students with an ASD had the highest STEM
  participation rates although their college enrollment rate was the
  third lowest among 11 disability categories and students in the
  general population. Disproportionate postsecondary enrollment and STEM
  participation by gender, family income, and mental functioning skills
  were found for young adults with an ASD.

Selected quotes:

Young adults with an ASD had a higher proportion of majoring in STEM
  related fields (34.31 %) than any other disability groups. The
  difference was significant for seven out of the 10 pair-wise
  comparisons. When we broke down the STEM related fields into computer
  science, engineering, math, and science, we found that the high STEM
  participation rates among young adults with an ASD was mainly driven
  by a high concentration in science or computer science majors. Young
  adults with an ASD were significantly more likely to major in science
  (12.12 %) than their peers with LD (4.72 %), SLI (4.71 %), ID (5.40
  %), HI (4.80 %), OI (1.45 %), OHI (4.55 %), TBI, or MD.1 These young
  adults with an ASD were also significantly more likely to major in
  computer science (16.22 %) than those with LD (4.06 %), SLI (5.90 %),
  or OHI (5.19 %). However, the high prevalence in STEM majors for young
  adults with an ASD was not found in non-STEM majors, such as health
  science (7.64 %) or social sciences (9.52 %)...
When focusing on STEM majors, the odds of STEM majoring were 13 times
  higher among males with an ASD than females...
These results provide the first national picture of postsecondary
  enrollment and STEM participation for young adults with an ASD as well
  as their peers in 10 other disability categories. Our analyses suggest
  that young adults with an ASD who attend college are most likely to
  pursue STEM majors. However, they also have one of the lowest overall
  college enrollment rates...
Despite a previous lack of national evidence, the idea that people
  with autism might be predisposed to choosing and succeeding in
  STEM-related majors and jobs has gained a footing in popular press
  stories and among advocacy groups (Moore 2006; Morton 2001; Ross 2006;
  Safer 2012). Our findings confirm that individuals with an ASD are
  more likely than the general population and other disabilities groups
  to gravitate toward STEM. The STEM major rate (34.31 %) for young
  adults with an ASD was not only higher than their peers in all 10
  other disability categories, but also higher than the 22.80 % of
  students in the general population that declared a major in
  STEM-related fields in postsecondary education (Chen and Weko 2009).
  In addition, this study found that young adults with an ASD in STEM
  fields were more likely than the general population to concentrate in
  science [12.12 vs. 8.3 % (Chen and Weko 2009)] and computer science
  [16.22 vs. 6.6 % (Chen and Weko 2009)].

Note that this indicates that people on the autism spectrum are more likely to choose certain fields, such as computer science and engineering, than is the general population - but people on the autism spectrum are also less likely to enter college at all compared to the general population.
This study links to many related studies, but only notes one other similar study in a single United Kingdom university that showed a correlation between autism and mathematical skill. All studies in total still make it impossible to compare higher and lower ranked institutions.
Finally, note that the mention of MIT is notable not simply because it's high ranked and famous - but because it is famous for a specific set of technological developments, related to AI (the topic of much of the interview in the OP), as well as engineering and computer science generally.
You can go about this in a rather sideways manner, however, from this one note from the above study:

Young adults with an ASD were less likely to enroll in a 2-year
  community college (27.66 %) or a 4-year college (14.95 %) than all
  other disability groups except intellectual disabilities (ID) or
  multiple disabilities (MD) (Table 3).

This shows that autism is less prevalent at unranked/low-ranked institutions period, so you could roughly infer that those with ASD who choose to go to college at all do so primarily at institutions which are more likely to be ranked (or ranked relatively highly). This is a rather weak argument, but it's about all we seem to have to go on.


text:
How much would it cost to remove pay-walls?
Is there any research/study/survey/... that tried to estimate how much it would cost to remove paper pay-walls so that all existing research papers are made publicly available free of charge?
E.g. France paid Elsevier 172 million EUR (mirror) so that 476 universities and medical center can have legal access to 2000 journals for five years. I wonder how much it would cost to buy the access to all papers so that anyone can access then.

