text:
Code sharing between co-authors
During a collaborative experimental project in my PhD, I developed a rather intricate simulation + data processing tool. The work was published with myself as the lead author. One of the collaborators, who is located in a different country, was keen on extending that work and, based on ideas and inputs during the course of the project, she got one of her students to prepare the experiment at their end. (Meanwhile, I finished my PhD and am now working as a Postdoc at a different group).
Recently, they got their first results and now to bring this study to a conclusion, the collaborator requested me to process their experimental data through that tool I had developed. I haven't been offered an authorship yet but chances are fair that I would be if the tool gives publication-worthy results (As also mentioned above: I have already contributed a bit in this study through ideas). My question however is, in the event I am offered a co-authorship, am I obliged to also share the entire code with them?
While I am certainly open to giving them a gist of how the tool works (or to even get it lightly reviewed) via code snippets, screenshots etc., I am wary of simply handing them all the files. This is due to the fact that we had had some authorship issues with the collaborator in the past (though I wasn't directly involved at that time). If they have the files, there is a good probability that they would obtain the results themselves, publish them, with my name -- at the very best -- being in the acknowledgements section.
Additional info in response to some answers: Certain parts of the code are generic and could be useful to the broad community. Being pro open source myself, I intend to release those parts publicly soon. The other part of the code is very specific to the current work and would be of use to only a handful of people, including the collaborator's group.

How broadly useful is the tool? Who else would use it? How would anyone else use it if you don't share? Do you expect co-authorship in perpetuity from anyone who might use the code? What, really, is bugging you here?

@JonCuster : I have modified my question to address the points you raised.

Weren't you were obliged to publicly release your code with your first paper?

I will give the answer I have given a million times already on this forum: Communicate.
If you're unsure whether or not you processing the data will yield a co-authorship, write an email asking exactly this before you do the data processing. If the other side is an experienced researcher, then they will understand that as a postdoc you have many obligations to juggle and that you need to spend your time on things that will yield publications.
If you're unsure whether or not you will be expected to share your code, write an email asking exactly this before you start working with them. They may ask for it, and in that case you will have to discuss with them under what conditions you would be willing to do that. Or they may not even want your code and simply be happy to rely on you this time and in future times to do the data analysis in return for co-authorship.
In both cases, you can spend your day worrying and speculating, but you will never know the answer unless you simply ask what's on your mind. Communicate!

From scientific point of view, the right thing to do is to release the code publicly. That allows for the code to be reviewed for possible errors, and makes it possible for other people to use it in their work, or build upon it. You will save many people lots of work.
For your personal benefit, this action might also be close to optimal. By giving away free useful tools you buy people's goodwill. As you are working on something else entirely, you lose no competitive advantage by doing so. By publicly showing off your work, you in fact demonstrate your main competitive advantage --- ability to create good, useful tools.
Last, but not least: People are likely to act towards you similarly to how you treat them. If you do not share your tools or ideas, they are likely to do likewise with their tools and ideas. Do unto others as you would have them do unto you :-)

Making the code available also greatly increases the chances that your earlier work will be used and cited by others.

This. No one would accept a proof of a theorem under "lightly reviewed", an overview of the proof, and a few pictures of the blackboard. Reproducibility is essential to science.

Don't forget that if they're using your code, they will hopefully be citing the earlier paper in which you explained it.

They can't really check your/their work without the code, can they.
Besides, check carefully who the code really belongs to. Here in Chile, by law whatever a student writes (homework, thesis, or programs) belongs to the school, not the author (it is considered "work for hire", essentially). So this might not even be your call to make.


text:
Sending a *digitally signed* email to prospective employer/supervisor
I have been digitally signing (and encrypting, whenever possible) my official emails for sometime. While I am not extremely paranoid (but serious, certainly) about cryptographic security, I also think signing the email is a signature [pun intended] that I take such aspects seriously. On a like-minded recipient, this could therefore make a good impression.
On the other hand, if seeing the

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

header has a high likelihood of annoying or confusing the person (to the point of them simply deleting my email), then I certainly do not mind sending an unsigned message.
I recently started applying for jobs (in the area of quantum information/communication to be precise) and was wondering if I should, in my first email contact with a potential employer or (postdoc) supervisor, also sign that email?

Well, are the positions in computer security or something else?

There are other digital signature schemes like PGP/MIME in which the signature appears as an unobtrusive extra attachment, which an uninformed reader can simply ignore.  That avoids the BEGIN PGP SIGNED MESSAGE header and may be the solution for you.

Just ask yourself: what is the main point that you want to communicate in your email? Is it, e.g., (1) "I can use PGP", or (2) "I am looking for a postdoc position"?

Borderline OT... @NateEldredge An unreadable attachment might also confuse non-tech-savvy people. Putting signatures in headers seems like a good idea in principle; I wonder why it never became popular.

Someone working in QI/QC should be well aware of PGP, shouldn't they? On the other hand, if they really know their cryptography, I'd probabily avoid using SHA-1!

Just one slightly pedantic technical remark: if you have not securely shared your key with the application board, the signature is almost meaningless. It is also pointless if they won't verify it or will accept an email in your name without one.

I cannot imagine anyone being too put off by the digital signature, although I would probably go with a detached signature.
I think if you are going to digitally sign your emails, you may want to make sure you understand what you are doing. This would definitely be the type of thing I might bring up as a "safe" small talk topic during a campus visit. Often the small talk conversations can influence a decision in a tight job search since the search committee is not only looking for someone who can teach the required classes and do great research, but also someone they want to work with.

I digitally sign any of my messages, and always include the following in the .sig: About PGP signatures: http://xkcd.com/1181/

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

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

sort: votes


text:
Potential consequences for a PhD student using a cracked software
A friend of mine, along with ~10 of their colleagues, recently received an email from the IT department saying the department is investigating those students for using two pieces of cracked software.  Apparently, the vendor contacted the university about this.
My friend was asked NOT to remove the software from his computer. Moreover, IT staff checked his computer without him being around (privacy breach?). They were emailed and asked several questions as well like: "Do you have the license?, do you have the software?, and is there an IT staff member overseeing your computer?"
They are now waiting to hear back.
My questions are:
How serious is this based on the above information?
What are the potential consequences?
Is it possible to get a fine for this?
Would there be any academic consequences?
Note: While using cracked software is obviously wrong, their research demanded using such software. The advisor knew this and allowed it to happen. So part of the responsibility should fall on the supervisor as well (my opinion).
Addition: This is a large North American university.

If it is a university-owned computer on a university network, why do you expect privacy?

It depends upon the laws of your jurisdiction and country as well as policies of your school.

Also, I'm surprised this happened. I've heard about software companies looking up researches who publish with their software to make sure the users have research licenses (rather than teaching licenses) for the software.

@Jon I think privacy on account level would be expected! I don't have a problem with IT finding an illegal activity through the network, but going physically to their computer, bypassing their password and looking through their files is a problem!

Well, in my non-academic environment it is quite clear - it is not my computer, it belongs to the company, and our security folks can and will run scans as needed to ensure compliance (including licensing). Large universities have large risks if they do not have cyber policies and procedures to deal with any number of risks.

I agree to some extent but not fully. I think this is different in a research academic environment where results should be kept confidential until they are ready to be published. Having IT (or anyone else) going through students' files, some of which are NDA protected, could be a big problem. I think procedures should be placed to prevent the illegal use of software while maintaining privacy at the same time. The way it was done in friend's case doesn't sound right to me.

You seem to think that a human is trolling through files. Network scan tools are highly automated to go find stuff like software without a valid license. And, of course, since the university signed off on the NDA, the university IT folks are bound by it - they won't disclose it. Again, if you are on somebody else's network, you should not assume any privacy.

@user18244 I think your expectations are misplaced here. Almost invariably, when you work at any large institution which provides a computing environment, you will be required to agree to conditions that give IT the power to investigate this kind of misuse. They couldn't do their job otherwise.

"So part of the responsibility should fall on the supervisor as well (my opinion)."  Arguably, but responsibility isn't additive - even if the supervisor should be disciplined also, it does not follow that your friend should be disciplined less.

Brent: I see. I have some personal information stored on my workstation which is why I thought what happened with my friend was odd. Looks like I need to remove my files from my workstation now.
Nate: I agree. It just annoys me that his advisor allowed this to happen for so many years with so many students. His role is to be a mentor and tell his students it was the wrong thing to do and they should remove the software immediately.

Every institution is different.  Where I worked, e-mail and data were considered personal.  Other than with a legal search warrant, admin did not have access to staff's data.  Just because the company paid for the pencil and notebook, it doesn't mean they have a right to read what's written in it.

There might be rules on whether the work station can be used personally, e.g. you might be allowed to use one folder with a special name for personal files.

It's been a while... Any news regarding the outcome of the story?

