What is the meaning of the various postdoctoral job descriptions in the US? As somebody who wasn't born or raised in North America, is there a schematic explanation what those various terms are supposed to be mean? Does it differ between the types of institutions? Are there specific fixed meanings to keywords such as

Assistant
Associate
Visitor
Fellow
Research

If there are not specific meanings, how do committees decide what to call a position?

As Jon Custer mentioned in the comments, there are no standards whatsoever, however generally speaking:

"Visiting" is a short-term position (I've never seen a post-doc with this title), probably even shorter than a usual postdoc, probably 9 or 12 months.

A "fellow" is usually a prestigious assignment, it may be a  university, college, or departmental soft-money position. For example, my university has "President's Fellows" although I'm not sure if they are funded specially or if that's just an award. However, nothing stops anyone from calling anything a "fellow."

An "associate" professor outranks an "assistant." However, I do not think there is any meaningful difference between "postdoctoral research assistants" and "postdoctoral research associates." One doesn't outrank the other. Probably, people just try to avoid using "research assistant," since that somewhat connotes an junior position.


Is it unethical to give a gift to my professor who might potentially write me a LOR? Undergrad going to apply for graduate school. I recently came back from a trip where I got some goodies - I thought it would be nice to give some of my favorite professors gifts. However, I am now concerned there might be some ethical issues at hand here. I will definitely ask them for LORs and it is unlikely they will refuse. However, will giving them the gift before requesting a LOR prevent them from being able to say yes to writing a letter? Also, is it just wrong to do such a thing - it might be considered close to bribery (but then again I am not deliberately stating that I want a better LOR nor am I giving them the gifts because I want such a thing).

Giving them the gift after having requested the letter is not an option as this goodie does have an expiration date. I am not sure how to proceed. (The goodie is less than $13)

Your first sentence tells us that you are still a student in the institution where these professors teach.  If you are currently in classes with any of these professors, or there is any possibility that you will be in their classes in the future, do not offer a gift, either prior to a request for an LOR or as a thank-you for having written one.

Giving anything of value to someone who will assign a grade is almost certain to make the professor uncomfortable and, although very unlikely, could cause the professor a great deal of difficulty.

Finally, consider that writing letters of recommendation is part of a professor's job.  You shouldn't think of doing anything that will seem like compensation for a professor having done the professor's job.

The things I value most from students for whom I've written LORs are notes telling me that they've been admitted and thanking me for my part in making that happen.  A particularly nice one was written on a postcard depicting the former student's new university.

Keep the goodies or share them with fellow students.  Send the professors a nice note after you've graduated and been admitted to graduate school.


First-year PhD giving a talk among well-established researchers in the field I am currently a first-year Ph.D. student, before that (as I have posted about before) I was forced to leave my Ph.D. program after one year because of a bullying supervisor. Previously, I made a good relationship with other researchers in my field and other scientific volunteering activities.

Now, there is a workshop at a highly ranked conference, and I asked about the possibility of sending a paper for the workshop. They don't solicit papers, however, I have a good relationship with the professor who is the main organizer of the workshop, and they voluntarily  asked me to be a speaker in the workshop for 30 minutes.

The other speakers are the most well-established researchers in my field, I felt excited but afraid in the same time. I don't have yet any publications concerning the current research. I don't know if I should apologize, maybe the professor does not know that I have been kicked out from the earlier program. I don't know what I should do, all the speakers are the elite and I think I am not deserving to be among them as I don't have the same experience.

Should I try or would this be counterproductive to my future career?

EDIT 1

Thanks for answers encouraging me to try, while there are pragmatic answers that I don't have to waste the audience time, honestly, I have self low esteem since all peers have papers published in top journals and conferences, I don't know why the organizers listed me as a speaker, I am not doing great as other students or there is no indication in the right moment that I am doing fantastic research.

Let's flip this question around and imagine that you, as a first year anthropology PhD student, are now visiting your high school. One of the students asked your former teachers if you would be interested in a local, anthropology-related research project they were doing (e.g., they could be investigating the attitudes of people towards those who are HIV positive, and contrasting how that varies between countries). The teacher promptly arranged for them to give a talk on their results while you were there.

The student feels excited but afraid at having to give this talk. She knows she doesn't have the pedigree you have, she doesn't know if she should apologize, maybe you don't know she flunked her latest exam, and she thinks she is not deserving to be giving the talk because she doesn't have as much experience as you. Should she go ahead and give the talk or would it be counterproductive to her future career?

I'm pretty confident you will say she should go ahead, and the same applies to you. These well-established researchers probably know (or can tell) you're a PhD student, and will not demand that you have done groundbreaking work on par with theirs. Instead of focusing on all the things that could go wrong, think of all the things that could go right: you get to present your work to a well-established audience. They're the people you most want to know your results. You get to network with them. You get to practice skills that you'll undoubtedly need later in your career. What's the worst that can happen anyway? Even if you give a truly atrocious talk they'll probably all have forgotten about it by next year.

tl; dr: stop worrying and do it.


Ways of encouraging companies to participate in survey for my doctoral reseach I am a doctoral candidate in Business Administration, researching the use of ERP (Enterprise Resource Planning) programs in companies. When I have explained my research to system administrators, the usual response is that it is an interesting subject. Despite the use of social media such as LinkedIn, a user group forum and direct mailing system administrators, very few companies have consented to participate in the research.

The research will be implemented via user questionnaires. In my opinion, very little time is actually required to complete the questionnaire (obviously I'm biased) and point out in the covering letter about the research that completing the questionnaire requires only about ten minutes. Of those companies who bothered to reply, almost all have stated that participating would require too much time.

Does anyone have any suggestions how I might encourage companies to participate? I know that basically I am asking them for something and not giving anything back in return.

From what you've described, you haven't done much, if anything, to provide a compelling argument for companies to participate in your research. Even though it doesn't, from your point of view, take much time or effort, it does take time and effort, both of which cost money.

If you're talking to a company that has 300 employees. You say it takes 10 minutes. Now multiply that by the number of participants and you have 3000 minutes or 50 person-hours. Then multiply that by the labor cost, say $80/hr (you have to consider the entire cost of the employee's time; salary, benefits AND the missed opportunity cost of NOT doing what something that would make the company money) that's $4000 for your 10 minute survey.

You need to think about what you can offer in return for their $4000 and sell it. Access to your findings? What would you offer them if you were asking for that much money to fund your research?


How normal is it to get email replies in ungrammatical English by a high indexed journal (in the context of lack of communication)? I submitted a brief report (2,000 words) to a high-indexed journal and after some five days sent an email stating that a preprint for the manuscript had been uploaded. A journal assistant replied he was to get back to me on the preprint as soon as they heard from the assigned editor (I thought: Whatever, it’s just a preprint notification.) However, after 20 days, there was no reply, and after a month, the manuscript was still at the With Editor stage.
I sent a short email to check whether an editor had been assigned and received the following reply: “Dear XY, Th editor has mailed to patience that he is working on the same. Best, XY” After the email, the status of the manuscript changed to "In Review". How would you interpret this?

There are a number of explanations, but the most likely two are carelessness or a non-native English speaker who is assistant to the editor. In a lot of places like, for example, NYC the workforce is composed of people from many lands. And some high end journals may have a widely distributed (world wide) staff. So, some awkwardness with the language can be expected, and I hope excused.
The other, carelessness, is that people sometimes get interrupted during their work and leave out a word. I know that here, since I'm old and may my typing is sometimes awkward, the spell corrector will substitute a word and I don't notice it.
And, of course a single word inserted, "recommend patience" rather than "patience", would make it just about right.
Don't overthink it.
Also, a month with no change in status means little, though it is worth pinging the editor as you did. Journal time, like academic time, can run very slowly, slowly, slowly. Some folks wait six months or more for a change. Mystifying, but there it is. And if you got back a quick reply to your query, you are luckier than some.


Is there such a thing as too much work for a Master's Thesis? My thesis  (Canadian Research Based, Computer Science), collects three separate research projects (with a tenuous connecting thread).

While collating these projects into a single document, I have looked into other theses coming out of my university and others in my field, and have realized that it's looking like my thesis is going to be very large. Probably twice the average length of others in my field.

Which makes me wonder: Did I do too much work for a thesis? Should I have pushed my supervisor, cancelled the final proposed project (#3) and graduated on the strength of the first two?

I'll be graduating 6 months after my target deadline, with multiple publications, and so burnt out that my initial plan to pursue a PhD has collapsed. Can't change the past, so I'm asking here mostly out of curiosity, and for other future students.

It is not clear how to judge the "size" of a thesis (page length or word count is probably not very good), but one can clearly do too much research for a Masters or Doctorate. That said a factor of two difference is not really that big since there is always going to be a healthy overlap between the "largest" Master thesis and the "smallest" PhD thesis. If your Masters thesis is larger than the average PhD thesis and larger than the vast majority of Masters theses, then it is possibly too large.

As a student you need to be asking yourself why you are getting the qualification. Most students put in much more work than that which is required to simply graduate. You should make sure you push your supervisor to help you achieve your goals.