If the question is unclear, you're welcome to comment on what is unclear.

made publicly available Please clarify who is the public? Your own country? Europe? U.S.? Developing countries? Undeveloped countries? How about Regions? (Hong Kong is not a country, it's a special region) The whole world? Vote to close as unclear.

@scaaahu public = all citizens, either in a given country or all countries.

Have you looked into SCOAP3? That covered (most of) one field but it should be possible to extrapolate

For an upper Limit just add up the market value of all the publishers... Then you make it all open access to everyone, and everywhere

@Andrew Thanks, this is the kind of initiatives I was looking for. However, from my vague understanding of What is SCOAP3?, SCOAP3 only focuses on paying publication fees when researchers submit new papers? i.e., it doesn't try to buy the right to make publicly available papers are paywalled?

Although an interesting subject I vote to close, not because it's unclear, but rather because the subject is apparently opinion based and a factual answer will be unlikely, unless a high executive from a publisher decides to gives us a ballpark figure.

@FranckDernoncourt as this question is closed here (in my personal opinion for no good reasons), you might consider reposting  it on OpenScience where it will most probably be perfectly welcome and on-topic to obtain additional answers.

@scaaahu Is the question still unclear to you?

It's still unclear. You said either in a given country or all countries.

@scaaahu Either is fine, but preferably all countries.

It's clearly not your question, but I cannot help underlining that France paid once for the researchers to write the papers, and a second time to buy their papers from a private company...

@anderstood Unfortunately this is what most countries do to some extent, although more indirectly: through funding from public agencies, tax rebates, etc. The French taxpayers shouldn't be the only ones to be pissed.

It's an interesting thought. Presumably, if you looked at the market capitalisation of some of the major commercial journal publishers, you could get a sense of how much it would cost to purchase both ownership of the intellectual property in such articles, journals, infrastructure and many other things.
I did a quick google and it suggested that the market capitalisation of Elsevier (for example http://www.bloomberg.com/quote/REL:LN) was 35 billion British Pounds (although I'm no expert in reading this stuff, and there seems like there is a lot of aggregation of companies into larger structures). My main point is that there is presumably a market value associated with the vast majority of the commercial publishing literature. It would be interesting to get an estimate of what this is (e.g., is it a half trillion US dollars or perhaps its much less, I'm not sure).
The main point is that it would be theoretically possible for governments to buy such companies or alternatively acquire the rights at commercial rates.
It would however be very expensive.
Alternatively, governments could change intellectual property law in relation to scientific journals or some category of material. There are a variety of ways that this could be done. A simple option would just be to mandate that articles in scientific journals need to be made accessible on a suitable repository (e.g., like pubmed) perhaps after some embargo period.
In general, a lot of this raises a number of broader legal issues. For example, it may be considered poor legal precedent to change the law after the fact. I.e., journals invested in publications on the assumption that their intellectual property would be protected and these rights are then unilaterally taken away by government. In some legal contexts, this may give rise to the publishers having rights for financial compensation.
The alternative strategy is to focus more on ways going forward that the published literature can be more accessible to the general public. For example, this can be seen in various conditions placed on grants that the publications need to be open.

Zero. The government of the nation you live in can pass a bill that mandates that all (existing and future) published research papers are made publicly available and redistributable.

Comments are not for extended discussion; this conversation has been moved to chat. Note that comments can only be migrated once; further comments cannot be moved to chat and may be deleted.

And how much would it cost to convince the government of my country to pass such a bill?

@JeffE Based on the current decision making: maybe you could win it over with a well-placed tweet.

I think that your example does not reflect the question. I didn't read the entire contract but it seems to me that France has just paid in advance the publisher's fees for five years for all the universities.
Probably they got a large discount, with respect to what they would have had to pay without such a large contract, but the order of magnitude is roughly the same.
For instance, in Italy all the university libraries are public, which means that any citizen can enter and read books and journals. Sometimes ago, I looked at the annual budgets of a few university libraries, and depending on the size of the university they ranged from a few hundred thousand euros to several million euros. Unfortunately there was no information on the expense breakdown between journals, books and databases, but I think it's reasonable to consider around 50 k€ for a major, possibly greedy, publisher (years ago I heard that IEEE journals where around 30 k€).
Hence, if you consider 50 k€ for roughly 500 universities and centers for five years you obtain 125 M€, which is of the order of magnitude of what France has paid.
Therefore, according to your example,

How much would it cost to remove pay-walls?