Usual disclaimer: I am not a lawyer and this is not legal advice.
Several things to consider here:

It is the university's responsibility to maintain their computers, including their contents. So if your friends have been using a computer provided by the university with cracked software on them, the vendor of the software will go after the university first. They just want to get paid what they're owed, so it's better to go after a large university than some broke students.
Normally, the university should have only provided students with user accounts, which do not allow the installation of software, which in turn is to be done by IT personnel with admin accounts. If they don't do this, shame on them, this is poor practice that warrants some fines here and there (and the cost saved with IT employees probably makes them insist on the poor practice).
If students had admin accounts to these machines, they have probably signed a contract/memo/agreement claiming they'd be responsible in such situation. Bad for them, but the vendor will prefer to go after the university first.
Part of grant money and department budgets are precisely meant to pay for tools required by research activities, which nowadays always include computers and software. There is no excuse for using cracked software over the long run.
To be clear, this is a matter of money, not of academic merit. As long as your friends behave during the process, they should expect to be fined, but not expelled. The university will come after them if they receive a fine from the vendor.
"Normal practice" (which I'm not endorsing here) when using pirated software for your academic work is to use it only in your personal machine and only if the department owns licenses for said software. In some large universities, they might even have "campus licenses" for software, making this ideia completely useless. The point is that you have the right to use the software, as your department paid for it, but instead of using it during office hours, you might prefer doing it from midnight to 6 am in the comfort of your bedroom.
If nobody has the license for the software, you might be in trouble to publish results obtained from it. But then again, you can first obtain results, then the license, then attempt a publication. You might even just ask for a trial license.
If these computers were owned by the university, there is no breach of privacy here. If they were owned by the students, IT should not have nosed around these machines without the students permission. And by the way, never grant someone the right to audit a machine of yours, specially if unsupervised. Everybody has secrets/nudes/browser history/work worth keeping private, all of which should only be kept/done in private computers.

My bet for the outcome (and please update your post in the future to inform us):

Students get away with a warning.
Advisor gets a warning and needs to spare budget to acquire the license, if the license is affordable. Otherwise, activities using this software will need to be dropped.
Story gets muffled, people will go around saying "It is yet to see what happens" until everyone forgets about the case. Then people will simply stop talking about it. This is to avoid having precedence of cracked software usage and preventing it from becoming common place.

EDIT
Just as an extreme example, there are software licenses that costs millions of dollars. Paying a fine over the value of license would warrant firing the professor who allowed its pirated use, as long as the university indeed pays the fine (unlikely) and had good policies to avoid it in the first place (further unlikely).
There is also software whose commercialization is restricted due to national security risks. Missile simulation tools come to mind. Here there is more than a "money problem", there is illegal usage of a controlled piece of software. But I'd hardly expect this to be the case.

Thanks a lot for the insight and the detailed input!

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


text:
May I upload the preprint version of my article to ResearchGate before publication?
Recently, I got an acceptance of a journal paper, where I am allowed to self-archive its preprint version in my own repository/website.
My question is whether I am allowed to upload it to RG before publication, assuming that my RG page is a personal web page. If 'yes', what should I mention in the publication date entry, knowing that it is compulsory?

Don't mention the date. Is it compulsory?

I must enter the date in the RG form. On the other hand, should I understand that I am allowed to upload it?

I supposed that acceptance does not mean a publication date and preprint should be the version submitted to the Journal which might not have a confirmed date of it's publication.

RG is not a personal website or institution repositories. It seems that there are many discussion here related to this issue (I saw earlier). Why don't you just upload abstract and link to the IEEE DOI?

Why don't you just upload abstract and link to the IEEE DOI? — Because that wouldn't make the paper freely available.

First you should note that ResearchGate is unlikely to be considered self archiving by the publisher. While they may allow it, you should confirm. You should also ask about embargo periods. Assuming the publisher has told you the publication date is compulsory when self archiving, it is not unreasonable to ask what you should do at this stage.
In the absence of guidance, you could use something like forth coming or in press in place of the date.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
How to network as a new graduate student in a new country
First of all, let me admit something from the beginning; I don't understand exactly what is meant by networking in an academic setting.
I am a new Master's student in a country where I never studied before (Germany). Until now, as an undergrad, I have done several internships, worked within a couple of research groups for some time, attended many seminars & workshops, taken several graduate-level courses. During each of those occasions, I had the opportunity to meet with several academics who could (I guess) help me while I am shaping my career, but I've never tried to communicate with people whom I didn't have to. Sounds quite a bit of lost opportunity, but in my defense, I don't like socially interacting with people whom I don't know and don't comfortable being around.
My first question is that what have I (possibly) lost by not networking?
Secondly, what is meant by "networking" exactly in an academic setting? Just knowing each other exists, or being some kind of friends, or just knowing who is interested in what?
Thirdly, how can a graduate student network in events where most of the people are way older, and academically more senior?

Addendum:
I've just come from my first, proper academic event. It was more for a celebration than a networking event, but still, I've met a lot of people and it was great. There were a lot of people who think in the same way as I do (not necessarily we agreed on everything, just our way of thinking were the same; analytical, based on data, etc.). I think I've made some "academic friends", and there was a lot of interesting discussion on almost everything but above all, it was really fun.
But, all the things were with the people whom I had already known a bit, and I found it a bit hard to join the discussion with the people I hadn't know.

What is your choice of career after you get your mentioned degree? Networking depends on your preferences.

@tachyon researcher positions

Since you

have done several internships, worked within a couple of research groups for some time, attended many seminars & workshops, taken several graduate-level courses

You have probably done a fair amount of networking already. And I'd say likely more than other Master students. You're maybe not as "connected" as someone who introduced themselves at seminars or workshops, but you still know better now what the various speakers are working on. This is a big part of what networking is about.

 Secondly, what is meant by "networking" exactly in an academic setting? Just knowing each other exists, or being some kind of friends, or just knowing who is interested in what?

Since you indicate you are in Germany, networking is about getting acquainted: knowing each other exists and what their professional interests and topics are.
You may also become professional friends (and since you are in Germany, beware of the difference between English friend and German Freund - which is reserved for close friends in English terms)

 how can a graduate student network in events where most of the people are way older, and academically more senior?

The most effective way is IMHO attending conferences.

If you are at a conference on your own (noone else from your group), attach yourself to various other groups that are there in somewhat larger numbers. Easiest IMHO to attach yourself to some fellow students, who are there with also postdocs or their professor around.
If you are attending together with more senior people from your group, I'd expect "your" postdocs or professor may introduce you to their acquaintances.

You can also attend e.g. PhD student seminars. There it should be quite easy to get acquainted with your peers. This is also very relevant and useful networking: a) you can get e.g. information on working conditions in their groups when you'll be looking for a postdoc position later on. b) Like you, they'll "grow up" academically/professionally. In a few years, they'll be your experienced professional peers, PIs and professors that you know already.
Last but not least, I think it also important to get acquanted also with a group of people outside your field. In Germany, I'd recommend joining some sports club/university sports or a theater group or... depending on what your hobbies are.

My first question is that what have I (possibly) lost by not networking?
Secondly, what is meant by "networking" exactly in an academic setting? Just knowing each other exists, or being some kind of friends, or just knowing who is interested in what?

These two questions are related, since what you've lost obviously depends on how you define networking.
In my view, networking is simply knowing and maintaining friendly relationships with people in your professional circle. It's nothing magical, it's just professional friendship. Those in your network may also be "social" friends, or they might be people you only ever see (or would ever want to see) in a professional context. Your network are those people who are more likely to take a biased and positive view towards you and your work, and for whom you also maintain a positive view of them and their work.
Thus, what you lose by not networking, is you lose a pool of people who might be willing to work together with you in the future, you lose those who might favorably review your grant application or journal submission, who might be willing to recommend you for a job or let you know about job opportunities in their orbit. On the flip side, you also miss out on having a group of talented people whose abilities and personalities you know and who you could recommend to fill a position in your own group or in your organization.

Thirdly, how can a graduate student network in events where most of the people are way older, and academically more senior?

I would say in this case focus on networking with your peers or close-peers (i.e. other students and postdocs). Networking is usually not about knowing people who are more senior than you, who have a ton more power than you, etc. Those relationships are typically more mentor/mentee, promotor/promotee. Your network are more likely to be made up of your peers. The people who are most likely to be in a position to benefit you in the future are your peers today, precisely because your relationship is not built on a transactional foundation. Those in positions above you in power/seniority are more likely to view things in what you are going to bring to them today/tomorrow, and already know enough people in their peer network that they're not in dire need of making a connection with you. Other answers about giving talks, asking questions and getting face-time with those above you at conferences is a good way to connect with those folks, but I don't think this will necessarily build a long-term network.
In terms of building up a solid peer network as a graduate student, you should start local. Take part in your school's student chapter of your professional society, take part in department events and interact with your group members. Beyond that, attend conferences as your schedule and advisor's budget allow. At conferences and other social events, don't travel just in a "pod" with your own group-mates. Take a chance to sit at a random table and introduce yourself around. If you see a talk from a student that you were really impressed by, tell them so and introduce yourself. You will probably be seeing those same folks at conferences for the next several years, so after the first meeting it will be more natural to grab lunch/dinner/drinks/coffee at future meetings.
Many of these people may not be those you have a strong personal connection with, but some will. For those whose company you enjoy, make an effort to stay connected between conferences and stay current on their career path. If in the future you're in a position to help their career, do so, and trust that they will do the same for you.