What to do when you reach a conclusion and find out later on that someone else already did? Say you've thought hard about a specific issue in your research and have elaborated a possible answer, interpretation, etc., to tackle it. (I'm not thinking about huge research subjects, but rather small ideas that articulate a demonstration.) You then discover later on, while reading a new paper, that someone has thought about the exact same thing. How do you present your idea on the issue?

On the one hand, you can't pretend that you haven't read what the other paper says about it, both for reasons of intellectual honesty and because the other author (or someone who read his paper) might think that you stole his idea. Citing the other paper is thus somewhat of an obligation.

On the other hand, it doesn't feel right to dismiss your demonstration and just cite the other paper, since, after all, you figured out a solution on your own. Conversely, it seems somewhat pointless (and maybe arrogant), to write explicitly that you reached the given conclusion and only then found the other article.

What to do in such circumstances?

Do not despair: your work likely still has value!

In my experience, it's almost never the case that work addressing the same problem has exactly the same solution or exactly the same approach to gathering evidence.  Existence of a previous publication will thus typically make your results smaller and more incremental, but not invalid or duplicative.  Some examples of what your work may provide:

A second, independent confirmation of a hypothesis
Confirmation of a closely related but different hypothesis
A different approach that has advantages in some situations and disadvantages in others

There are even good journals like PLOS ONE that explicitly invite replications and "non-notable" incremental work.  Thus, if you've got a set of results in hand and you discover somebody else has done much the same, you should still write up your work---just be straight and honest about the smaller size of contribution based on the prior work.

If you're still at the "ideation" stage where you're just thinking up possible work to do, however, then it seems more appropriate to move on and work on something else instead---maybe building on their results.


How are office hours for PhD classes different from office hours for undergraduate classes? I plan on attending office hours this week for a PhD class (in math, to be specific).  This would be at a U.S. university, at a strong math department.

My question is:  are the expectations different from undergraduate (and masters) class office hours, when the time is mostly spent on HW questions?

If you're a professor for PhD courses, what do you expect to talk about with your PhD students during office hours, if you indeed have different expectations and rather not discuss homework?

At every level of education, the purpose of office hours is to give students an open-ended opportunity to discuss the material that they are learning with their instructors, and particularly to get help and clarification in their understanding.

As an instructor, I found it greatly frustrating when students (or any level) reduce this opportunity into simply asking for help on homework questions.  I believe there are many other instructors who feel the same. In fact, I felt so strongly about this that I personally had a policy of refusing to help with homework questions per se, and would instead offer to work a related but different problem in order to try to get the student to learn the material rather than just solve the problem.

I find this attitude most widespread amongst undergraduates, but many graduate students have it to.  Hopefully, you are actually interested in the material that you are learning, rather than just your grade.  That attitude, then, can easily translate into requests for help that are about the material, rather than the problems.  For example, consider:

"Can you help me with problem 5?" vs.
"Problem 5 made me realize I don't really understand Urysohn's Lemma.  Can you help me understand that better?"

Whether graduate or undergraduate, if you ask questions of the second sort, any good instructor who cares about their students' learning is likely to appreciate it.


Do STEM PhD admissions committees check a candidate's Statement of Purpose for plagiarism? Or is that not really possible, given the high volume of applications?  Do professors have a plagiarism-detecting application to launch investigations, if necessary?

What if, for instance, a successful math PhD applicant to University X gives his Statement of Purpose to his friend for him to apply next year at a similar PhD program at University Y?

I am just asking out of curiosity - I have no intentions of plagiarizing :)

Also, there are plenty of admissions-consulting businesses that are around, particularly for business school applications, so I wonder if such services are offered for PhD applications and whether PhD admissions committees have a way to say, "this Statement of Purpose was definitely not written by Candidate Z."

At my institution there is no such practice and I haven't heard of it at other institutions.

  What if, for instance, a successful math PhD applicant to University X gives his Statement of Purpose to his friend for him to apply next year at a similar PhD program at University Y?

It is quite common for people do consult other's statements as a reference, that is why you can find many of those (besides teaching statements, research statements, etc.) on various academic web sites. However, a blatant plagiarism would probably hurt your application more, no matter how good the original statement is. The reason for that is that such documents are usually personally tailored. They are written to highlight the writer's ambitions, goals and plans and make them compatible with the school's (or adviser's) vision. It is very hard to find statements that can fit multiple students, except if they are very generic and thus rather bad. Also, don't forget that the statement is a part of a larger package, which is also tailored to tell a convincing story why a student should be admitted. Part of that package are also face-to-face interviews. All of that taken together makes it undesirable to have one document sticking out, and it will stick out at some point of the process.

Personally, even if I found a student that has plagiarized another's statement, I wouldn't call it plagiarism but rather a disappointing lack of dedication. If you can't be bothered to put together a few paragraphs on what is important to in your future and also find it easy to blend into another's view of theirs, it's a way more serious problem then plagiarism.

Finally, as said before, the statement is only one part of the application, it is by no means the most crucial one. So, even if you "get away" with plagiarizing it, it won't guarantee your acceptance.


What is a social strategy I can use to respond to "How's your PhD going?" I was surprised when starting my PhD as to how much I get asked this question and how much I fail at answering it. Whenever I attempt an answer, I fumble around and the subject immediately changes after. If I state exactly how it's going, the stress of publishing and intensity of the program comes off overly negative. If I state what I'm working on, I either lose them or bore them.

What's a good social strategy to respond to this question?

"It's going well, last week I made some good progress on X. How're things with you?"

The vast majority of people are just asking to be polite. If they're actually curious for specifics, they'll follow up with a more specific question. I personally like to have some kind of a cute story about my research because nobody has any idea what pure math people actually do. (I draw fractals for a living, so I have some pictures on my phone to show around.)

EDIT: Some of the comments bring up relevant points about cultural differences. If the local culture is one in which asking out of politeness is frowned upon (ie German @O. R. Mapper, or grad students @JiK), I think it would be still best to start an answer of the above form. This allows people to either gracefully exit or pursue a more in depth description according to their own interest and cultural mores.


What terms should be better to set when creating a Startup with your PhD supervisor? What terms should be better to set when creating a Startup with your PhD supervisor?
I had the PhD project idea before starting the PhD and working on it for some years. Now my PhD research looks promising for commercial use and I am thinking to create a startup. I recognize the prestige of my PhD supervisor and he is willing to participate in the startup.
Which are considered fair terms for both me and the professor for our new startup, based on the fact that i have done all the development (spending countless hours of work the past years) and came up with the project idea, but the professor has the prestigious name to make the startup more credible (and maybe better funded)?
Share equal equity? Have equity based on hours spent on the startup? Something else?

I strongly suggest that you hire a lawyer to get this advice. Failing to do so could lead to a huge amount of conflict later. It is likely that your interests don't completely align with those of your advisor.
I'm not a lawyer so can't help much, but it might be possible to set up a joint meeting with a lawyer and the advisor to work out an equitable arrangement. Your joint venture will need legal advice in any case.
But you also need to consider what a conflict would mean for finishing your degree. Don't put that in jeopardy.


Do non-ACM events/conferences publish & index their final proceedings in the ACM digital library? I am looking into options to submit my research paper to this conference:
- http://www.icbdr.org/ or - http://www.iccbdc.org/index.html

Both of the links indicate that after acceptance, the paper will be published in ACM library and indexed in Scopus and EI. But after I discussed with my colleagues they said that there is a chance of being a scam.

I checked the ACM main events but did not find any of the above-mentioned conferences but instead, I found them in Non-ACM Events http://www.acm.org/conferences/non-acm-events.

Does it mean that the work will be published and archived in ACM library?

UPDATE: I contacted the Elsevier Ehelpdesk and got the following reply:

  Dear xxxxxx, Thank you for reaching Elsevier Ehelpdesk regarding
  Scopus Indexing.   The 2017 International Conference on Cloud and Big
  Data Computing (ICCBDC 2017) is set to be published under the
  International Conference Proceedings Series by  ACM as seen on their
  site http://www.iccbdc.org/index.html.   I can confirm that the
  International Conference Proceedings Series by  ACM is already indexed
  in Scopus which has several conference titles already indexed.   Once
  a conference is is published, the publisher will be processing the
  title to be included in Scopus to be indexed.   I hope I have provided
  you with everything you need. Should you have further query, please
  don't hesitate to email me back. Kind regards,

Yes, but there are rules.

There are three ways for conferences to have their proceedings published in the ACM Digital Library.

What most people mean by an "ACM conference" is a conference that is sponsored by ACM or one of its special interest groups.  Proceedings of all ACM-sponsored conferences are published in the ACM Digital Library.  ACM sponsorship must be advertised in all conference publicity, including the conference web site and call for papers.

Conferences can also be held in cooperation with ACM.  In-cooperation conferences can apply for their proceedings to be published in the Digital Library, but not all such applications are approved.  Cooperation with ACM must be advertised in all conference publicity, including the conference web site and call for papers.  In particular, in-cooperation conferences cannot claim to be sponsored by ACM.

Conferences can also apply to publish their proceedings in ACM’s International Conference Proceedings Series without sponsorship or cooperation.  These conferences are allowed to use a special ACM-ICPS logo on publicity materials to advertise the publication agreement, but they cannot claim to be sponsored by or held in cooperation with ACM.  This is the agreement advertised by ICCBDC.