It costs as much as the total fees.

In other words, if you want to pay Elsevier a one-time subscription rather than many smaller ones, they are going to ask you for the same amount of money that they make now. Their business expenses are not going to change, so they need the same amount of money to keep their business going as it runs now.

50 k€ for how many journals? I agree that the example is a limited version of the question, which I tried to specify by mentioning "France paid Elsevier 172 million EUR so that 476 universities and medical center can have legal access to 2000 journals for five years."

@FranckDernoncourt Usually publishers sell the whole package of their published journals: it's a way to sell also the less read ones.

@MassimoOrtolano Thanks, so in the example it means a University has to pay 50 k€ to obtain access to 2000 journals for one year?

@FranckDernoncourt Yes, roughly. As you can see from the obtained total, I might have a bit underestimated that amount.

Is there any research/study/survey/... that tried to estimate how much it would cost to remove paper pay-walls so that all existing research papers are made publicly available free of charge?

I am not aware of any such study. The cost however, could be pretty minimal if the governments of a couple of key countries (e.g., US, UK, Germany, etc) decided to make it happen. If laws were passed to outlaw restrictive licenses on research publications, this would effectively remove pay walls.
A few years back, the NIH mandated that all publications resulting from NIH funded work be made freely available after an embargo period. While the NIH is still willing to provide funding for publication and open access fees, if they stopped, people would be forced to publish in free (both as in beer and as in freedom) places. Similarly, there is discussion that in the future in the UK the REF will only count open access publications. Again the research councils provide funding for publication and open access fees, but if they stopped, people would publish in free places.

Note that the government of the UK seems to think that "gold" OA is a bad idea after all. http://www.nature.com/news/uk-open-access-movement-sways-towards-low-cost-repositories-1.14953


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Getting notified when an article I cited in one of my papers gets retracted
Is there any way to get notified (e.g., by email) when an article I cited in one of my papers gets retracted?

Perhaps you could set up a Google Alert or set up a similar event handler at http://www.changedetection.com/.
I have tried both of these services.  Once in a while they both catch the same thing, but for the most part they complement each other.


text:
Why did journal subscription prices increase by 25% between 2013 and 2017? (vs. 5% for US inflation)
I read on https://journals.ebsco.com/products-services/explore-content :

Why did journal subscription prices increase by 25% between 2013 and 2017?
That's much more than the US inflation (~5.1%  between 2013 and 2017 (mirror)):

(source of the image: http://www.usinflationcalculator.com/inflation/current-inflation-rates/  (mirror))

Three words: because they can.

^^^ Journals have an effective monopoly on intellectual dissemination. Authors want to publish in the "best" journal in their field and publishers will bundle 99 non-best journals in with the best journal to sell to libraries, which have no choice but to purchase the bundle.

Sci-hub. They lost so much money due to sci-hub, they just had to increase their prices.

@Mark Is it true? Probably, most of their revenues come from institutional subscriptions, and I doubt that these have been significantly affected by sci-hub.

@MassimoOrtolano I don't think so, but they said so. "Elsevier gave the court a list of 100 articles illicitly made available by Sci-Hub and LibGen, and asked for a permanent injunction and damages totalling $15 million" (https://www.nature.com/news/us-court-grants-elsevier-millions-in-damages-from-sci-hub-1.22196). But then, many people who use sci-hub do so because it's easier than going through their institutional subscription. Hence my view that they didn't lose anything.

On a more serious note: are there any numbers on the differences in earnings through open-access and (classic) paywall papers? The former gives a one-time big financial boost, the latter relies on "small" fees every time someone wants to access the paper (and cannot get it through institutional subscriptions).

@Mark: Elsevier presumably said so because it sounds better than "because we can get away with it".