You are confusing between being social and interacting with people in developing professional networks. Professional networks could be strictly career-oriented and collaborative with no personal attachment. Your professor, for example, is in your network and you do not need to socialize with them.
Coming to answering your questions. Why do you care about what happened in the past? Just start networking now. If you can find Linkedin profiles of those people, feel free to connect now with a nice message on LinkedIn. Though, I believe Germany uses some other professional network.
You build an academic network in many scenarios. For example, you discuss someone's work over email or in-person and exchange feedbacks. You can apply for funding together. Look for organizing conferences or some sessions in a conference together. Invite them to your universities for guest lectures and also get invited. Let the PhD students in the groups exchange ideas.
What do you gain from it? You get votes and citations to your work. People who know your work would probably be nicer when they review your paper and vice versa. Without going into many of those things, you can collaborate on interesting ideas and push the boundaries of science and technology faster than you would be able to do it individually.
Focus on these goals and networking will follow suit. Do not put the cart before the horse.
There are people of all ages in most events. And in Europe people are not as hierarchical as in Asia etc. So you can talk to even people who are more senior to you while showing respect. Eventually, it is those people who will give you PhD and Postdoc positions.

People who know your work would probably be nicer when they review your paper and vice versa. They shouldn't, though. And under double-blind peer review, they thankfully can't.

@henning--reinstate Monica   Not all conferences are double blind. And even in double blind conferences and in A ranked conferences I have seen cases when papers were sent directly to 'friendly' chairs a day after the deadline.

@kosmos I know. That's true and wrong.

My first question is that what have I (possibly) lost by not
networking?

This is a hypothetical question, and we will never know. But, depending on the setup that you've been, you might have lost couple of interesting discussions that could have generated some ideas. Don't dwell on this...

Secondly, what is meant by "networking" exactly in an academic
setting? Just knowing each other exists, or being some kind of
friends, or just knowing who is interested in what?

Mostly the first and the last, but not the one in the middle. People will keep it professional, you should not expect to become friends with people that you will meet in a networking event.

Thirdly, how can a graduate student network in events where most of
the people are way older, and academically more senior?

Targeted networking: in such event you usually know the participants upfront. If any of them are of particular relevance to you, you can easily approach them. If they are relevant, you will already have an idea of the topic to talk about. "The seniors" in academia usually deal with people younger than themselves, i.e., their own students. So, you can expect them to be open to discussions, but you will probably not get their full attention. They are there for networking as well, for their own interest. This should imply that the theme" of the networking event is relevant. If it is meant for the young, i.e., a PhD forum, you will have your opportunity. If it is a lunch break in a top conference, people will stick to their ranks.

a downvote but no explanation whatsoever... why though?


text:
Is it common in academia to not have any written "contract" when you get a scholarship?
If you are been accepted into a Master's program which grants a scholarship to its participants, they just send you a letter outlining the scholarship in a brief manner. Is this common in academia?
Question:
Is it common in academia to not have any written "contract" when you get a scholarship?
Edit:
I am mostly interested in Europe (in particular Germany if it makes a difference)

For some of us there is a very real difference between "getting a scholarship" and being accepted into a program, either MS or PhD. A "scholarship" often means that there are no duties involved other than remaining a student in good standing.  Can you explain more what you are asking? I'll note also that the policies are extremely variable around the world.

@Buffy Thansk for the comment; is it clear now?

Is it a bona fide scholarship, i.e. a bunch of money with no strings attached? Or do you actually have a lot of duties, like attendance, and taking orders from your advisor/head-of-lab/PI etc.?

What country is likely important in this case.

@StephenG see my edit please.

I have had a scholarship in Germany where the letters (their offer and my acceptance letter) together were the actual contract.
A scholarship in Germany is a mostly one-sided contract: the funding agency grants the scholarship. There are almost no strings attached for the recipient of an academic scholarship since the purpose of the scholarships is basically to give the recipient carte blanche to pursue their research/studies (usually there is a requirement to write a reports about what was done/achieved every so often, there may be requirements to present your work/achievements if asked to). But the scholarship cannot enforce working hours or the like (that would make it an emplyoment contract), and also no outcome (that is not even possible for an employment contract).
Since scholarships are exempt from income tax in Germany, it may make sense to take the grant letter to the local service desk of the tax office and have them check that it fulfills their criteria.
They'll tell you (at no cost) whether any further information is needed, and whether you need to submit a tax declaration/where to put the exempt income.

Caveat: A US view, and there are exceptions even here as noted below.
There will, I think, always be an "agreement" even if it isn't a formal contract. It probably isn't something that is negotiated, with the student having any say. But accepting such a scholarship is a formal agreement to abide by some set of rules, that may be just statements of policy somewhere, perhaps visible on a web site. All the details may be spelled out in the letter of acceptance, but it is more likely that the student simply makes agreement to obey the rules in force.
The most common "rule" is that the student maintain "good standing" which involves something about GPA, perhaps, and not being sanctioned for misconduct. Whether it rises to the level of a "contract" however, depends on too many things (local law,...) to have a definite answer here.
I suspect that in many cases the (informal) contract can be modified by the university without explicit consent of the student. The student's only likely recourse is to accept the new terms or stop receiving funding.
Note also that this differs (drastically) in some places and some situations. It also depends on what you mean by "scholarship". If there are specific duties attached (not the common case in US) then the contract is more likely to be a formal one. In particular a TA position has certain duties and so additional requirements.
If a scholarship has no duties attached then it is probably also possible for the university to terminate it for many reasons, including financial ones. But the student can also leave the university (possibly needing to return pre-paid funds) without penalty. This might be different if there were a formal contract.

A scholarship in Germany (Stipendium) can have only very few strings attached by legal definition. E.g., it cannot have working hours specified. Typical requirements that are possible are: written report after each term, possibly presenting at the funding agency if asked to, duty to take at least n workshops out of a list of workshopy they hold (at the cost of the funding agency).

@cbeleitesunhappywithSX, yes, and thanks for your Germany specific answer.

EDIT:  Answer not updated for changed question.
Yes, the letter often functions as a contract.
If the position is unionized, the contract between the union and the university applies to the person who accepts the letter.
This is not legal advice, and this is not the law stackexchange.

AFAIK, a scholarship cannot be unionized in Germany since by definition a scholarship is very much not an employment.

@cbeleitesunhappywithSX The question changed.

Instead of writing "Answer not updated for changed question", you could better write to which country your answer applies, which would have been useful anyway.

@MassimoOrtolano Country does not necessarily determine unionization, so no, that doesn't work.  In my opinion, the answer is still correct, just not specific to the more narrow question.


text:
Where to get help when we can't understand something done in a paper?
I often face the following situation:
I am reading a technical paper, and I can't figure out a calculation shown in the paper, whose details are not given. There is no reference in the paper about the exact calculations. It is not possible to get an answer from the author(s), either they are dead or they don't answer even if I did (even if they did, it takes a lot of time for them to respond). I can't write to my advisor; for him to help, he also needs to read the paper and practically this is neither ideal nor realizable in a short amount of time. I can't write to my friend because I don't have any friend who works in the same field as I do. I won't ask the question in one of the stack exchange websites, because it is often the question is too field-specific and technical that I don't receive any helpful answer in a considerably short amount of time (assuming that I will get a helpful answer, which is not the case most of the time).
So, in the end, I try and try to understand what the heck author did in that part of the article that I couldn't understand, and it takes a considerable amount of time for me to figure that out (if I can).
Question:
Assuming that I am not the only one who faces such problems, where can we get help in such situations?
Note: I am working in a field of Physics.

I would try to understand what the authors are trying to calculate.  So base on previously presented concepts, say A, and the aim, say B, I would then fill in the gaps myself trying to go from A to B.  It's possible that the authors' answer or derivation is wrong.

@Prof.SantaClaus just to get an idea, how often do you see wrong calculations in peer-reviewed papers?

quite often.  Also, most reviewers (in my experience) do not check calculations.

@Prof.SantaClaus good to know; thanks for the comment

If it is in math, you can ask at Mathoverflow.

Assuming that you've exhausted a reasonable degree of effort to try and understand what the author is doing, you can always just contact the author directly. There is usually contact information on the paper for the corresponding author.
There have been a number of papers that I have read and needed to reach out to the authors for to get a better understanding of what is going on in their paper. Professors are people too. As long as you have demonstrated a reasonable degree of effort prior to reaching out, asking for some clarification from them is a reasonable thing to do.
In the case of an author having passed away... then you will want to communicate this to your supervisor and explain why you need help to understand the paper. If you cannot figure it out for yourself, do not have any peers you can talk to, or are unable to contact the original author, then you have your supervisor as a work colleague.
If that all fails, then you will just have to try and drudge through understanding the computation. While I understand you want the answer quickly, all things worth while do not come quickly, and you'll need to cultivate and demonstrate resilience in the face of that struggle.