Nothing on the ICBDR web site suggests that their proceedings will be published in the ACM Digital Library, so they almost certainly won't be.

(Indexing is a separate question.  A very small number of proceedings series like VLDB are indexed in the Digital Library even though they are not published by ACM.)


Education sections in an Job Application Form I'm trying to fill in an Application Form for a position as a Spanish Teacher in United Kingdom, and I came accross these 2 sections: Educational/Training and Academic qualifications and Further Education.

What am I supposed to write in each of these sections?

Assuming I have obviously primary school and college, as well as 2 degrees and 2 postgraduate courses (all relevant for the position), where should I put each of them?

It's been a while since you asked this question so I assume it's no longer needed, but in case others come across this hoping for an answer...

In the UK, further education typically refers to any education completed after finishing GCSEs - which are typically taken at age 16 - and beginning a university degree - which typically starts at 18/19. The most common form of further education here between ages 16-18 are A levels, taken at a sixth form college or school. See: http://en.wikipedia.org/wiki/Further_education

In your case, I would enter your college course in further education, and your subsequent education in the education/training and academic qualifications section.

But, ultimately, I agree - this is quite a confusing example of an application form.


How do I use/add first name (or forename) in citation? I like to use first names (or forename) to cite the work of others.
It has become even more relevent when I found that somebody working in my field shares my initial and surname.

However, this is not the most common practice and in many cases, I do not know the forenames of the people I would like to cite.

Do you know of any pratical way to find these information ?

I usually resort to Google and Google Scholar search but that does not always solve the issue and can be time consuming (considering it is a detail).

It's a little tricky trying to expand someone's name, since you might inadvertently arrive at a form they never use (for example, some people have never been called by their first names, but have always used their middle names instead, and may prefer to be cited as "F. Middle Last" rather than "First Last", "First M. Last", or "First Middle Last").  Some people also prefer to use initials when publishing, for example out of fear of prejudice or bias.

So if the published paper uses initials, then it is safest to retain them when citing it, unless you are really confident that your expanded version of the name won't confuse readers or offend the author.

On the other hand, if the published paper gives a first name, then you have your answer.  Other databases may also give first names (for example, MathSciNet or the Mathematics Genealogy Project), but which databases are relevant depends on the field.


Is being the second author always good? I work in an institute where I am more concerned with Development of systems and solutions rather than actual research, but of course the head is a professor and writing papers is an important task when it comes to productivity.
My ordeal is that I would rather be:

  on the programming, developing side of the research, where I like to give things a try than just writing ideas and concepts

I have however been a second author on a couple of papers; one a demo/poster paper and one for a conference (in the pipeline).

I have been stressing myself because I realize that writing papers isn't my thing but the work that I do is still enjoyable and fun and I would like to continue working as much as possible

Is being a second author most of the times accounts to something similar to publishing things as a first author?

This depends strongly on the field. In some, it is a big deal, in others not so much. But it is always a good thing to be an author, wherever you appear in the list.

If you are comfortable with it, don't worry too much. Your preferences may change, of course, in which case you may want to take more of a lead in the research and thus in the "perceived rank" of authorship.

Of course, your institution might put more emphasis on "first" authorship and it may affect your advancement. Don't neglect that.

In some fields we don't worry at all about that and just list names alphabetically, assuming that if they are listed, they contributed.


How to respond an email for postdoc process I live in Iraq and my postdoc application for a Dutch position has been accepted. Now, the PI has sent me an email:

Dear XXX,
Ms YYY (in Cc) and Ms ZZZ will now start the procedure of your
appointment. Please let us know from which date you can be available.
Note that it may take about two months to arrange your residence
permit.
Kind regards,

I have ambiguity about the sentence:

which date you can be available?

Does she mean the date on which I can start the job (for example as soon as my visa gets ready) or she means the day on which I will be available for HR calls? (for example tomorrow)
Thank you.

Congratulations on your new job!
They want to know at which day you can start the job, in order to include the starting date in your contract, which I presume ms. YYY and ZZZ are drawing up as we speak.


Are cover letters sent to referees and should you highlight the contribution of your paper in the cover letter? How to write a cover letter to journal when submitting a manuscript?

In the letter, it is expected that I propose 5 referees. Is this the only reason to write a cover letter?
Will the cover letter be sent to the referees or only to Journal's staff?
I feel reluctant to praise my contribution in the cover letter. The article should defend it itself. Is the praising important part of the cover letter? Is it required?

It is also polite to write a cover letter, even if nobody asks for it. And the purpose is often to ease the process of finding the referees, so helping to do so by giving insights about the paper that cannot be write in the paper is a good thing.
If you mention potential referees, I guess it will not be sent to the chosen referees. Otherwise (in my experience) it is.
You don't have to praise your results in the cover letter. Just state shortly the results (say more than the abstract, less than the introduction). If you think that there are issues related to the paper, this is also the place to state them (conflict of interest, new way of considering something - which can hurt someone's feelings -, direct negative comment on related work, etc.). If you think that, because your paper is gap-bridging, you need reviewers from several fields, you should say it as well.


Are DOD Young Investigator Research Program (YIP) grants transferable to new universities? Backstory: a colleague has a YIP with the AF, funded, and has been hired by a new university. The Program Officer is on personal leave (3 months now, no end in sight). He is pushing harder, and hearing non-options like 'don't go to the new post' and 'reapply'. Has anyone seen a DOD YIP move successfully?  If so, how?

The answer to your colleague's question is specific to his funding award, his program officer, and his specific situation. Only his program office or someone else from DoD could answer his this question. That being said, a quick Google search found another funding request that describes general DOD grant policies:

  Transfer of Award to New Organization: Unless restricted by the specific Program
  Announcement, a change in organizational affiliation will be considered on a case-by-case basis
  by the USAMRAA Grants Officer. If approved, the PI’s original organization will be required to
  agree to relinquish the award. The new organization will be required to resubmit the entire
  application on behalf of the PI, including regulatory documentation. Extended times for transfer
  may put the award funding at risk. A transfer will not, unless under extraordinary circumstances,
  be allowed for any organization that includes a study site/clinical trial at its location.


How I can subscribe to conference/seminar/workshop alerts? Can anybody please provide me link from where I can subscribe to alerts for international conferences, seminar,  workshop etc or postdoc positions ? This could be very useful for me as I generally miss important conferences/seminars/workshops.

There are several sources I get information from:

Mailing list: See if you can find a mailing list specific to your area. Ask your advisor and colleagues about them.
Friends and colleagues in the field.
Word of mouth at other conferences: Ask participants about their favorite conferences & workshops.
Invitation emails of various kinds.
The academic sub-twitterverse
Wiki CFP: http://www.wikicfp.com/cfp/

Note that there are many conference/workshops that are not worth going to. And some of them are right out scams. I've read a number of horror stories about them (e.g. https://scholarlyoa.com/tag/predatory-conferences/). I suggest you choose carefully.


I think I may have violated academic integrity last year - what should I do? I think I may be overthinking things, as I’m known to having a huge guilt complex.

As an undergraduate last year, we were given a coding assignment to complete that was worth 15% of our overall mark for the course. We often worked on it at computing practicals where students worked together in computer labs along with postgraduates who could assist you if needed.

Towards the end of it, I had managed to complete the first two parts of it, but struggled with the final portion, and there were no more opportunities to ask for help at the practicals.

Eventually, a friend of mine’s close friend (who I was still becoming closer with) figured out how to do it, and showed us a screenshot of his code. I initially copied it down so I can see what he did, and then spent some time reading it to understand how I was meant to go about answering it properly, and then tried to write up my answer knowing the right way to go about it, but it couldn’t be done in a way that didn’t look very similar to what my friend did. So I fear I copied.

I didn’t think anything of it at the time, and submitted it, and it was marked and that was it. I think there may had been a plagiarism checker but I can’t remember.

Recently, I’ve since been worried that I’ve breached good academic practice. I don’t know why I’ve never thought about it much until now.

As well, in a module I took last semester, I had worked together with friends on homework sheets that we handed in but people often completed in groups, which I think was perfectly permitted. I only worked in groups if I couldn’t solve anything, so there was a time last semester where I went to a friend who went over with me how to do the homework assignment (helping me through almost all of it) which allowed me to get a decent mark on it as I now knew how to do it with his help and instruction (they also were intentionally meant to help our understanding more than assess us apparently). I’ve also had trouble saying no to people who want to look at my homework for help, as I’m not very assertive.

I’ve figured out that this could be poor academic practice as I’ve aided and gotten aid for assigned work recently.

I just don’t want to think I’m an unworthy academic. What should I do? Should I contact someone? Should I just let it go? I’ve told myself for now on when asking for help from colleagues that I will never ask for answers but merely understanding, and to my knowledge I’ve not done anything else that’s improper other than this.

Should I be ashamed of myself?

Is this situation a common thing, even among academics? I’m going to be at an internship over the summer with very esteemed academics. Am I likely different from them in my academic scruples given this described past behavior? Should I look down upon others who’ve done minor things like this who don’t feel guilty about it?

The past is the past and cannot be undone. Whether you are ashamed or not, you need to move on. But you don't need to invite external punishment for past misdeeds that haven't harmed others.