Why shouldn't they? https://www.youtube.com/watch?v=UJOjTNuuEVw

@Mark Let's ask: Earnings generated by open-access papers vs. (classic) paywalled papers

Did you read the 2018 Serials Price Projection Report on the same page where you found this graph?  That says quite a bit about increasing journal prices.

The direct answer is "because they can". Demand for journals is pretty inelastic - increasing the price doesn't cause much of a fall in demand. Can you imagine your university not subscribing to a journal like The Lancet or Science?
Behind that answer however is a storm of interlinked factors. Here're some of them:

Publishers are under pressure from their shareholders to show revenue and income growth. This is no different from university administrators pressuring their faculty to show research output growth, university ranking growth, and so on.
The total number of academic papers being published worldwide is increasing quickly. To shareholders this sounds like an excellent opportunity for growth! But not all these papers can be published in top journals, so a lot of them end up in not-so-good journals.
Most of the papers in these not-so-good journals are actually very seldom used. For example take the Elsevier journal Wave Motion. It's got an impact factor of 1.575, which is pretty medium. I picked a random paper, "An elastodynamic computational time-reversal method for shape reconstruction of traction-free scatterers", Vol 72, page 23-40, July 2017. Then I went to Web of Science, found the paper, and checked the usage statistics. Guess how many times it's been used in the past 180 days - three times (!).
Since the usage is so low, libraries are incentivized not to subscribe (and remember, this is a solidly middle-of-the-road journal - imagine what it's like for the bottom-tier ones). But if libraries don't subscribe, the journal makes a loss. What is the publisher to do?
Let's take the obvious thing to do, and one commonly argued for, which is to close the journal. If publishers did this en masse, there'd suddenly be no more journals except the few top-tier ones. Remember that the papers published in these not-so-good journals aren't necessarily bad - they're usually just rather boring, low-novelty papers: the backbone of science. Without the journals, these papers would never be published.
Another thing about these not-so-good journals is that they're crucial to researchers from developing countries. It's true that these researchers might be slightly less capable than those in developed countries, but it's also probable that they simply have fewer resources. If one is not able to access the Large Hadron Collider, one is also not likely to make breakthroughs in particle physics. Hence one ends up with boring, low-novelty papers that won't make it to top journals.
On top of all that, let's add the fact that some academics think that they write papers, they edit journals, they serve as reviewers, they deserve to be paid for it. I'm not saying that they're wrong, but you can see the tension this belief causes.

And then there's open access. Most forms of OA ties the revenue to the number of papers published (there are other models, but those journals are loss-making and only stay afloat because of an external source of funding). This means there's an immediate conflict of interest for the publisher, which is why there's predatory OA publishing, and in turn is why there's a backlash against OA. Also consider what it's like from the publisher's and library's points of view.

Publisher. If you convert a journal to OA, you're giving up subscription revenue. A bird in hand is worth two in the bush. Further, many academics prefer to publish in subscription journals even if they have access to OA funding, since if they publish OA they have to jump through some administrative hoops. There're also lots of academics in developing countries that simply cannot pay for OA. There's no guarantee that your 100-papers/year journal will still be 100-papers/year after you convert to OA. Do you dare? Remember your job is on the line (see comment above about shareholders).
Library. OA costs money. You need to free up funds somewhere to fund OA. In theory you should be able to use subscription money to pay for OA, but in practice, you're either subscribed to a journal or not. You can't just pay $3000 less for a subscription and use that for OA for a single article. The only way is to unsubscribe, which effectively removes access to every paper in the journal.

Finally, let's not forget that publishing is a notoriously poorly-paid job, and the publisher also has to keep its employees happy.
tl; dr: it's a difficult world out there. If you have a solution, you'd be in contention to win the Nobel Prize in Publishing.

@NajibIdrissi I visited my university's press a few months ago. We touched a bit on profits - turns out their net margin was -50%, and they only remain afloat because of funding from the university.

Certainly nothing we should be discussing in comments. I won't say any more, other than if you have a better model to handle academic publishing, you can try starting your own journal or publisher. As for net margin of commercial publishers, Wiley, Elsevier, etc are publicly held companies. You can check their annual reports.