Thanks for the answer; the effort is not a problem, but ideally I would like to get the bottom of the issue quickly, so that I can use the calculations in the paper in my own research.

They may be depending on something done in one of the references. Traditionally you follow those back to see what is there. And, there may be no quick solution to understanding.

+1 for "While I understand you want the answer quickly, all things worth while do not come quickly"

@Buffy Thanks; I didn't think the author could be using a calculation given in an earlier reference. But, I remember that I have seen such (failure of proper referencing) cases in the past, so I will keep that in mind next time.

From the question and your comments it seems like you are actually capable of reading and understanding the paper, it would just require effort on your side. It would therefore be easier for you if someone else would exert that effort.
Allow me a bit of a harsh reply, then.
It is not the job of the author of said paper to provide a pedestrian introduction - they wrote a paper that is apparently both readable and correct.
It is not the job of random people at SO to answer very field specific questions about a specific paper at someone's request. One might get lucky, but asking SO requires patience. And luck.
It is in general not the job of your supervisor to read papers, and give you a Reader's digest version of it. It is, however, the job of your supervisor to help you overcome specific hurdles you encounter when trying to understand a paper, ie. a specific calculation you cannot reproduce.
So: Use the resources at hand, and start reading :).

Sir, no need to be harsh; I know it is my job to exert the effort, but even after two days of working on the same calculation, I can't figure out how the author go from one equation to another.

"It is, however, the job of your supervisor to help you overcome specific hurdles you encounter when trying to understand a paper, ie. a specific calculation you cannot reproduce."


text:
Is the PhD thesis needed for a faculty appointment?
I applied for a full professor position, and after the interview, I was asked for a copy of my PhD thesis.
I was confused and want to know if it is the common and normal procedure or happened for me based on a specific reason?
Because, my strong works were done after my PhD, and I didn't know that my PhD project would be used for judging me (frankly, I'm not proud of that project).

It's a little odd, I must say. Similar to asking assistant professor applicants for their "Ph.D GPA" :).

It looks to me more like asking assistant professor applicants for their undergrad GPA. At the career stage where you're applying for a full professorship, your Ph.D. thesis is not nearly as relevant as a lot of more recent work.

One of the general prerequisites in this day and age for a faculty appointment is an earned (as opposed to honorary) PhD from a (typically accredited) degree-granting institution.
Consequently, asking to see either a PhD thesis, a transcript, or the degree certificate is would be ways of ascertaining that you do, in fact, have a valid degree. This by no means implies that only your PhD matters in the hiring process; just that it's part of the process to ensure you're eligible. I wouldn't read too much into this beyond that.

sorry I didn't get your answer. I understand that proof of the terminal degree is mandatory, and the proof is diploma and transcript. Why the PhD thesis is needed as a proof? Thesis is a scientific document, not official.

It's not unreasonable for them to want to see the quality of the thesis as well. It's another data point for them to use.

I assume you are applying to a junior faculty line (your use of "full professor" would suggest senior faculty but this is belied by the rest of your post).

After they make the short list, we commonly ask junior faculty who do not yet have a research monograph to submit their dissertations. We do this for several reasons:

If they are ABD, it is an easy way to ascertain whether they will complete. If it is March and they say they are submitting in April and they only have 3 chapters, then we know to be cautious.
If they are recent PhDs, then often the PhD is the only piece of research writing that they have in their dossier. It remains one of the best gauges of their research competence until they complete more publications.

After responding, I looked at your profile and it seems that you might indeed be applying to senior positions. In that case, I'd be puzzled too -- unless you don't have many publications and/or your dissertation was at a university that is not well known. Or, alternately, the institution you are applying to has not had much experience with senior hires, and is defaulting to the junior practice.

Personal Aside: I'm a tenured associate. If I applied for a full position and they asked for my dissertation,  I would be puzzled but not be offended IF they had also asked for everything on my CV. I would assume they are just being extremely meticulous in making my case to the Provost for the senior line. But if they asked for just a few of my publications and my dissertation, I might tend to becoming annoyed (by the insinuation that my PhD was suspect).

It depends on the field. What they generally want to see is a Terminal Degree, or exceptional achievement in lieu thereof. But in some fields no widely recognized PhD level really exists, and the Masters -- plus professional experience -- is as close to a terminal degree as it gets.

How does this answer the question? The OP is asking whether it's normal for him to be expected to show the hiring committee the PhD thesis, not whether he's expected to have earned a PhD.


text:
Who is earning money when users buy access to a research article?
I'm a software engineer, but I used to have to read a lot of papers about neurology. I am slightly disappointed by the high price for access to the full text of research papers. I can understand a pharmaceutical company could pay that amount of money, but I don't think private people can afford to pay $30 for reading a paper.
Does the money from article sales go to the researchers, the journals or somewhere else?

The discussion on this question has been moved to chat. Comments are for clarifying the question, not for extended discussion.

Related: Do researchers receive no income from revenues arising from their published papers?

Regardless of political considerations, the answer to your question is that publishing companies are collecting the revenue from subscriptions and individual article sales. Some publishers are commercial operations, some are non-profit (such as the American Institute of Physics).
The price you pay at this time is related only to the publishing process (organization of submission process and peer-review, typesetting, archival strategies, printing, administration, etc.) and all other aspects of a commercial company including, of course, a margin. Some people have strong opinions about what this margin should be.
The actual research is paid for by other means, including government grants, university salaries, non-profit and foundation grants, funding from commercial companies, etc. If you had to pay for the actual research behind a given paper, chances are it would cost you something closer to 30k $.
There are various other business models for publishing, some where the whole process is paid for by an institution, and is thus free for both authors and readers, some where authors have to pay to publish, etc.
There are important aspects in keeping money out of the editorial board - publisher - reviewers - authors relationship, because it reduces the risk of conflicts of interest (although author-pay open-access advocates think otherwise).
Options to obtain scientific papers without paying (yourself) include: going to the library of your local institution, checking out pre-print servers and government-sponsored repositories or ultimately, contacting the authors to obtain electronic copies. More on that subject in this useful thread.

I would think in the field of neurology, 30k could many times be a very low estimate.  Just paying for a single research subject to study the brain on PET scans can cost 1k $ on just incentive, not including paying for equipment (or rental fees)

@user1938107 suppose 50 people read the paper, you would get a million and a half, a good start for a research project. Anyway this was just a way to illustrate my point.

ah now I see your point, I read "if you had to pay for the actual research behind a paper" to mean the actual cost of funding the research, which you dont need to because the research is paid for by grants etc.  Now I see what you mean, which would probably turn research into kickstarter projects, asking people interested in the subject to pledge money until there is enough to conduct it.

Notwithstanding the above, the funding of the research may well be 30k, but the value of the output may be far less. More often than not, without connotation, research results are purely incremental, and relying on them is only wize if they have been further discussed in other articles, and/or reproduced or challenged by complementary approaches....


text:
How can an international student get accepted into a PhD program in an area different from his MSc?
First off, I realize my question is too broad as it depends on the country, but I would be interested to hear mostly about the process in Canada and in western Europe, where it is common to complete a Master's degree before one's PhD.
I am an MSc mathematics student, and I am considering to switch to a different field for my PhD studies. I am thinking about certain directions in Computer Science or Electrical Engineering, which are completely unrelated to my current research.
Within my university such a switch is not uncommon, as the duration of a PhD has quite a soft upper bound, and a student coming from a different background can be accepted and simply required to learn the necessary basics of the new topic. Also, students who have received their MSc from the same university are not required to present official letters of recommendation when applying for a PhD, and the acceptance depends pretty much solely on the new advisor.
However, I imagine such a process would be much more complicated when applying to a different university, especially in a different country, as the department (or the potential advisor) has no way to evaluate the student's potential in the new field (assuming his MSc has nothing to do with the new field), and the student can't present letters of recommendation from researchers in said field.
Are such cases common? Are students coming from a different background at a significant disadvantage when competing with applicants from the same field, and how could one raise their chances of acceptance?
Thanks!

A lot depends on how strong your application is and the field you apply to.  Much of CS and EE is just thinly veiled math, so math -> CS/EE is easier than CS/EE -> math. It is impossible to say if you will be at a disadvantage.  You should email specific programs and directly ask them.

I have a friend who has changed his area from Computer Science to Theoretical Physics, but at MSc, he graduated the first, continued with the PhD, and was one of the best graduates.


text:
Does dropping a Coursera course look bad in a PhD application to the university offering the course?
A few weeks ago I've enrolled in a Coursera course offered by university A, without asking for a certificate. I've completed some of the work, but now my university holds a course on the same topic, to which I am enrolled for credit.
Consequently, I decided to stop doing assignments from the Coursera course and focus on the course I'm enrolled in.
University A is one of the universities I am planning to apply to for my PhD studies next year, possibly in the topic of the course (or even with the professor teaching it).
How likely is it that the professor and/or the committee will check whether I've already been enrolled in something offered by them, and will get a bad impression because of me dropping the course? (e.g they might conclude that I'm not serious/committed when it comes to studying.)
Do committees generally look for academic information on applicants other than in the documents they provide in their application?

this seems very unlikely to matter.