It is best if you do your own work, of course, since that maximizes your learning. It is worst if you copy since you haven't really learned anything. In between is getting hints about things, with various graduations of that. The best hints come from your instructor, since s/he can give you a minimal hint to get you past a block so that you can advance. Getting hints from others is worse since those others may not be taking your educational development in to account.

So, for the past, let it go. For the future think about the goals of the exercise, not just the end point. Seek appropriate assistance that won't hinder  your learning rather than inappropriate assistance that might.

Probably you transgressed norms since you describe it yourself as copying. But treat it as a learning experience and move on.


How can I cite software documentations? As my bachelor's thesis, I'm developing some software (a mocking framework for MATLAB). As such, I often need to reference software documentation - both from MATLAB and the software which serves as my inspiration. It would also be nice to be able to reference the documentation of the specific feature I'm referring to (the analogue of referencing a specific page in a book). However, I mostly access this documentation online and by its nature it tends to exist just in electronic form, which is not really recommended in publishing. So far, the best I've come up with is this:

@misc{mockitoFeatures,
 author = {{\em mockito} developers},
 title = {Features and Motivations},
 note = {\url{https://code.google.com/p/mockito/wiki/FeaturesAndMotivations}},
 urldate = {2013-04-24},
}

(ok strictly speaking, this isn't part of the official docs but it serves the same purpose: it's a specific page and it's only available online)

Specific questions:

Who should be the author? In the case of MATLAB I guess it's Mathworks or somesuch; I guess listing open-source projects as "xx developers" is the best I can do.
How should I mention the version? Urldate helps in general, but if I'm referring to a particular software version, where should I put this info? In the title?
Are there any "official" MATLAB citation recommendations? MATLAB is used in research a lot, perhaps there's a suggested way of doing it and I'm just missing it. The rest of the question still applies for other software, though.

In general, I would treat software documentation depending on how it's distributed.

If it's published in book form, then it should be cited as a book. The version number goes where you would put the edition, and the company that manufactures the software is the "publisher."
If the manual is distributed electronically, then you should cite the website from which it is obtained as the "source."
An exception to this is if you are asked in the documentation to reference a specific work (for instance, a research article, or a website) when citing a code. Then you should follow the specific guidance provided.


What can I do to get an admit in a Neuroscience program? About me:

I work full time often more than 60 hours a week but I want to go to
college to be a neuroscientist.
I live in the US and have bachelors
degree in Chemical Engineering.
My goal is to get a PhD in
neuroscience.
I work in the IT department in a corporate but do
mostly documentation.

My plan is to begin by doing the following -

Preparing for Bio, Psyc and Math GRE subject tests
Subscribe to Scientific Weekly and Scientific Mind to get current research news
Read a college level Biology textbook to get some background on
Biology.

Can you please help me with the following -

Offer some advice if I am headed in the right direction.
What else will help me get into school/neuroscience research.
Any pointers on getting scholarship/aid.
Will I be able to get into a Masters program (with some pre-requisites) or do I need to start from undergrad?

I completed my PhD doing almost all my research in neuroscience, so I can give you a few tips from my personal experience.

Neuroscience is by nature a very cross-disciplinary field. I was coming from a psychology background, and my classmates had backgrounds ranging from biology to computer science to mathematics to pre-med. You will be at a disadvantage given your relative weakness in biology, but not a very significant one. Your math skills from the bachelors in engineering will serve you well as you learn about neural and systems dynamics, and the chemistry you learned will be of immeasurable use in understanding the biochemistry of the nervous system.
Given your background, you should definitely be able to apply directly to a MS or PhD program without having to retake (too much) undergraduate coursework. Do note that you may be able to get into the program with the caveat that you will be required to take some undergraduate courses during your first year; this was a common practice in my program. Given how long it takes to complete your PhD anyway, it should not delay you much, if at all.

Coming from an IT/engineering background, you may be interested in computational neuroscience, a subfield which attempts to understand how the brain works—both at a systems-level (i.e., whole brain) and cell-level (i.e., individual neurons)—using computational models. There are entire departments dedicated to such research; it's a fairly large field.

Your action items listed above are all excellent ideas, and should serve you very well. The only suggestion I would add is to simply google the term "neuroscience research labs" and begin browsing around the web to see what types of research is being performed. As you search, google again using narrower terms, to see how broad each subfield is. Consider writing down some of the schools that house labs that sound interesting to you for future reference.


I've been working for one year. Can I apply for grad school in CS in Canada? I planned that I could make myself money to continue education (by obtaining a master's degree), but what am I supposed to do to continue my education? It would be nice if it's going to be a part-time education and I don't have to attend to school all the time.

My candidate would be University of Toronto or McGill.

I looked at their homepage, and the application information describes undergrad for high school applicants, or application directly from undergrad students.

On top of that I am not Canadian citizen (but a resident). Is there any chance for me to restart my education?

Your best bet would be to get in contact with a specific professor who is an active researcher in an area of CS in which you would like to complete a Masters degree. If you find a supervisor who is keen to advise you (which you will need, anyway), he/she can help you negotiate the university admission process.

However, be forewarned. Many professors receive a lot of unsolicited emails from candidate students and are unlikely to respond. You need to make it very clear from first contact why it would be in his/her interest to supervise you, in particular.


Can I cite information from a report summary, if the report is locked behind a paywall? I've found a market research report which has some really useful information for me, but the report itself is locked behind a paywall, and I've received no response to the mechanism for requesting a free copy.

My question is, can I just cite the info from the report's summary (it's actually still quite detailed) and if so, should I cite that as a separate source (webpage) rather than saying that I'm citing the report itself?

If you are able to read the information in the report, even if it was only in the abstract, you can cite it.

Cite the report and the complementary references you have found.


How is sexism unknowingly perpetrated in academia? Some sexism is obvious, blatant, and/or deliberate. Fortunately, my understanding is that this kind of sexism is mostly a thing of the past.

However, female colleagues have told me that more "benign", but still harmful, sexism is still very prevalent in academia. In particular, I've heard that implicit assumptions that women are less capable, or more inclined to be teachers than researchers, are distressingly common. As a mathematician, the results are distressingly obvious: most math departments are overwhelmingly male.

What are some ways in which sexism is unknowingly perpetrated by well-meaning people, in academia in particular? And how can those of us who are well-meaning make sure to avoid doing so?

And how can those of us who are well-meaning make sure to avoid doing so?

If you see something, say something.

You're correct that blatant sexism is mostly gone.  I'm a female computer engineer, and I have never been told that I can't do the job because I'm female.  What remains is "death by a thousand paper cuts" sexism.  For example, I was recently at a conference, and the small group I was in was discussing one of the presentations.  An older professor in the group remarked that the presentation was particularly good because the presenter was beautiful and wearing tight clothes.  Nobody called him on it: after all, he was trying to give her a compliment, mentioning it would be rude, he's older and things were different then, and so on.  And it's hard to blame them, because if that were the only sexist comment I heard that day, it wouldn't be such a big deal.  But shortly after that, someone jokingly said I should marry my PhD supervisor.  Then someone said a new tool is so user friendly that "even your mother could use it".

Each of these incidents on its own is fairly mild: most people probably don't even realize they're saying something exclusionary.  Unfortunately, if you're a woman, each one reminds you that you don't belong, so the cumulative effect is very discouraging.  However, if you correct every person who says something mildly sexist, you get a reputation as a bra-burning feminazi.  As a result, most women keep quiet, or only point out the particularly insensitive comments.  It would make an enormous difference if other men would call out the ones who make inappropriate comments.  You don't have to be dramatic or rude about it, but a quiet "I don't think that's appropriate" would take a lot of the burden off women.  And naturally, you can try to be more aware of the things you say to make sure you aren't accidentally discouraging women.  A lot of sexist ideas are so deeply ingrained that otherwise fair and open minded people will say them without a second thought (like the "even your mother" comment).

I don't want to downplay the other valuable things you can do, such as volunteering at math/science camps for girls, but if enough men followed this rule -- even part time -- 80% of the sexism I encounter would disappear. To modify Edmund Burke's quote a bit,

  All that is necessary for sexism to triumph is for good men to do nothing.

June 27, 2014: After a year of comment trolls, I think it's time to add a point about men's rights activists.  The key mistake that MRAs make is treating rights as a zero-sum game.  The fact is, gender stereotypes hurt everyone.  They hurt women who want to be engineers; they hurt men who want to be nurses.  They hurt women who don't want to have children; they hurt men who want to be stay-at-home dads.

Sometimes, these stereotypes result in a disadvantage for men.  For example, Doug Spoonwood points out that American men have to register with the selective service system to get student loans, while American women do not.  MRAs point to these cases and try to claim that feminism oppresses men.  This is, at best, willfully ignorant: all these inequalities come from the same outdated beliefs and stereotypes, which feminism opposes by definition.  The fact that these cases exist just indicates that gender equality is not a solved problem.  (Women in the American military were not allowed to be in units tasked with direct combat until 2013.)

My answer discusses a woman's point of view because that's what I know and that's what the question asked about.  I would be thrilled if a man in a predominantly female field added an answer discussing his experience.