If you can write a supplemental answer filling in the blanks in mine, I'd be interested to see it.

@NajibIdrissi : "This whole answer […] assumes a capitalistic way of publishing" Indeed, but I guess it still answers the question properly, as the alternatives I know of to this way of publishing do not use subscription (free access through on-line archives, typically), and hence do not play any role in the increase of the subscription prices.

@NajibIdrissi I don't think Allure is saying that your criticism is invalid, he's saying that it can't be developed in comments, and I agree with him. I agree with your remark that journals published for free can play a role in the price of subscriptions, I was short-sighted, but I still believe that it is a minor role compared to the role played by greed.

Since OA ties the revenue to the number of papers published, not always. There are lots of so-called "Diamond OA" journals that don't charge authors or readers.

@DavidRoberts not really, relatively speaking there are very few such diamond OA journals. Since they don't charge authors and readers, they need external funding. They also don't offer typical publisher services such as copyediting (of course, the authors from first-world countries indulging in these diamond OA journals don't think they need it, but there are a lot of authors from non-English countries that do) and marketing. Finally these diamond OA journals don't scale well - see comments by Paul Ginsparg and Dan Kulp here: https://www.aps.org/publications/apsnews/201602/arxiv.cfm

@Allure "very few such diamond OA journals" - not according to DOAJ A 2013 study found that only 28% of journals in the Directory of Open Access Journals (DOAJ) required payment by the authors; however, this figure was higher in journals with a scientific or medical focus (43% and 47% respectively), and lowest in journals publishing in the arts and humanities (0% and 4% respectively) (from WP https://en.wikipedia.org/wiki/Open_access_journal#No-fee_open_access_journals and citation is given as https://doi.org/10.1002%2Fasi.22972) and there are more recent figures than this

@Allure if you are thinking about volume of papers, then of course, that's slightly different. For detailed analysis I refer you to http://www.lulu.com/au/en/shop/walt-crawford/gold-open-access-journals-2011-2015/ebook/product-22758863.html (that's a free e-book) and data available here: https://waltcrawford.name/goaj.html

@DavidRoberts Thanks for link. That's news to me, but I'm skeptical of the results. Eleven of the first twelve journals' website in the raw data did not load for me, and the sole one that did was not in English and did not look like a journal's website. Random attempts later in the dataset also led to a lot of dead links, and I only hit three journals' website. One was diamond OA but subsidized by a society, one charged 350,000 IDR, and one actually charged a subscription but called the journal "open access".

I'm mostly unconvinced I'm afraid. Diamond OA, if it's ever successful on a large scale, must simply shift the costs somewhere else. It might be a society, a publisher using its other activities to fund the diamond OA journal, or a university, but someone is paying for it. The people managing the journal must still put food on the table after all. It seems probable that the ultimate payer is still authors (in the form of membership fees to societies), universities, etc. Also we're way outside the scope of the comments section. If you want to discuss this somewhere else, I'm in.

@Allure I don't disagree about the cost of publishing and the scalability of Diamond OA. Just wanted to correct the idea that OA publishing = author pays, and give a sense of the scale of how many journals don't fit that mould. The main specialist journal in my subfield is Diamond OA and has been so for over 20 years. It's well regarded, so it's not a new concept for me. I think we had better not chat too much, either. :-)

A fair objection. I'll see how I can edit the answer.

If we read the question not as "why is there an increase in price" but rather "why is the increase in prices occurring now?", is this answer basically saying "since there are more people wanting to publish, there is an increase in demand?  Regardless of how the supply curve looks, it seems possible to me that the increase in demand is so much so as to increase prices a lot, but this would be stronger if the supply curve were also inelastic...


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To what extent does the wealth, connections and alumni donation of a parent help their children be accepted into a college in the US?
Is there any research/study/survey/dataset that looked at to what extent the wealth, connections and alumni donation of a parent help their children be accepted into a college in the United States?
(E.g., a notorious case: John F. Kennedy's Harvard application)

@NateEldredge Thanks, I am interested in both undergrad and graduate.