There's almost no way they would know. They could, but this is a very low-value thing to check.

Your identity is not verified when you take a Coursera course without a certificate. Anybody can register with any name; l could register under your name if I knew it. Even if anybody on the admissions committee cared (which they don't), they still would have no way of unambiguously connecting the PhD applicant and the MOOC dropout.

I don't think they're going to take attendance at football games either, but you never can be too sure.

AFAIK Coursera is not for credit, thus should not impact your phd record in any way.

Is this answer based on an assumption that only things that are for credit impact a PhD application?

Certainly not.
I highly doubt any university even has a mechanism for looking this up easily (since it isn't public info), or if they are even allowed to do so (might be against their privacy policy).
Also, MOOCS have extremely low completion rates (this says 15% on average) to begin with. These online courses, unlike traditional university courses, don't require a commitment or have any real effects from not completing it.

Things happen! People drop courses all the time for various reasons. In no way should it look bad. If you weren't going for a certificate, it doesn't really matter.

@djechlin And in many countries no-one cares.

authors: Vladimir F Героям слава


text:
Is it polite to ask about scholarship/assistantship opportunities during a Ph.D. interview at a UK university?
I am scheduled for an interview in August for a Ph.D. program that I applied to at a UK university. However, even if I get an offer of place on the program, I would not be able to accept it unless I also receive funding. So, is it okay to ask the panelists after or during the interview about the scholarship/assistantship opportunities that the university offers? Thanks!

I wouldn't expect them to have any more information than is already on the university website.

Yes, it's both a polite and sensible thing to ask.

There is quite a bit variety in how funding for UK PhDs works, but I am not aware of any situation where you would apply for a scholarship via the university AFTER an admissions interview. Instead, I'd expect one of the following setups:
A. For a university with a lot of attached funding (eg Cambridge), you indicate that you want to be considered for scholarships on your initial application. Funding and admission are then mostly aligned, although it is still possible to get admitted but not funded. At the moment you could be interviewed, the funding deadlines are long over.
B. A university with limited scholarship funding will usually advertise scholarships or RA positions directly, and the admissions process is integrated in that. Most scholarships will be restricted to UK residents. If you apply directly for the PhD programme, you are exected to have external/your own funding.
So unless the university you've applied to follows a different model, you may have wasted everyones (including your own) time already.


text:
Correcting and improving a submitted article
Recently I wrote a paper and submit it to a journal. Currently it's under review.
Later, after checking the preprint over and over, I noticed typos (for example instead of considering $\mathbb{N}^*$ I wrote $\mathbb{N}$) and I made modifications (not significant): grammar errors, improving the content.
During the review most of the above will be noticed.
If I was asked to make revision should I include the typos... ?
Also, is there any problem if an unnecessary remark - which isn't used and doesn't have an influence on the paper, it's remark of the form theorem x and theorem xx are true if we replace $P_1$ by $P_2$ a result which can be concluded trivially - is removed ?

First, I would endorse the two answers already given. As far as the issue of removing superfluous or unnecessary material goes, I would be inclined to remove the material, but with provisos. First, before removing it, consider whether the material now seems superfluous to you because of your familiarity with the subject. It might not be considered superfluous by a reader who is less familiar with the material than you. Indeed, unless the material is simply annoying because it interrupts an otherwise clear chain of thought, I would be inclined to leave the material as it stands. If the reviewers found the material obtrusive, they would say so. The second proviso is that if you do delete the material, you should highlight the fact in the covering letter for the revision and make it clear that the material could be restored if necessary.
I've done this several times in resubmissions (both with mathematical papers and others), and have received both kinds of responses from editors along the lines of either "please restore the deleted lines", or "yes, I agree that the deletion makes the paper flow more smoothly". In one instance, I was asked to put my proposed deletion into an appendix, smoothing the flow of the main paper, but providing a supplementary support for some readers who wanted it.

Typically, if you find any errors (even if the reviewers dont notice them), you should correct them during the review process. Regarding all the issues you noted, it should be possible to submit a revised version with your corrections and an answer to the reviewers in which you must include and comment on all changes to your manuscript.

If I was asked to make revision should I include the typos... ?

Yes, you can and should make any appropriate edits when you submit a revision. Note what you changed, like any other. If you receive no requests for revisions, you can make these changes at the proof stage.
I'm not in math, so I won't address the second part.


text:
Is it possible to do labs in a college separate from the one I'm enrolled in?
I'm currently living abroad in japan and looking to start college online from an American university. The problem is that any biotech course I'm interested in requires a lab portion to be done physically. So is there anyway to complete a lab assignment, specifically a biology based one, at a foreign college? And if so would there be any catches like having to pay a fee?

I've never heard of anything like this but I can't imagine how it would work. Assuming this is an undergrad degree, the lab work isn't about the results (as it might be in a Masters or particularly a PhD) but about learning through doing. If you aren't receiving instruction from course leaders, you aren't learning what they want you to learn. Another potential option might be to start at a university in Japan then transfer - others may know more (part of why this is a comment not an answer).

It seems to me that this question has no generally useful answer. Clearly it is technically possible to complete the assignment in any physical location where you have access to the necessary facilities. Beyond that it is entirely up to the two institutions involved whether they are willing to participate in such an arrangement. Voting to close as 'depends strongly on individual factors'.

With Covid, places have scrambled to figure out the lab thing. Having a university student in the family, I have some insight into one institution. They did a mix of in-person and virtual for freshman physics labs, working in teams of 3. One would get to go do the actual physical stuff in the lab, the other 2 would do some research, and all would contribute to the lab report. One of my kid's team mates was fully virtual (not on campus). Perhaps not surprisingly, the remote person was the least invested in the course and mostly did not do their share of the work, but could have.

Ask the American university, and look before you leap. If they are offering online programs, then it's their responsibility to provide a pathway for you to satisfy the degree requirements.
In my estimation, the odds that a Japanese university would be willing to supervise an American university's lab assignments are low; the odds that they would do it for free are lower still. You might be able to take entire lab-based courses at a Japanese university, and then apply for transfer credit.
Before enrolling in any online program I recommend that you first ask lots of questions and make sure that their program fits your needs.

It's possible depending on the collaboration you can make with the varsity that you want to run your lab sessions. And this can be done with the other help of the varsity that  you are in enrolled in. So it's your duty to discuss with the management of your University so that you can be given legitimate papers for you to run lab operations in the other university.

Yes, it is possible.
My college advisor has a good impression on me. I graduated few years ago, but recently we make contact and start to collaborate on projects while I am still taking a full-time job. So from my humble experience, it is all about time management and trust from others on you. But I do keep this secret from my co-workers to avoid troubles.


text:
Venue name structure for citing papers
I have noticed in some citations that the journal or conference name is split up, for example "Neat Stuff, International Conference on" instead of "International Conference on Neat Stuff." For example:

Ragsdale, Daniel J., et al. "Adaptation techniques for intrusion detection and intrusion response systems." Systems, Man, and Cybernetics, 2000 IEEE International Conference on. Vol. 4. IEEE, 2000.

Is there any reason for writing the reference this way?

Where did you get this specific citation example? If it is from a journal, then the answer might be the specific citation style. My guess is, that in this case, the journal wants to have it that way?!

Here is the conference page: http://ieeexplore.ieee.org/document/884952/

If you click on the 'Browse Conferences', you see that the links/conferences are listed by year and then the name. This might be the result of the specific citation style...

There are a virtually unlimited number of conferences whose title is of the form:

"[Society] [International] [Conference|Workshop|Symposium] on XYZ"

where "International" is optional and the optional "Society" is a big organization like IEEE, ACM, ACS, etc.
Since there's basically no information in the first part, the organizers and attendees of these conferences will tend to refer to them as the informative "XYZ", ignoring the preamble.  Citations often do the same (e.g., just "XYZ" as venue, and sometimes even just the initials), particularly in page-limited publications such as standard IEEE proceedings.
The "XYZ, IEEE International Conference on" form is then a hybrid compromise that some venues use to put the informative bit up front while still keeping the full title.

If I recall correctly, "Xee Yay Zat, IEEE Conference on" is the standard style of IEEE bibliographical data, i.e. if you get it from them, it looks like that inside. I've always edited it to the (arguably) canonical "IEEE Conference on Xee Yay Zat" or even "Conf. Xee Yay Zat" if the place was scarce. "XYZ" is probably too ambiguous, but I was guilty of that few times, too.


text:
What is the norm in PhD internships in terms of their duration, tasks, and location.
Context:
I am on my third year doing a PhD in Engineering in a North American University. The norm in my institution is that a PhD is 5-6 years long. I was funded through the past period of time through a scholarship. The "understanding" is that the advisor funds students after the initial three years but nothing is formal.
Situation:
My advisor found an internship opportunity for me and "strongly" suggested that I take it. In this case, the company pays me while I am there.  During that time, he gets matching funding from the government. The idea is that he would use the matching funding to pay me after the internship ends. He basically takes the money and gives to me back later. I trust that he will do that. I am not sure if this is considered normal or not in acadima but that is not my question.
The problem:
The problem is that some aspects of this specific internship seem abnormal to me and I want to get feedback from the community about these aspects.
Questions:
1- The internship is for 9 Months. It is full-time internship and I will not have time to work on my PhD. This means that my PhD is extended by 9 Months (5-6 Years + 9 Months). Is this a normal period of time for a PhD internship? I have seem people go on a 3-4 Months internships and even 6 in one case but never 9.
2- The tasks of this internship seems to be a long the lines of a Full-time engineering job. There does not seem to be any research involved. My thinking was that a PhD internship would help me develop my research skills and this seems to be an internship for a masters student or an undergrad. Is it normal for an PhD internship to be a full-time job in disguise?
3- The internship is located in another city. I have to move there for 9 months. This would require me to completely change my living situation twice in 9 months. Is this considered normal?
I am considering passing on this opportunity and finding a more suitable one myself. I just wanted to get feedback from experienced people before doing so. I would appreciate any input.