How to suggest merging papers with a more senior author? Here is my situation: A well-known senior researcher - let's call him Prof. Bigshot - wrote a paper. His paper is based on a good idea, but the implementation of that idea is (in my humble opinion) messy. After much thought, I, a lowly PhD student, cleaned up and extended the implementation and wrote a follow-up paper.

Both of our papers are publicly available on arxiv. I know (via gossip) that Bigshot's paper has been rejected twice already. I have not submitted my paper anywhere yet.

I believe his paper is being rejected because it is a conceptual paper without any meat. And I worry that my paper will also be rejected because it is incremental. However, if we merged our papers, I think it would be a strong paper as it would have both conceptual and technical contributions.
Thus I think it would be mutually beneficial if we merged our papers. (My advisor concurs with this assessment. Merging papers is reasonably common in my field.)

How do I go about suggesting to Prof. Bigshot that we merge our papers? I don't know what the etiquette for this situation is. I worry that he will think I am trying to take credit for his idea. Should I just wait for him to bring it up? or should I actively suggest it?

I have interacted with Prof. Bigshot before and I also sent him a draft of my paper, to which he responded positively. So this is not coming out of the blue for him, but I need to be diplomatic nonetheless. In particular, I want him to feel comfortable saying no without anyone's feelings being hurt.

Let met just get some stray observations out of the way: "Professor Bigshot" publishes a paper with flaws that are obvious to a PhD student, who knows just how to fix them and happens to know information about the status of Professor Bigshot's submissions.  This "gossip" seems perhaps a smidge unseemly (although I don't want to claim that I never talk about this sort of thing myself).  In my field, well known senior researchers rarely write papers with an obvious shoddy aspect (they may make some kind of subtle, critical mistake -- everyone does sometimes -- but that's not the same thing).  I find it a bit curious, but it doesn't affect my answer.

Sure, if you and someone else have two unpublished manuscripts that would each benefit from being combined with the other, you should suggest the combination.  I would have given the same suggestion already given in the comment: maybe get your advisor to broach the subject.  The advantage of this is that your advisor is (surely?) much more senior and established than you, so if the request comes from him in the formal sense, it comes with his imprimatur.  Putting myself in the Professor B's place, knowing that your advisor has endorsed the action is at least useful information.  If your advisor is someone I know and respect, then that does put more gravity behind the request.

(By the way, you didn't just wake up one day with a "followup paper" on your hands.  In deciding to write the paper, you knew you would be putting yourself in your current situation.  I hope that when a PhD student decides to write a new paper, he mentions it to his advisor!  What advice did you get while you were writing the paper?)

I don't mean to insist that going through your advisor is a key point.  Given that you have already corresponded with Professor B, it most likely will not be.  Anyway, let me assume that you will do the asking yourself, because that's the more difficult case.

  How do I go about suggesting to Prof. Bigshot that we merge our papers?

Assuming you want to do it yourself (to be sure, there is nothing wrong with doing this), you write to Professor Bigshot, send him a copy of your paper, and ask for his feedback on it.  You mention that the possibility of merging them has occurred to you, and you would be interested to hear his take on that.

  I don't know what the etiquette for this situation is.

I don't think there is any specific protocol here.  In dealing with academics, especially senior academics, you want to be (i) informative, (ii) respectful and (iii) reasonably concise.  There are many ways to do so.

  I worry that he will think I am trying to take credit for his idea.

Suggesting coauthorship is not trying to take credit for someone else's idea.  It is possible that he thinks that the idea is so precious, even with its shoddy implementation, that he doesn't want to share authorship with someone else.  Okay, he can say no, but you haven't done anything wrong.  It would also be possible, by the way, to describe your respective contributions in the paper itself, in this case crediting Professor B with the idea and you with the implementation.  That is not done as much as it should be, but it is sometimes done.  But wait -- in this case you have separate arxiv preprints, so the origin of the contributions is rather publicly known.  I don't see that you have much to worry about.  If you wanted to, you could cite both preprints in the paper: this would be an unobtrusive, easy way to show any interested party the provenance of the paper.

  Should I just wait for him to bring it up? or should I actively suggest it?

You should actively call his attention to the possibility of the collaboration.  There is no prize for the meek here.


Journal changed the ordering of the authors. What to do now? I am facing a very difficult situation. I sent a paper for peer-review in a SCOPUS indexed journal. My supervisor though did not contribute anything rather than reading my draft insisted that I put his name in the manuscript. I had put his name as the second author as otherwise he would stop my funding. Now my paper has been  accepted and published online. To my ignorance the journal has re-arranged the author names in alphabetical order making the name of my advisor to appear first.
In our university, it is mandatory for authors to be listed in the order of their contribution. Also it was me who did all the hard work. My advisor had no idea about the reviews sent by the reviewer.
Though I had clearly made myself the first author and my advisor as the second author in the TeX file I had submitted for publication, the journal has changed it.
The journal did not send me the page-proof before publishing it online. They just changed the author ordering in the TeX file I had sent and published it as it is.
They put my paper in "RECENTLY ACCEPTED" section with no DOI and no VOLUME NUMBER but it is posted online and is accessible.
What shall I do now? I mailed the journal. They are not replying, it's 2 days already.
Can someone please help. Shall I withdraw the paper from the journal?

You seem to be in a Math department, and are having a problem that is going to effect everyone in that department.  I suggest you speak to the chair of the department.
There are journals in mathematics, good ones, that insist on an alphabetical order of authors.  This is also the standard in most of pure mathematics.  If you have your facts correct, your university has policy that will make it very hard for anyone in pure mathematics to publish.  Applied math is a bit different but this still will be a problem.
As an example, the journal Results in Mathematics explicitly requires alphabetical author order.


Publishing software in a convenient way I create a software in order to solve a step of an specific problem. The results obtained (aided by the software) are going to be published in some journal. The focus of the publication is far away from that step.

The software may be very useful for other people because that step is involved in many common problems. It is not a huge code, but neither me or my collaborators known about other similar software for the matter. We know many researchers that solve it manually in long time.

I want to make the software available online. I wish to do it in some way that it can be cited (and the cites counted).

I can include the code in the supporting information, but I think that it has some downsides:

Hard to find compared to a site like github.
Impossible to polish and improve it.

If I don't attach it to a paper, then I don't know how it can be cited.

In short I want to: Make the code widely avaliable in some way that let me collect cites, and make me free to modify/improove the code after publication.

Is there any way? Which are my best options?

What do you mean by "and the cites counted"? Do you mean something like Google Scholar will index it?

If so, then the common route in CS is to publish something that introduces the program (although the code often lives on github). Then people will often cite that paper and or the repo whenever they use your program.

That isn't necessarily a ton of work either. Many conferences have workshops  or industry tracks (in case you are an engineer and not a researcher). Also, see dgraziotin's answer on publishing a paper in an open access journal so that others could cite his work.


What are the steps to find a publisher and strike a deal to publish the proceedings of a workshop? I help organize a workshop in a conference on machine learning where the conference doesn't publish proceedings for the workshops: the workshops have to do it themselves if they want to.
What are the steps to find a publisher and strike a deal to publish the proceedings of a workshop? (where to find the list of publisher in a given field, what are the typical contract clauses and negotiation points, etc.)
I know that we can publish it ourselves (since in the end publish = hosting some PDFs online) but I'm curious to know how the old-fashioned publishers work.
If that matters for the answer, all papers are written in English and one requirement is that papers are open access or allowed to be posted on arXiv.

I went through this a few years ago for a conference for which I was the program chair.
Since you want open access, you'll find that the big commercial publishers will want to charge quite a bit (thousands of dollars per paper) to publish your conference proceedings.  For open access publishing, there are a few reputable publishers and lots of disreputable publishers that you'll want to avoid.
One reputable publisher for topics likes yours is Dagstuhl's LIPICS series.
If the society that sponsors the conference has its own in-house publishing arm then that can be a good choice too.


How many candidates are usually invited for a campus interview? I am currently a candidate for a few jobs, and have a few campus interviews.

How many candidates are typically invited for a campus interview?

I am mostly interested in answers for positions for the range of positions, tenure-track, non-tenure track, lecturer positions, and postdocs.

For tenure-track positions my department generally invites 3 candidates for on-site interviews after doing phone screenings. This is what I have seen from a lot of universities in the US.

Other types of positions don't have standard rules. Non-tenure track and adjuct positions are filled as needed, don't involve as rigorous of interviews, and may never be brought on-site. Postdocs are usually hired by the individual PI rather than the department.


what are my options if the degree i want is not available on my country? Hello this is the first time i post something here:

I live in Argentina and I'm 18. Currently, I'm giving my evaluation exams to enter UTN university (It's one of the best universities in Argentina, it's public).

I wanted to study software engineering but that is a rare degree in Argentina, however i found a private university (Not as good as the public ones) but i don't have any reference of it. So i don't know if it is going to be worthy studying 5 or more years there at all.

The actual problem is that in UTN i'm studying systems engineering, is the closest degree i know it's going to be worthy but i don't want a systems engineering job in the future. (Although i know people who has a Systems E degree and works as a software E instead).