I would say they are so different that there should be two separate questions for undergrad and graduate admissions.  The undergrad one might get closed, though.

@NajibIdrissi The question is not "loaded", since the extent could be 0.

@NajibIdrissi I see. Of course the study could take care of confounding factors.

I don’t see this as off topic. It’s about how universities work. Would there be a better place to ask this question?

Thanks for the interesting link. This is a bit off-topic, but I find Kennedy’s explanation of why he wishes to go to Harvard perfectly articulate and logical, and much more honest than the loads of BS prospective students are required to come up with these days. Perhaps JFK did get in thanks to his family connections, but this excerpt from his application shows no evidence that he was undeserving, nor do I see anything that’s “mediocre” about his writing, despite what the blog author says.

@NateEldredge This is not a student asking how to be admitted to an undergraduate degree. It's a question related to a general aspect of the US university system, and it can be quite on-topic here. Please, as discussed several times on meta, let's not fall into the trap of considering off-topic anything that contains the word undergraduate in it.

This is an important question for understanding the system of American higher education. (I do not read it as being an off-topic request for "How do I improve chances of admission to college?" especially since changing a family's wealth is a much more difficult course of action than, say, paying for tutoring.)
There has been some quantitative study of "legacy admissions," with Hurwitz (2011) estimating that the odds of admission are multiplied by 3 for students with a parent who attended the school, after controlling for other factors. (For instance, legacy students in his data tend to have higher SAT scores than non-legacy students.)
He explains that favoring students whose parents attended has benefits similar to favoring those who apply early or sports stars:

Highly selective colleges face the challenge of maximizing the academic profile of their student bodies, with the understanding that sacrificing some academic talent now will enable the college to preserve or improve its selectivity in the future. In other words, from the college's perspective, an exclusive focus on academics in the admissions process is not sustainable. ... Other tradeoffs might include relaxing admissions standards for early decision applicants to decrease acceptance rates and increase yield rates, and consequently to appear more selective (Jensen & Wu, 2010). Or they might involve admitting academically lackluster star athletes to maintain the successful sports teams that encourage alumni giving (Holmes, 2009; Meer & Rosen, 2009). Relatives of alumni (legacies) offer enthusiasm and familiarity to colleges, and the special treatment awarded to them in the admissions process helps to preserve generational ties that also are intended to motivate financial generosity. (from section 2.1)

His data do not include parents' giving rates, but they compare the same student's admissions across multiple colleges, showing an advantage at a parent's alma mater.

For some historical background, in a legal review of legacy admissions, Lamb (1992) explains how legacy admissions policies came about. Harvard and Yale kept out most public school students with a Latin requirement through the end of the 19th century, and only had to deal with selective admissions upon dropping that requirement. Their (at least somewhat) meritocratic process that followed let in "too many" Jewish and Catholic applicants. Columbia started asking for family information (religious affiliation, father's name and place of birth) in 1919, and other elite schools followed. In 1926, Harvard announced it was taking things like "personality" into account in admissions and started requiring photographs with applications; they used the photos and the discretion to make it harder for Jews, Catholics, and (likely) black students to gain admission, while increasing the proportion of legacy students. (p. 494)
So, the example of John F. Kennedy's 1935 Harvard application is an interesting one. He had famous parentage and family background at Harvard (and by WWII 1/4 of Harvard students were legacies, according to Lamb p. 495). In his case, his Catholicism was probably not held against him.
Lamb also reviews data from a Department of Education Office of Civil Rights inquiry into Harvard admissions. Circa 1992, the Harvard admissions process benefited legacies, and gave additional weight to children of alumni who served on the "Schools and Scholarship Committee" (p. 502), which is apparently a group of alumni interviewers. (My guess would be those who give time are more likely to also give money, but I do not know that donations would change the odds of being accepted as an alumni interviewer.)

In the graduate realm, my guess would be that graduate programs that charge admission (especially for professional training) are much more likely to have legacy preferences than academic programs. However, in subjective processes where a department is hoping to get a good yield of applicants or hire a faculty member who will choose them, I'm sure that there is some benefit in being able to say in an interview, "It's great to be back at this university! My parents met here..."