I suggest you reformulate the question title to better reflect what you are asking. As it stands it's terribly vague/broad: a lot of things can be considered normal for an internship, that may or may not be relevant to what you are asking

I reformulated the title. Thank you for your input.

For research internships I think doing a bit longer will result in better outcomes. In my experience it takes 1-2 month to get into a new work environment/topic and doing serious research in 2 month is unlikely.
The best way to find out is to talk to your supervisor (at the internship) about this. The internship should not be a pure engineering task (it is still a full-time position though). It is probably to be expected that you do some hands-on work but you can ask about the topic and the probability that this will result in a publication. Depending on what your PhD topic is, you could also see this as an opportunity to get some real-world experience.
This is quite normal (I moved to the US for 6 months, I know a lot of people who did this). Of course if you do not want to do this, your supervisor should not be pushing you.

It would be best to consult with your advisor before searching for something else yourself. Maybe he just wants the additional funding for you but maybe there is something else about this internship that makes him think it is suitable for you.


text:
What if an undergraduate concentrated on research on the account of his study?
I am studying medicine. We study different disciplines and different specialties during our undergraduate years.  My subject grades aren't very good. Then, I rushed to research and biostatistics -maybe to veil my low grades- and have made a little good progress at them while I am still undergraduate. Will doing this help me in my future? (I mean if I continued doing bad at the subject exams and concentrated on research methodology and biostatistics)

Improve your grades and do the research. Those things are not mutually exclusive. Otherwise you are crippling your research future.

This might be different to medicine, but, in general, for undergrad, good grades are good/necessary, research is bonus...

Changed "faculty" to "subject."  I hope this is what is meant (the use of faculty didn't make sense to me ).

When you say you're studying medicine, I take it that you hope to be a doctor.
In which case it doesn't matter how brilliant you are as a researcher, if you can't acquire the necessary medical knowledge and clinical skills you'll never be competent or safe to practise medicine and your medical career will never get started. You may have a fantastic career as eg a medical statistician awaiting you.
It's great if a doctor is research competent too, but being able to do research is not essential. Being able to examine, diagnose, and treat patients is.


text:
What to do if my professor won't give me a grade for a test?
So I took this online class and the professor didn't grade our exams till the end of the semester and I was surprised to learn that I got a 0 on the first one. Now I remember taking this test and while I may not have gotten a perfect score, I don't think I did bad enough to deserve that grade. So I talked to him about it and he said he has a couple of blank scantrons and can't figure out which is which so he gave a couple of us a 0 instead. The thing is, the testing center at my college won't let you turn in a test unless everything has been filled out and I'm 100% sure that I didn't knowingly take the test without putting my name on it.
What do you think I should do? He also mentioned in the middle of the semester about losing his laptop or something like that, do you think he's lying about the blank scantrons to cover up the fact that he may have lost them and won't take responsibility for it? I was talking to him through email yesterday and now he won't respond. It really hurt my grade and he won't do anything about it. I NEED HELP!

I lost a student's test once.  With no way to assess the student's performance, I assigned a grade of 100%.  For the remainder of my career, I checked that each test had a name on it before allowing the student to leave the exam room, and came prepared with a giant binder clip.

@BobBrown I second this. When in doubt, error on the side of benefiting the student. This professor seems to have done the exact opposite.

If this is accurate, you should talk to the Department Chair.

Is the professor claiming that there are scantrons missing names or completely blank of answers?  If the scantrons are missing the names (who knows, maybe it happened) and all other names are accounted for, I would think that, at the very least, you can make the argument that the unnamed people should receive the lower of the two grades, rather than a zero.  This is a problem that is definitely compounded by the professor grading the tests so late in the semester.  I completely agree with DC541 that there is something odd happening here, but proceed with caution.

In my assessment, the professor acted somewhat negligently here. (Albeit maybe not lying).
I find it odd that he claims that he had a few blank scantrons without names, so he just gave people 0 points on the test. Really? He doesn't even have the presence of mind to email students and ask if there had been a mistake? This seems incredibly lazy. (Not to mention the fact that he waited until the end of the semester to grade the tests). I'm not sure it would be too far beyond the call of duty for him to have at least email students to verify if what he is seeing is correct. I would have done this for students I have, especially if they were turning in the homework and completing other assignments.
I do wonder how in the world your testing center would return blank scantrons to a professor. At every school I have ever taught at or attended, the testing center produced scantrons with student names computer printed on the top. And the testing center always scored the scantrons. Does this professor have his own scantron reader?
Moreover, every testing center I have ever interfaced with kept records. Surely your university keeps digital records of which students have taken the test, right? I'm pretty sure my undergrad institution kept computer-based testing center records even in 1996.
As Buffy says, I would stay away from accusing the professor of being a liar. But make this professor account for testing records recorded by the testing center. I'm of the opinion that this is actually part of his job description (implicit or otherwise).

I doubt that he is lying. There is little, if anything, to gain. I think the best you can hope for is to ask him if he will let you take a retest - even if it is a quick oral exam on the "missed" material.
I'm not sure why you haven't learned of this before now. Is there something you neglected to do earlier. If so, it is harder to get any satisfaction at this point.
But is your professor who can help you, not the people here. Email isn't a good way to handle things like this. You need to go see him if it is at all possible.
If you don't get a quick reply from email the reason could be benign or not. If you can't go see him and you don't get a reply, ask his superior to have him contact you. Don't make an initial complaint, I think, until you have tried other avenues.
It is possible, of course, that a scoring sheet was lost, but also possible that it was lost by someone else in the system. Be careful about accusations, especially of those who have power over you. Investigate first.

If the class is online, I wonder how feasible it may be for the OP to go to the professor in person. If possible to go in person, I would agree that it is best to try to find the professor face-to-face.

@user102164 "Be careful about accusations, especially of those who have power over you. Investigate first." I think that's all you need to know.


text:
How far should I help students with learning extracurricular skills?
I am currently a teaching assistant for both master and PhD students. Part of my work included helping and supervising them during several lab experiments (physics). One task of the lab experiments is to write a program to numerically calculate values and simulate them afterwards. The students are allowed to use any programming language they want to use (except stuff like Brainfuck and Whitespace, of course), as long as they provide the source code with the result.
While the master students are not having any problems with the problem, I got was asked by the PhD students if I can help them do the programming in Excel, as that is the only thing they can use and know for "programming".
How far should I now go and help them? I know that doing the task they are assigned to is impossible to do in Excel, but they never used any other language or programmed themselves. I am able to teach them how to achieve the programming goal, but based on their current knowledge that will take a lot of time, which I also need for my own lab tasks. Should I thus simply tell them to drop the course, or should I try to help them, and if yes, in which extent?

Your class should mention pre-requisites, which would include knowledge in one of a list of acceptable programming languages. Does it not? If it does, it's fair to refuse help in other languages; if it does not, well, that's bad. Also, is this an elective class or a core class? Finally, are you sure it's impossible in excel? The VB background is turing complete, isn't it, and it's part of excel; so while it's backward, it should allow you to do any task?

This is an elective, non-necessary class for the PhD students. As far as I know there were no requisites stated beforehand. Concerning Excel: I did not consider VBA, that is correct. But in that case I am not able to help them, due to my lack of knowledge in VBA...

You would be amazed at what can be done in Excel. Not the tool I would choose for hard core computation, but it can do likely anything in a canned physics lab. I've certainly seen it used extensively in current research projects. I may give the PI some flack on 'Excel abuse' but it does the trick. The hard part is Excel does not lend itself to letting somebody else (say the TA) actually understand what is happening in the same way that straight code can.

@JonCuster: Thus your suggestion is to let them do that in Excel, but I can not help them in case of a problem?

Recall them that You shouldn’t use a spreadsheet for important work (I mean it)!

@arc_lupus - well, I wouldn't waste time debugging their spreadsheet, but I would not debug someone else's code either. You have them tell you how they approach it, and show you how the did it. With the excel folks you may have to probe deeper...

You can model stochastic differential equation in Excel, so there is quite a lot that's possible in Excel, and it's kind of fun to learn how to do this stuff, although it is of the category of mental exercise rather than true work skill.