So i don't know what to do. I wouldn't mind move to another country, the problem is i really have no idea of what to do then, i can't move to another country but not knowing for sure if i was accepted by the university or not!
Also i don't know another's country's universities.

I only speak Spanish and English, but does anybody have an idea of a country exchange or something that asures me i that i have been accepted in university, so then i can move to that country to study?.

From your question, it seems like there is a misunderstanding about the process of studying abroad:

If you want to study abroad, you first apply for admission (and possibly scholarships). Only if you are accepted (and you accept the offer), you start your preparations to move to the place of study. There is no need to move before having been accepted.

You also don't need an exchange program between countries in order to do that. You just apply to a university that you are interested in, using the documentation of your previous studies that you have (e.g., high school degree). Applications from abroad are quite normal in many institutions.

On a related note: for most countries in the world, in order to study there, you need a proper visa. You will only be able to get a visa that allows you to study there after you have been accepted for a program.

As to finding out where you should apply to: this is the more difficult question, as this is quite subjective. There are university rankings that give you an idea of what very good universities are out there. Note that these rankings have their own problems, but they are often a start. Then, you can search for research papers in some sub-area of software engineering that you find interesting. If you find very strong research groups in that area, you may want to find out about the courses of study being offered at their institution.


What typically happens when a research field becomes "dead"? I'm interested in knowing what typically happens when a research field is largely regarded as being "dead".

Do professors in the field treat this dead period as a permanent effect and look to build new skills to do research in another field?

For instance, I recently had a conversation with a well-known topologist; he mentioned how topology had become dead ever since the Poincaré conjecture was solved by Perelman.  And now, he looks outside of mathematics, to physics, because he feels many questions in physics can be formulated as questions of topology.  Is this the typical thing to do when one's own research area becomes dead?

Topology is surely not dead. Maybe geometric topology, or its specific parts that were targeted at the Poincaré conjecture?

Even then, there are several inequivalent definitions of deadness. One meaningful watershed is when advisers stop suggesting the field to their grad students because they don't believe the students can build their career on it anymore; a lot of fields are dead by these standards. Another, more restrictive, criterion is when editors can no longer find referees for papers on the field.

None of these things dooms the field to eternal dormance (in fact, many dead fields have recovered, some many times), and in fact people do sometimes work on dead fields: some because they don't care about building their career (e.g., since they already have a steady job, or since they are too idealistic to care), some because they feel like they can revitalize the subject, some because they hope to find things of use for other fields, and some simply because they don't know that it's dead.


Principal investigator requests transfer of GitHub repository with my code to his account I am a senior postdoc and have recently published a bioinformatics algorithm in an academic journal. For that publication, I was listed as the first author of the manuscript, and my principal investigator (PI)/supervisor as the senior author. Both of us were listed as corresponding authors.

As a follow-up we decided to submit an application note pertaining to that algorithm. Once again, the same authorship (and corresponding authors) was maintained. Additionally, the algorithm had been developed into a webserver that was placed on the PI's lab website.

The PI asked me to put the algorithm on Github. Accordingly, I created a repository on my personal account and later added the PI as a collaborator. I am a Github novice user but my understanding is that this would be sufficient to push/pull the repository and generally make modifications to it.

However I was very surprised that my PI specifically requested a Transfer of Ownership of the repository from my account to his account. The other solution is to fork the repository onto his account, but the PI doesn't like this solution on the basis that it makes it harder for him/her to maintain a copy in their lab.

So the questions:

Is the request to transfer ownership a fair request? My rationale is that since I created the code, the repository should be on my personal account! And since the algorithm is broadcasted on the lab website and the PI is the senior author, then he/she has been properly acknowledged and their ownership of the algorithm is also properly represented!
How will transfer of ownership affect my future career prospects and search for Assistant Professor jobs, especially as my field (bioinformatics) is heavily dependent on coding and algorithm development?
What other GitHub alternatives are there (besides forking and transfer
of ownership), which would still allow me to keep ownership of the
repository and have any changes directly synchronised to a copy on the lab account?

The PI asked me to put the algorithm on Github. Accordingly, I created a repository on my personal account and later added the PI as a collaborator. I am a Github novice user but my understanding is that this would be sufficient to push/pull the repository and generally make modifications to it.

It is. The problem is that a personal account is, well, personal, and not overly suited for professional activities, such as research projects. To this end, GitHub uses the notion of "organizations", which can also own repositories. AFAIK there is very little practical difference between having a repo owned by a personal account and an organization, only that having it under your personal account gives the impression that this is a project of yours (as opposed to a project of your lab).

  However I was very surprised that my PI specifically requested a Transfer of Ownership of the repository from my account to his account.

From your personal account to his would be a little weird. From your account to an organization with the name of your lab sounds like entirely fair game to me if for no other reason than to maintain the "corporate identity" of your lab.

  The other solution is to fork the repository onto his account, but the PI doesn't like this solution on the basis that it makes it harder for him/her to maintain a copy in their lab.

Well, if you end up having to maintain both forks your PI is correct. Forking is easy, but keeping two forks up-to-date is unnecessarily cumbersome.

  Is the request to Transfer Ownership a fair request? My rationale is that since I created the code, it the repository should be on my personal account!

... and since you likely created it on grant money of the lab, having it under the account of the lab is at least equally fair.

  How will transfer of ownership affect my future career prospects and search for Assistant Professor jobs, especially as my field (bioinformatics) is heavily dependent on coding and algorithm development?

If bioinformatics isn't completely unlike any other computer science field, then very little people in a hiring committee will care about code in the first place, and nobody will care about whether the repo that contains the code is yours, or the one of your lab, or even the one of your PI where you committed a lot to.

  What other Github alternatives are there (besides forking and transfer of ownership), which would still allow me to keep ownership of the repository and have any changes directly synced to a copy on the lab account?

You can set up a Git repo with two origins, and you always push each change to both origins. However, that seems somewhat cumbersome for rather questionable gains.


Could I plot data from other papers in my figures for comparison? It's necessary for my current paper to compare some values from my work and previous work. Since the mean and std values of previous work are shown in their paper, could I plot some bar chart for the comparison between mine and theirs(of course I'll specify the source of the data)?

Yes, you can do this. Note that data per se isn't copyrightable in most places. But citation is proper to avoid any charge of plagiarism.


Can both a grad. student & faculty member cosign a recommendation letter? Can two people, a professor and a graduate student, sign a recommendation letter? The concern here is that the professor knows little about the student and the graduate student knows all about the student.

My concern here is that if the professor is contacted, he will not be able to provide further information, where as if I was listed as the primary contact: I could.

Like Noah, I had a situation where two advisors co-signed a letter of recommendation. I should mention that the people reviewing the letter found this an unusual situation—and had claimed that they had not seen that in twenty years of reading recommendation letters. So this is definitely not standard practice. I suspect it would be memorable, but I am not sure it would be actually useful.

However, the difference was that my two co-signers were equal in rank. Your situation has a professor with a graduate student providing most of the insights. I suspect you will need to have the professor adapt the graduate student's comments, and then sign the letter. In the case where feedback is needed, the professor would then need to get the relevant details from the graduate student.


Should the distinction between bibliography and reference be maintained when writing a paper? There is a small difference between a bibliography and a reference: the former includes all works consulted and the latter only those that are cited in the paper. Should we maintain this technical distinction when writing a paper?

Some journal templates require the title of the last section to be 'References'. Does this mean all the references must necessarily be cited in the paper?

From a practical point of view, whenever you send your paper for a peer review, they check if you have all citations both in your text and in sources. It means that "yes" they must be cited.

Saying so, there is normally clear advise from a journal how to cite and produce bibliography. You should do what it says.

At last you can always solve the problem by adding one sentence in your text: "Additional information about ... can be found in [your references]." With this sentence everyone should be happy.


In US, is it possible to have a non-tenure position for the whole career As it is very competitive to have tenure, I wonder if there is any case that someone holds a non-tenure position (e.g. associate professor) until the end of his/her career, i.e. until the retirement. If there is, is it a normal practice?

In the US system, it is generally not possible for a person to hold a tenure track but non-tenured position, such as being a tenure-track assistant professor, for longer than a few years (I think the typical tenure clock is 6 years plus extensions for life events like new babies).  After that, the person will either get tenure or else they will have to leave or switch to a different class of position, such as "research scientist."

Research scientists or non-tenure-track professors, however, can easily have a full and comfortable career with nothing even vaguely like tenure involved, all the way up until they retire, go emeritus, or succumb to old age.  This can happen both in traditional academia (see, for example, Dave Clark, or non-tenure professors at medical schools) or in alternate academic settings such as national labs and research companies.


How to cite from a paper using a different citation style? When writing a paper where you are citing from another paper which uses a different citation style, how should one cite portions of text that contain in-text citations? For example

    “Malnutrition has often been referred to as “the skeleton in the hospital closet”, as it is often overlooked, under-diagnosed, and untreated [69,70].Despite this, the negative consequences of malnutrition have been widely reported..." (Barker, Grout & Crowe, 2011).

An alternative format would be

    "Malnutrition has often been referred to as "the skeleton in the hospital closet" , as it is often overlooked, under-diagnosed, and untreated (McKee, 2011; Busby, 2008; in Barker, Grout, & Crowe, 2011). Despite this...."( Barker, Grout, & Crowe, 2011).