As a backdrop to this question, there is a longstanding literature that admission into selective colleges, attendance at any college, and graduation rates from college, depend strongly on family socioeconomic status, including level of parent education and family income.
For instance, Duncan, Kalil, and Ziol-Guest (2017) find:

Across 31 cohorts, we find that increases in the income gap between high- and low-income children account for approximately three-quarters of the increasing gap in completed schooling, one-half of the gap in college attendance, and one-fifth of the gap in college graduation.

Controlling for family structure does not explain much of the difference they find, but some of it is related to maternal age; the "maternal age gap" between higher-income and lower-income families increased over the time period they're looking at. (It is not clear whether maternal age is causal or a marker of other family differences.)
Chetty, Friedman, Saez, Turner, and Yagan (2017) look at intergenerational mobility by parent wealth, finding that children from rich families are much more likely to attend college--and fancier colleges--than their poorer counterparts.
Family connections and legacy admissions will not shape these overall enrollment statistics, because the kind of students whose families have that pull are very unlikely to be on the margin of not attending any college.
Instead, sociologist Annette Lareau's idea of "concerted cultivation" is probably much more relevant. Middle- and upper-class parents know the pathways for success and train their children into the attitudes and behaviors that prepare them for success in this society. The example aeismail gives of volunteering to work in a lab runs along these lines.

@FranckDernoncourt After your JFK edit, I added a historical update. Up to 1/4 of JFK's class would have been fellow legacy students, and there is some evidence that (in the early 1990s) Harvard weighed different alumni parents differently.

I want to offer some commentary on the graduate situation, and why it's so hard to find comparable results to the level of research available for undergraduate admissions.
It’s going to be very hard to find studies of graduate admissions in the US, because admissions are handled at the departmental level, so data sets are smaller, and because financial need and socioeconomic status are not something asked for or measured in graduate applications. Thus, they’d need to be “add-ons” in a study.
While I can’t say they’d have no impact, graduate admissions by necessity tend to be more meritocratic than undergraduate admissions. Admitting someone who is clearly not competent for graduate studies makes the department look bad, and can act as a drag on future recruitment efforts. That said, if the candidate is otherwise qualified, a history of donations to the department from the candidate’s family certainly wouldn’t go overlooked.
Another possibly overlooked aspect of a family’s socioeconomic status that can indirectly impact things is that their financial security enables opportunities that someone who is not similarly advantaged might not have. For instance, someone who comes from a well-to-do family could offer to volunteer in a lab for credit, while someone who needs to “pay their own way” or help support their family may have to do something outside of research during the summers, thereby being at a disadvantage by virtue of having a smaller research profile.

I added a paragraph about that. Basically it’s going to be hard to find studies because grad admissions don’t ask about financial need or socioeconomic status.

@MassimoOrtolano: That's fine. My goal is still to point out that there isn't going to be the same level of data available at the graduate level for various structural reasons that simply do not exist at the undergraduate level.


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Can instructors fail honest students when tests are too hard because most students are cheating?
I am in Nursing school.  I can prove that 80-90% of students have cheated every semester.  They pass test banks around in email, text or Instant Messenger.  Every semester I've come forward (5 instructors) but nothing major has happened.  In 3 semesters of nursing school the faculty has never condemned nor said a word about using test banks.  This semester I tried to warn instructors before the first exam, but they didn't listen.  Now a few of us simply can't pass the exam because we're not cheating.  The exams are that hard.
Test banks from previous semesters were being passed down from the semester ahead of us.  I looked back at these test banks after the exam and found 21 questions just in one chapter.  That's when I emailed them the test banks that were being passed around.  It's a fine example of how academic dishonesty cheats everyone including the ones being honest.
Every semester Instructor makes the exams harder and harder because "statistically" the instructor data shows statistically "These are good/not too hard questions".  But I have the documentation to show WHY people are able to pass.  Had I used these test banks I would be passing.  Honesty is earning a few of us a 60.00% on each exam.
What can I do?  I warned them; they didn't listen. I plan on filing a complaint and a grade grievance.  My question is: can an instructor fail students who are being honest?  When there is clear proof of compromised exams and academic dishonesty throughout the class. Is it our fault they can't catch it?  Is it our fault they have no idea what a hard question really is? Can instructors really fail people for being honest and choosing not participate?