Writing a simple free-standing program in most programming languages would be easier than using VBA in Excel.

So: If there were no advance requisites stipulating the need for programming skills, then where did this programming task come from? Whoever created this task put the situation out-of-synch, and they have a responsibility for rectifying it now.

@arc_lupus 'due to my lack of knowledge in VBA': If you can deal with students programming in any language they choose then VBA is really not going to cause you problems. It is the first language I was taught, and I sat down for a weekend and got the hang of it.

If you are a TA and have questions about what to do, almost always the first thing you should do is ask the instructor.  The instructor should clarify exactly how you should be assisting them, and what the prerequisites for the course are.  I would be wary, as a TA, of suggesting students to drop the class.

How far should I now go and help them?

You probably shouldn't be spending any time whatsoever teaching prerequisite skills one-on-one to any individual students. As you say, it is not anywhere in your expected priority queue of work that the university expects you to be doing (plus: it's simply an inefficient use of the time resource). Perhaps the most that is reasonable is to point the student in question to a relevant class, book, or tutorial from which they can learn on their own (and as an aside, to explain why it's a bad idea to use Excel for a task like this).
That said, you note in a comment that "As far as I know there were no requisites stated beforehand". This is, indeed, very bad. I would say if that's the case that the instructor may now have a responsibility to give them an alternative and equivalent assignment that does not involve programming, if that failed to be stated up front in university prerequisites, or on the first-day syllabus information.
Definitely speak with the teacher of the class (and advisor if that's a different person), tell them there are students in the class who don't know any programming, and ask about how to handle this case.

"you may now have a responsibility to give them an alternative and equivalent assignment" - I assume the "you" here refers to the instructor of the course, not the teaching assistant who posted this question?

Giving them an alternative assignment is not possible for me, after I got the assignment from the teacher to do the given experiments and help them with the evaluation afterwards. Thus I have no influence on that.

Thanks, I did indeed misinterpret the situation. Edited a bit to reflect that the asker is not the teacher. Definitely inform the teacher about this situation.

This is definitely an issue for the instructor.
Perhaps programming should have been mentioned as a prerequisite for the course. On the other hand, the prerequisites probably did not list "Must be able to find the physics lab given a campus map.", even if that is required for success on the course. The instructor may have, not unreasonably, assumed that graduate students in a STEM subject can do simple numerical programming in at least one language.
You may want to have a list of options to present to the instructor:

If the assignment can actually be done using a spreadsheet, show you how so you can help the students do so.
Set an alternative assignment.
Pick a time period when you would normally be doing TA activities, and tell the students who cannot program to meet you then. Teach them really, really basic programming in some language with which you are familiar.

Personally, my go to is to provide as many resources that are available to them, and then it is their prerogative to take advantage of what I have provided to them. There are a number of excellent resources for students to learn how to code and program in all the languages available online, and for free! I've have used both the free options, and they give practical and immediate feedback on their progress.
Being a TA takes a lot of time, and it being a post-secondary education course these students should be responsible enough to seek help and use the resources available to them. You could put a task from these sites as a lab, or do quizzes based on the activities in each module on the sites below.
If you are looking for free options I would recommend:

Free Code Camp
Code Academy

A paid option is Udemy
Free Code Camp is a collection of many resources from all over the Internet. It has 300 hours of total practice available, all split by the different programming languages.
Code Academy is a website that has a built in lab with it that requires the user to successfully write the code in order to advance through the module. It also has a support community for people to ask questions if they get stuck.

It would be nice if you provided URIs.

https://www.freecodecamp.com and https://www.codeacademy.com

I'd state my competences (where I can help without having to study a week to come up to speed) beforehand, and tell them I can't be of much help outside that range.
That said, being able to use Python (perhaps as part of sagemath), or perhaps some language like Mathlab will be very valuable for them later on. Yes, spreadsheets are Turing complete, but that doesn't mean anything. It is much more important that the program is clearly written, and can be fixed/extended by somebody else (even yourself after not looking at it for a couple of weeks).

Well, Brainfuck is also turing complete, but I still would not advise anyone doing serious stuff to use it...

@arc_lupus, don't compare a language designed (and widely used) for serious work with something created as a sick joke. Search for "Turing tar pit".


text:
How should one acknowledge assistance received via sites like SE?
I have been working for some time on a paper that I hope to submit to a mathematics journal. Buried deep in the guts of the paper is a technical lemma that I struggled with for some time before finally posting the question to MSE, where it promptly received an answer.  What is the proper way to acknowledge this assistance in the submitted manuscript?

Related: Attributing contributions to academic work that occur in Stack Exchange.

Also, can you please clarify: Do you want to know what kind of acknowledgement you should use, i.e., citation or acknowledgement section or how the acknowledgement should be worded?

I was assuming that the correct way to do it would be to use the acknowledgement section -- but perhaps citing the answer as a source is better, after all.

Then maybe you should first make up your mind about whether you want to cite or acknowledge (perhaps by changing this question to ask about it) and when you have done so, ask a separate question about the form of citation/acknowledgement.

In your case, the user who helped you participates under his real name (he's from my hometown :)). I would include his proof, with a footnote at the page bottom "This proof is due to ...", and additionally thank him where you usually thank people (I've most typically seen this as footnotes on the page of the abstract, but whatever is normal for you). To cover all bases, I'd finally contact Hagen by simply leaving a comment under his answer with @(name) either linking to this question, or outlining what you intend to do, and getting his sign-off to do so. I think in any case where you can identify a user by name, mention of MSE is optional.
The same generalizes for those participating not under their real names. You should then just discuss in your @(name) message under which name (if any) user would like to be quoted. If user agrees to using their proof but prefers to not be mentioned by name, then thank an anonymous user of MSE.

The proper way to acknowledge any source other than your own brain is to formally cite that source in your bibliography; whether that source is a textbook, journal paper, proceedings paper, preprint, StackExchange questions, blog post, newspaper article, movie, cereal box, bathroom wall, or your mom is utterly immaterial.  If your source is a StackExchange site, then you must cite the StackExchange site.
See meta.math.SE, meta.cstheory.SE, and meta.SE for a discussion of when, whether, and how to cite StackExchange questions and answers.
(Full disclosure: I have cited blogs, StackExchange questions, Usenet posts, newspaper articles, movies, and video games in my refereed journal papers, and at least one of my StackExchange questions has more citations than at least one of my research papers.)


text:
Does the American Mathematical Monthly allow ArXiv posting?
This is a follow-up to the question Posting to ArXiv a longer version of a submitted journal paper.  The general consensus on that thread was that it is probably okay to do what I proposed, but that I should check with the editor first to make sure the journal does not have any kind of policy against ArXiv posting.
I've sent an inquiry to the editor in question, but haven't heard back (of course, it's summer and people's schedules are wonky, so I don't necessarily think the silence means anything).  I thought I would ask here:

Does the American Mathematical Monthly have a policy prohibiting posting to ArXiv a longer version (or a preprint version) of a submitted manuscript?

Yes, they do allow arxiv postings at any stage.  However, starting in 2015 the Monthly has moved to a double-blind reviewing system (which, for general readers of this site, is all but unheard of in the field of mathematics).  Posting on the arxiv before or during submission would of course cause a serious risk of ruining the anonymity of the author.
I happen to know through direct experience that the Monthly views such ruination as being the author's prerogative.
It should be emphasized that this is a recent development, and whether it will be continued in the future is up to the board of directors of the MAA (and not the editorial board of the Monthly, a fact which I found surprising).
Added: Some remarks about the laissez faire philosophy of the Monthly's double-blind policy can be found here.  The difficulty of preserving authorial anonymity in an arxiv culture is mentioned.

I'm very surprised by double blind referreeing. I suppose it makes some sense to prevent any undue prejudice towards an author, but it's still surprising. In the hard sciences, it makes a good bit of sense since there can be a lot of infighting, but I have not really seen such a situation arise in math personally.

Could you clarify what you mean by "the author's perogative"?  Is that to say there are few (if any) consequences?

@Antonio: I mean that the editors did not take any action in response to a submission being posted on the arxiv, even when this was called to their attention by a referee as compromising the authorial anonymity.

The real difficulty with double-blind reviewing in math is that even without the arxiv, there are many very small subfields and people who have distinctive style's of proofs and techniques used. This may be likely less to be an issue for the Monthly given the  nature of its articles.

Your link is dead. Correct link: https://web.archive.org/web/20150926134330/http://blogs.ams.org/jmm2013/2013/01/11/the-day-of-missed-talks/

Note the current (as accessed online Nov 2, 2018) policy--
https://www.maa.org/sites/default/files/pdf/pubs/AuthorInfo_Monthly.pdf
says not to post. It states under “Peer Review“ that “Authors should also refrain from posting papers to any website until an editorial decision is made.“

@user2357 I guess John is referring to the "Authors should also refrain from posting papers to any website until an editorial decision is made." part, which makes sense given double blind review.

Please edit your answer to include/quote the relevant text. Link-only answers are frowned on, as the link could stop working at any point.