This seems an awkward and redundant solution. Would this be considered correct for APA style? What about other citation styles; MLA,etc.?

Echoing the other good comments and answer, I'd encourage you to think in terms of "forthrightness", rather than compliance to semi-random formal criteria. Think of the function of your citations, and thinking of the idealized version of scholarship and such. The goal is not conformity to style guides, but useful contributions to human knowledge, blah-blah-blah, ;) But, yes, that should be the way to think about such questions.

To my taste, citations in-line should be sufficient so that the reader does not have to "flip to the end" to see what "[46]" is. The space spent on fuller references is a good investment!!!

That is, yet again, if one thinks that the function of one's writing is to help the reader, all in-line references would be optimally helpful, as opposed to "proper-and-possibly-unhelpful".


How many graduate credit hours are generally required teach in a department? I've heard some conflicting reports on this, but in general, how many graduate credit hours are required to teach in a department or secure a professorship in it?

I'm an interdisciplinary PhD student with a heavy focus on computer science, but I will have close to thirty credit hours in social sciences when I'm done and I'd like to know if it is worth getting the count up a bit.

In the US there isn't a standard requirement.

If you have a PhD, you could potentially become a professor. If you have a master's, you could potentially be an adjunct or instructor.

Although, I have seen smaller schools and community colleges advertising a requirement of X graduate credits to be an adjunct, where X is rather small (e.g., 6 classes).


Language certificates when applying to positions in the USA I am non-US citizen and I want to apply for an academic position in the USA.

At which point do I need to show up a language certificate? For example, together with the job application, or together with the visa application?

Normally TOEFL is required for admissions in USA. However, you must check the requirements that are required by the University first to secure admission that may or may not include TOEFL beside other tests such as GRE, GRE subject, GAT etc.

Second is the visa requirements, make sure if the TOEFL is required or not for the visa, as in that case, you may get admission but denied visa or vice versa. so get eligibility criteria from different universities, compare them and find out what are the common requirements for all the universities, and then check the visa requirements.

Time of showing language certificate depend on the university, they can ask in advance or later.


Common file-formats for writing research papers This is a rewrite of a question that was perhaps-naively posed. I rephrase...

What file formats are ok/good/ideal/common/long-term-viable/archivable/useful for research papers?

And, also, there's the history-question:

What is the story of viable file-formats in the last 20+ years?

plain text/markup language

For mathematics, I think TeX/LaTeX is the way to go.  This is the standard way to write papers in nearly all areas of math (perhaps not biomath, where collaborators necessitate Word), so there's little extra cost.  One advantage of this approach is that it's easy to automate outputting in almost any format you want.  Furthermore, as new formats develop, we will almost certainly develop tools to convert TeX source to these new formats.  The arXiv is a great example of this model.


Can my supervisor prevent me from publishing by affecting reviewers opinion? Lately, and after long time of work in my PhD, I was able to get a result that is brand new, very strong and important. My supervisor though seems jealous and wants me not to publish before finishing my PhD. But I sense he wants to scoop me once I leave. The time is short and I haven't enough time to work in lab that will guarantee a paper. I insist on publishing though, can he contact any of the journal editors and affect their opinion?
I can't take the risk, so what should I do to avoid this?

In a biology / bio-engineering discipline, the authorship standards almost certainly dictate that you must have your supervisor as a co-author.
As such, worrying about contacting journal editors is beside the point: you can't ethically publish without your supervisor's permission---not because they're your supervisor, but because they're your co-author.

The biology focus also may help explain your supervisor's reluctance to publish, as it's (unfortunately) common for biologists to spend years building up a "perfect publication" with no incremental publications in order to try to get into a "glamour" journal like Nature or Science.

Given this context, I would recommend simply including the work you've done in your Ph.D. thesis (which does not preclude glamour publication).  That will make it very clear that you have done the work, such that your name must remain attached to it.  Beyond that point, I would recommend not worrying about the author order either: in biology, it is typical to put the student first and the supervisor last; since "last author" is also a significant and prominent position, I would expect that your supervisor is unlikely to have a problem with you being first.

Finally, I would recommend that you have a clear discussion with your supervisor about the criteria for publication.  Not "when will we publish?" because the answer to that will probably be "when it's ready," but "what else needs to be done before we publish?"  Get that agreement clearly worked out between you, then confirm it afterward via email to create a timestamped written record, and then you can also feel it is less likely that publication can be delayed by shifting goalposts.


Why do the rankings from U.S. News & World Report list some schools twice? The 2014 rankings of US statistics doctoral programs compiled by the U.S. News & World Report lists a few of the schools twice. I assume that the rankings are probably for different types of statistics programs (Harvard for example has both a statistics department but also a very good School of Public Health, which I'm sure has a biostatistics program), but the methodology section does not address this problem and I am doing research which requires analysis of this list.

Question:  Why are some schools listed twice in the rankings?

I cannot request this information from U.S. News & World Report directly because they only release this information to university officials.

If you click on a school's name, you can see the rankings of its various departments, including both Statistics and Biostatistics if applicable (example). This is pretty inconvenient, as it requires going through the schools one-by-one, but I'm not sure there's a better way to get that information.

There is also a post on gradcafe separating the rankings, though I'm not sure if it includes the entire list.


Deferred admission but funding not guaranteed I received an offer from a top US school for PhD this March and accepted their offer. Due to some family circumstances, I would not be able to join the program this year. I am an international student, and I have to remain in my country due to some personal and family reasons.

I asked the program about possibility of deferring admission. After hearing my reason, they have decided to defer my admission, but I am not guaranteed funding. Basically, I need to compete with the next batch of applicants for funding (fellowship, TA, RA, or none). I agreed to the same, and I would be getting an offer sometime before April of next year along with funding allotment (if any).

In this context, my questions is: Can I apply to more programs to make sure I have a funded PhD offer for next year?

I realize that there is a certain commitment when deferring an offer, however does the same hold true even when funding is not guaranteed. When I asked the program about my chances of funding, they replied that it is "likely" but "not guaranteed". I am not sure if I can take a "likely" and live with that. What if I don't get any funding (which is basically a rejection) and don't have any other offers? That will be a very sad scenario.

I would like some advice, IMO it is shrewd to apply to more programs, but is it ethical? I don't want to explicitly ask the program this question, since there is a likelihood that they may ask me to simply reapply, which I don't want to. I got off a wait-list, hence not very confident of my chances! Also, since funding is not guaranteed, do I even need to ask permission for applying to more programs? I mean, do they honestly expect a student to commit to a program without the program committing to financial support? I think that is asking a bit too much, and gives the program a complete hold over the student.

Also note that there is one other program (call Y) that I was admitted to this year, which I really liked. I had a very hard time choosing between the two offers, and had I not got into the program that I have accepted and deferred (call X), I would have gone to Y. I think I can get into Y again next year if I apply, since they tried hard to recruit me, but in the end I chose X because of better location (both were equally strong in research). So if X doesn't give me funding next year (effectively reject), I would like to go to Y.

Please share your thoughts. Thank you.

In brief, in academic mathematics, if you are "accepted" but without promise of funding, it's a very weak offer. The fact that you got funding this time around is certainly positive, but there's so much volatility involved that I think it would be a dangerous mistake to view the situation as so much promised to you (it's not) so that you have a complete obligation to go there and nowhere else. A promise of funding should be construed as obliging you to either keep your promise or decline in advance, but mere admission, without funding, while not nothing, is barely something, either.


How much time should I spend to prepare to teach a class? In the last few years,
I've taught a course which was developed by my colleagues.
The first year, I spent about 6 hours a week
preparing for a 3-hour lecture.

I'm currently teaching a course for the first time.
I find that I'm spending about 15 hours a week
preparing for a 1-hour lecture + 2-hour lab.
In addition, the course material is often floating around in my brain
even when I'm not actively preparing for the course.
I feel like I'm spending too much time and energy preparing for classes
and this is hurting my research productivity.

I'm looking for rules of thumb about how much time is "normal"
to spend to prepare to teach a class.

Question: What is a reasonable amount of time to spend preparing to teach a class?

Question: What is a reasonable amount of time to spend preparing to teach a class?

That question cannot be answered in general. Many factors go into what is a "reasonable" amount of time to prepare.

As commenters have argued, the first time you teach a class necessarily takes significantly longer as bootstrapping the teaching material can be the most time-consuming aspect of teaching. 15 hours per week for a new 3-hour course seems on the long side to me as well, but if the preparation for the lab is time-consuming it's probably not excessive. Labs in general vary widely in terms of their time commitment, based on the nature of the lab and availability of TAs.

What I have found is that it pays to be pragmatic: when I am teaching a class for the first time, I generally avoid time-consuming experiments and I do not provide much material outside of lecture slides, book (chapters), and papers (that is, I do not prepare custom readers or much else that needs to be created from scratch aside from lecture slides). I also try to go for a lab model that is considerate of my own workload in the first year (i.e., I'd rather try to have a project that students can work on more freely rather than something that requires constant hand-holding, if possible). In the following years, I will step-by-step create additional material or change the labs. This also has the advantage that by then I know better what additional material students actually need.