Where I come from, it is taken as given that students are aware of previous exams and grading schemes are adapted to this. Just that this isn’t considered cheating. If this is not the case at your institution, this is indeed a problem, but it can only be reasonably solved by officially recognising and allowing that everybody is aware of previous exams.

I agree with the previous comments: could you please explain why you feel that using the test banks from previous semester's exams are cheating given that "the faculty has never condemned nor said a word about using test banks" and that the faculty change the questions every semester?

I agree that the policy seems to be that using previous years' tests to study is allowed. However, if this is the case, the faculty should say something and make sure that all students have equal access to previous tests. It is the unequal distribution of these tests that is a problem!

Related: https://academia.stackexchange.com/questions/42841/is-it-ethical-to-use-past-years-final-exams-that-the-professor-hasnt-explicitl

Not sure if it is a real duplicate. This is asking retrospectively. That was prospective.

I agree that the policy seems to be that using previous years' tests to study is allowed. However, if this is the case, the faculty should say something and make sure that all students have equal access to previous tests. The fact that some students are unaware that using previous tests to study is permitted is a problem, as is the unequal distribution of tests. I could easily see a student who was marginalized from the group for some reason (sex, race, nationality, etc) not getting these unofficial emails, and then it would be an issue of discrimination.
I would recommend the faculty post the previous year's tests to the website to make sure everyone has equal access and is aware that these are permitted study aids.
As a student, I would push for a clear statement in class on whether or not these aids were permitted. If faculty refuse to make a statement or take any action I would recommend speaking to your academic advisor about the issue.

I will add that this also happened to me as an undergraduate. When I complained to the teacher that some people were getting tests from older friends, he told me "you need to get better friends." I didn't understand that he was telling me that using previous years' tests was considered proper in his course, and went on to get a mediocre grade. As a first- gen student I didn't understand the norms!


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How do new tax rules apply to a Ph.D. student receiving a fellowship?
I read that some revamping had happened in the recent times with respect to the tax policies in the US. Say,I get an admission for Ph.D. for Engineering at New York University with a fellowship which offers $2600 stipend per month. How much will be the tax I have to pay OR what is the 'real' stipend I will get?
Edit: I am an international student planning for Ph.D.

The local tax office may be a good place to start...

The major policy change for grad students was relate to tuition reimbursement and did not go into affect.

@SolarMike: The US doesn't really have those.  (They exist, for some values of "local", but in most cases they're not a practical way to get assistance.)

It will depend on many things: your country of origin, your visa, the funding source...

Unfortunately (as you know) tax laws in the US are pretty complex, and you're in a relatively unique situation as an international student with a fellowship.  Many universities have a page on their website that discussed tax issues, and I noticed that NYU has one as well.
You'll notice near the bottom of the page that your taxes also depend on the tax treaty that the US has with your home country, and there also might be technicalities related to whether the school classifies your pay as a fellowship or assistantship for tax purposes.  For example, according to my university, my funding is through a "research fellowship," but because I'm expected to work a certain number of hours per week in my advisor's lab, the tax forms classify it as an assistantship.
It is a good idea to reach out to someone at your university to ask this question.  They may not be able to help you, but the worst that will happen is they'll ignore your email or say "Sorry, I can't help."  I would start with people in the payroll department or (if there is one) the office for international student admissions or support.  Sometimes students (or potential students) are shy about asking for help, but they shouldn't be.  People like to help other people, and the people you'd be reaching out to are literally employed to help people in your situation (among other things).
When I ask people in the business office, finance office, etc. for help, I usually explain what my question is and then end the email with something like "I wasn't entirely sure who to ask for help, but thought you would be a good person to start with--can you help me figure this out, or recommend someone else for me to reach out to? Thanks so much for your help!"  That way, even if I'm "bothering" them with something that's outside their responsibilities, they usually point me in the right direction for who to ask next.