Upvoted, to counteract the false comment that "this does not provide an answer to the question." On the other hand, I agree with the other comments recommending that the relevant part of the linked instructions be copied into the answer, just in case the link stops working.

Almost certainly they have no policy prohibiting this. Indeed, I don't know of any math journal which has and enforces such a policy.
You can probably find the answer to your own question on the journal's web page. In the meantime, here is some evidence that if there is any such policy then it is frequently disregarded.

Looking at these search results now and comparing arXiv submission dates with the received/accepted/published dates on the Monthly's Taylor & Francis website, it appears that some authors are following the requested policy: arXiv submission after an editorial decision.


text:
Should I write a peer-review in third person?
While it is generally accepted to write papers using the collective we, what is a common practice for writing peer-reviews: I, this reviewer, or something else?
For example,

This reviewer has a minor concern with how pink elephants are defined in this paper. It would have been helpful if authors defined an elephant first, and then added the color pink.

I have a minor concern with how pink elephants are described in this paper. My recommendation is to define an elephant first, and then add the color pink.

This user would find a review using constructions like "This reviewer" extremely strange.

Since it sounds like you're a first-time reviewer and that you've not received many reviews of your own papers, I'm guessing you're a PhD student. I'd strongly advise that you have a chat with your advisor about what is expected when reviewing papers. Obviously, do continue to ask any specific questions here, but a general chat with somebody who is already familiar with reviewing in your field will be very helpful to you.

@DavidRicherby I just graduated. The reason I asked the question was because my adviser always required me to use "this reviewer" phrase, while I have never seen the style in the reviewers I received, and it does not match my style. Now, that I am on my own and forming my own style, I thought I would ask a larger community for feedback.

@Orion OK -- that makes sense. Since your advisor's use of the phrase "This reviewer" seems a little unusual, it might be worth having a general chat with somebody else, too.

I recommend the first person.  Like most good linguistic constructions, the reader passes over it without explicitly noticing it, whereas your first construction with "this reviewer" holds up the entire mental process for a split second.
The idea of using the third person to "soften" the criticism: well, Paul Garrett knows how much I esteem him, and we usually see eye-to-eye on things.  But this time I simply disagree.  The reviewer is empowered -- nay, enjoined -- to supply an opinion on the work.  If you want to shade your opinion, explain very carefully and explicitly why you are doing that.  Switching to the third person should not convey that you are less sure of yourself, and it does not convey that to my ear.
[Imagine my answer began with "This academic".  Wouldn't that have been more distracting?]

Even though (in math) I always know the names of the authors, I do always refer to them as "the author" or "the authors".

@Oswald: Me too.

I wouldn't even say the criticism is always "softened" by using the third person. I emphasizes that the statement expresses one person's subjective opinion, which may well be unreasonable or different from other people's opinions. This reviewer, on the other hand, emphasizes the position the person is in, thereby underlining the implicit assumption of authority and making the criticism kind of irrevocable, much more severe than with the I.

Unrelated to that, I'm not sure I'd consider passive voice the correct term here.

@O.R.Mapper Indeed: it's the third person, not the passive voice. The passive voice is the construction "This sentence was written in the passive voice", as distinct from the normal "I am writing this sentence in the active voice." In the passive, the natural object of the verb ("write") becomes the subject of the sentence.

@O.R. Mapper: Yes, you're right.  Looking back at my answer, I was even a bit surprised to see that I had used the term.

I have a third take on the issue: this is not about the reviewer nor the author, is about the work and as such, I think that it should be the subject of the sentence:

The paper could benefit from a redefinition of pink elephants, possibly defining elephants in general at first and then by adding the color pink

In my opinion this has the benefit of making the review less personal and make it come through as more objective.

This is, of course, always the best option, and it is good to be stated. However, my question was intended for the situations when you want or need to add a personal take.

Shades of meaning. If I think something is very unclear, I'll say that "The definition of pink elephants is unclear": that makes it fairly clear that I think it's the authors' fault I couldn't understand their definition. If I think it might be me being a bit dim, I'll say that "I found the definition of pink elephants hard to follow." Bear in mind that a review is, explicitly, a personal opinion on the paper. Sometimes, it's not really appropriate to make your subjective opinions look objective by writing in the style of "The definition is unclear."

@DavidRicherby I was following the example provided in the question and in that case it seems to me that an impersonal take would fit better. The meaning of the review does not change, how it is received by the author does.

@Federico Whether you say "This reviewer thinks the definition is unclear" or "I think it's unclear" makes no difference. But "This definition is unclear" does carry a different weight, by being presented as an objective fact rather than a personal opinion.

@DavidRicherby "This definition is unclear" is simply a stronger version of "a better definition could improve the paper". Which is better to use it all depends on the context (not given in the question). I sincerely do not understand what your point would be or, where my answer would be wrong acconding to you.

@Federico You seem to be saying that it's always better to write reviews in the style of "The definition is unclear" rather than "I found the definition unclear"; you say that this comes across as less personal and more objective. I disagree. The "I found the definition unclear" phrasing carries a different meaning and you should use whatever phrasing carries the meaning you intend to convey. Reviews are necessarily subjective and phrasing a subjective judgement as if it were an objective fact is not necessarily accurate.

If you're writing a review that will be read only by the editor, you can use "I", but if you want to simplify the editor's life by giving them something to cut-and-paste, or forward, to the author:
In English, in mathematics at least, the contemporary style for publicly-consumed reviews seems to be to refer to oneself, the reviewer, as "this reviewer". Thus, "in the opinion of this reviewer...", "this reviewer cannot understand why the author is so dense..." :)
There are some observable exceptions, where a reviewer is enough of a big-shot to not merely "suggest" that the author has erred, but to be snarky about it, and in either first person, or an exaggerated third-person. My own opinion is that it is not nice to do this. That is, a forthright voice is best, and choice of voice not depending on status is tasteful.

Does "publicly-consumed" mean "will be seen by the author" or "will be seen by everyone" (such as for the AMS Bulletin or Math Reviews)?  As an author, I've certainly received reviews of my papers written in first person.

I don't think the difference between first and third person should have anything to do with the amount of confidence in the assertion.  Moreover, referring to oneself in the third person is in most contexts awkward and stilted.  There are places in which it is done as sort of an in-joke or hat-tip to the format: e.g. journalists sometimes refer to "this reporter"; in MathReviews one often speaks of "this reviewer".  But I think that's an affectation, which happens to in certain very specific circles be accepted.  In a referee report I would (and do) certainly write "I".

On MathSciNet I do avoid "I" and "We* in reviews.

I think the editors of Mathematical Reviews (= MathSciNet) routinely change "I" and "we" to "the reviewer".  As for referee reports, I don't think I ever explicitly thought about how to refer to myself, but, looking back at a sample of reports that I've written, I found that I consistently used the first person.

I don't see any need to write in the third person just because the editor is going to forward your report to the authors. The authors understand perfectly well that, if a referee report says "I think your paper is awesome", it means the referee, not the editor. Most reviews I receive are written in the first person.


text:
Pros and cons of doing PhD in a research group with a high number of post-docs?
What are the pros and cons of doing PhD in an experimental/theoretical research group with a high number of post-docs?
For example, if there are a lot of post-docs, this means that the group is doing research on many different problems, in general. However, this also means that the P.I. (i.e your advisor) will have much less time for you, but since there are lots of post-docs, it might be possible for the student to make it up with the post-docs. However, it is much harder to assess a post-doc than a P.I.

Experimental or theory or simulation? Experimental more postdocs is better - more hands on experience around.

@JonCuster it would be good to have an answer for both cases, because most of the time PhD students choose their field and working method (experimental or theoretical) after joining a lab

Number of postdocs, in isolation, is not a useful data point.

@AnonymousPhysicist but I am asking you to assess a particular research group, I am just asking that if we had 2 identical research group except with different the number of post-docs, what would be the pros and cons of choosing the one with more post-docs.

@onurcanbektas That is not a real situation.  If it were a real situation, I would say there are no meaningful pros and cons.  Real postdocs are not fungible.  It isn't their number that matters.

There are too many variables for a general answer. How do the post-docs work? Do they work together? Is the lab environment friendly and helpful or cut-throat. Are they willing to help you? Are they new at this or beginners? All the combinations could balance out to something good or bad.
But most important is how interested your advisor is in helping you and spending the necessary time for it. The rest is probably just noise.
But a cooperative staff can be quite helpful if you are getting started. There is a lot of experience to draw on since the post-docs come from different institutions.
But do what you can to keep everything friendly and helpful. Establish a working relationship with your advisor. Don't be shy. Ask for help when you need it. Give help when you can.

Plus, a "high number of post-docs" is very field dependent. What is "high," in the OP's opinion?

@AzorAhai, and relative. In math "high" would be about two. The OP studies math and physics according to the profile.

@AzorAhai high ~ 16

@onurcanbektas That's a crazy number. I would definitely be worried about any PI being able to manage 16 post docs, to say nothing of grad students and RAs

@AzorAhai well, there is such group which I am considering working within, and looking at the research output, the PI manages them quite effectively, but I should also point out that some of the post-docs work with multiple PIs.