  I feel like I'm spending too much time and energy preparing for classes and this is hurting my research productivity.

Well, I would lie if I said that teaching a course ever did not impact my research productivity. It is a fairly seizable chunk of additional work and mental load, after all. In general, this should be built into your tenure- or promotion requirements, as it is true for pretty much every university faculty member (i.e., when your, for instance, tenure requirements are drawn up, people don't plan for you working full-time on your research). Also, try to figure out whether this is a one-time happening (for instance because the course is new) or whether you will always spend 1/3 of your work time on teaching going forward.

If you feel your current teaching load will prevent you from reaching your next career stage, you should either attempt to reduce the time you commit (e.g., be more pragmatic about how you design the course or how much you prepare for lectures) or talk to your department manager about whether it's possible to reduce your teaching load (e.g., give you more TAs next time, etc.). I feel making a data-driven case ("this is how many hours I spent on task A, B, C, because of reasons X and Y, how can I improve this for next year?") works best here, especially if your teaching load does not look extraordinary on paper.


How best to increase the reach of conference proceedings / papers? I am helping to organise a conference which has been running for a number of years. Conference papers are peer-reviewed by a well-respected review committee and the conference has a good reputation and attendance within the country. However, papers from the conference are rarely cited, don't rank highly in google scholar searches, aren't included in Scopus. For for example, my papers from this conference are read and cited less than some of my (frankly, lower quality) papers from other conferences.

We are exploring ways to increase the reach and citations of the conference papers.

Currently, the conference proceedings have an ISBN but are just published on our own website. We are exploring the option of publishing the proceedings as a special edition of a journal, but this is unlikely to happen this year.

Would it help if we assign DOIs for each paper and/or the conference proceedings? Does it matter which?

How do we improve search rankings on google scholar?

How can we get the proceedings included in scopus?

What else can we do to increase our reach?

Realistically, the main thing to increase the probability of the papers coming out of your conference being taken seriously is to:

Convince a professional organization such as ACM, IEEE, or USENIX (to provide some examples for Computer Science, your field will surely have similar organizations) to print the proceedings and include them in their digital libraries (if existing), or
Partner with a reputable journal to print your proceedings as some recurring special issue, or
Have a really high-prestige organizing committee back your conference and vouch for the quality of papers.

In short, you will, unfortunately, need to piggyback on the prestige of some other entity (a publisher, a journal, or a bunch of well-known individuals) to get your proceedings off the ground.

To answer your specific suggestions:

  Would it help if we assign DOIs for each paper and/or the conference proceedings? Does it matter which?

DOIs are cheap, and even many spam- or borderline-spam journals happily assign DOIs. I can't imagine this being seen as a seal of quality.

  How do we improve search rankings on google scholar?

IIRC search rankings on Google Scholar are a combination of citations and match of the paper to the search query. I don't think there is much leeway to game the system (aside from citing previous papers in the conference, of course - but thinking this thought through to its natural conclusion quickly ends up in rather unethical practices).

  How can we get the proceedings included in scopus?

I have little knowledge about Scopus given its low relevance to Computer Science in my area, but to the best of my knowledge they don't index proceedings at all?

I should also say that nowadays the barrier for national conferences (and if I understood your question correctly yours sounds like a national conference) to be taken seriously as a prime publication venue is extremely high. There is an abundance of international meetings to choose from, and most researchers choose those to publish their novel and exciting new results. National conferences are really meetings, first and foremost, not places to publish new results. Some of the more prominent national meetings in Computer Science have moved away from printing proceedings altogether, and focusing on what a conference should arguably be about in the first place - to present and discuss ideas and previous work, not to publish new results.


If someone conducts unethical research unbeknownst to anybody, but produces positive results, what would happen to the research once discovered? I was just wondering about this specific scenario.

Say someone was researching nature vs. nurture, but his experiments involved keeping babies in a controlled environment for the first 10 years of their life. His research is secret and he has ways to smuggle children for his research (don't ask how).

After 15 years, he publishes a paper and confirms that there is a set amount of characteristics that can be transferred via genes.

What would become of the researcher and his research? Will the researcher be jailed, but the research results recognized?

This question is about unethical research in general, not just ones involving human subjects.

P.S. No babies were harmed in the making of this post

Unfortunately, history has already forced this question upon us, and the answers are not entirely clear.  The Nazis inflicted widespread and breathtakingly horrifying human medical experiments on their victims during the Holocaust. These yielded quite a bit of medical data, that some want to unearth and apply today.

This has ignited quite a bit of debate on the ethics of using this most obviously and supremely unethical research.  The science may be dubious as well, given the circumstances under which it was performed.  An excellent discussion of the dilemma may be found in the article "The Ethics Of Using Medical Data From Nazi Experiments" by Baruch Cohen.  In essence, Cohen argues that in certain extreme cases it may be possible to use the data, but only when accompanied by strong condemnation of the methods and only when it concerns information that is both otherwise impossible to obtain and of life-saving importance.

Nazi medicine is an extreme case, but unfortunately by no means isolated, and the judgement of history and science on these studies contains less uniform condemnation than we might like.  The modern consensus, however, seems to be that except in very unusual circumstances, unethical studies should not be rewarded in any way by recognition.


Advisor recommended reuse excerpt of master's dissertation in Ph.D. Thesis I am finishing writting my Ph.D. thesis and a bit short on time. Part of my Thesis would be a review of literature, regarding the method used. This method was used as well in my Master's work (under the same advisor) and thus, my Master dissertation contains a portion in which a literature review is performed. My advisor suggested that it would be good to reuse this from my dissertation.

Now, I went to look at my dissertation to select the excerpts, and I see that it amounts to around 16 pages in a 150 page dissertation. My thesis is currently with 103 pages and I believe that in the end it will have approximatelly the same length as my dissertation.

Of course, when I saw the numbers, a red light of self-plagiarism lighted up. Of course, there would be some addaptations. For instance, there are occasions in my dissertation where I refer to a previous chapter, which would need to be adapted. And of course, I would clearly state which parts are repeated.

However, it is a large excerpt, which makes me really scared about this and I seek a second opinion on the matter.

I would treat a long excerpt of your own material acceptable provided that you also cite it, listing carefully that it is an excerpt and pointing to the original source. I'm assuming that you hold copyright on the early work, not having yielded it to another publisher.

Don't confuse the two issues, permission to create a derived work, and proper citation. The permission is obvious if you hold copyright and by citation you avoid any claim of self plagiarism.

Note that the main purpose of avoiding self plagiarism is to let readers find the original source of material and, thus, learn its complete context. By citing, you make this possible.


CS Master's admission after academic dishonesty I got a B.S. in Math several years ago. I'm applying for CS MS this fall, but I still need some coursework before admission. I spent the past year at College X as a non-degree student. I did well last fall (all As), but was caught cheating on an elective CS class this spring (googled some answers on one homework assignment). The result is a B- in the class (instead of a B). I realize I'm fortunate for a pretty minimal penalty -- I just got a 0 on the assignment, and a one-semester probation (which doesn't affect me since I was only a non-degree student here and I'm not continuing here anyway). I don't have an excuse for this, and I don't know why I decided to do this. This is the only time I've cheated. For whatever it's worth, it's not indicated on my transcript, only in some confidential file the university has somewhere. My questions are:

How badly does this affect my chances for admission? I was planning on applying to just one top 20 school that I doubt I'd get into anyway, but most of the schools on my list are still ranked in the top 50.
More importantly, is there anything I can do to repair the situation? I don't have years of time before application season to be able to say it happened a long time ago. That said, I'm taking two classes this summer at College Y, and another class in the fall at either College Z or Z'. The advice given in a similar thread here was to do very well in classes from here on out, but would people reading my application even believe the rest of my work is honest after committing academic dishonesty?

If I go to College Z this fall, I could also retake the same class from this spring. It wouldn't do anything to help my GPA at College X, but my GPA there is > 3.6 anyway. I believe I could do well, at least an A-. The class also covers an extra couple chapters, one of which is related to my CS interests. Would it be worth "retaking?" It's basically the same class, so it feels like it might be a waste of time, especially since one B- isn't that bad. If I go to College Z' this fall, I could probably take an advanced class related to the class I took this spring. This advanced (joint undergrad/grad) class seems to cover a lot of material specifically related to my CS interests.

My overall application is pretty strong (3.7 GPA, GRE 170Q, 158V, 4.5A, 2-3 strong LORs, 75%ile Math Subject GRE). Hopefully it helps that three schools I'm considering are Colleges Y, Z, and Z', so maybe having a little bit of coursework done at two of them could help.

Thanks for any advice.

Based on what you stated, it doesn't really sound like this will follow you anywhere. You were caught, they gave you a token punishment, and everyone moved on. It's not as though you have to state your dishonesty on your resume or whatnot. I would recommend treating it as a lesson learned, and unless someone specifically asks you about it, don't bring it up.

To directly answer your questions... no, you really can't do anything to fix it. It's part of your history now. However, it may not affect your application, as they receiving university will probably never find out about it.

Note that all of this is based on the assumption that your dishonesty does not go on your official transcript, based on your having stated that in the question text. If it is on the official transcript—the one that one university will send to another when asked—then your situation is a good deal worse.