Can I add my middle initial to my author name in preceding articles? So I'm not sure what to do. I've been listed as a co-author on my first publication in X journal, with a decent impact factor. Now I just realized that my middle initial wasn't included on the first publication.

Can I start using my middle initial in future publications? I know it's only my first, but that paper could get plenty of citations in the near future. (just hypothetically)

What do you think?

Is there a way to link the 2 names? Could I link them if I publish again in that same journal, specifically an ACS journal?

In the modern day of vastly intelligent computer software and important internet presence, it is highly unlikely that a missing middle initial will be the cause of "nonrecognition" of your name. As Stephan wrote, a bigger problem is name confusion; it is definitely a good idea for you to start including your middle initial(s) in future publications. I'll answer here focused more on how to make sure the names are "linked".

My Google Scholar profile, which is compiled entirely by a computer (my only contribution there was identification of duplicate entries and removing them), even picked up some of my undergraduate term-reports which I put on my website many years ago (and which are now no longer available). Of my published papers, I've listed at various times my name as

Willie Wong
W W Wong
Willie W Wong
Willie W-Y Wong

and I don't seem to have had much trouble*.

If you want better control over the articles associated to your name, you can always register for Web of Science researcher ID and/or an ORCID which are both designed to help alleviate the problem of name collision and name changes throughout the career of a research scientist.

For fields which encourages the use of arXiv, the author identifier also helps group all of your pre-prints, and allows you neat things like a Javascript widget for your own website showing your recent pre-prints.

For mathematics, the AMS maintains author profiles (they recently upgraded this!) to which you can also submit corrections to include omitted paper or to exclude misattributed papers by other authors. (The AMS author profiles are only accessible through a MathSciNet subscription.)

I am not that familiar with other fields, but you should look around to see if your scholarly society provides a similar service to help maintain a comprehensive publication record for authors.

*With Google, at least. Microsoft Academic Search has some trouble coming up with my complete list of publications.


Postdoc without letter of recommendation What if my PhD advisor doesn't want to give me a letter of recommendation, because he doesn't want me to leave on postdoc? No one of his young assistants have never been on any postdoc or fellowship exchange.

Based on your comment responses, I think that you are working for a young faculty member who is trying to build his group and encouraged his first two PhD students to stay on after they graduated. It's an admirable goal to start building a research group, but in the US it would be discouraged to do so by keeping all of your own students in my experience. US academic research has a bias towards sending one's students out into the world to cross-pollinate ideas and avoid stagnation and closed-mindedness.

That being said, refusing to provide a letter of recommendation to a good student for this purpose is borderline if not outright professional misconduct and wouldn't be tolerated at most US universities (though I'm constantly surprised what weak administrators let star faculty get away with sometimes).

I think you should sit down with your advisor and explain your life goals to him. Include the fact that you are eager to get out into the world and learn more in a different environment. Try to convince him to see it from your perspective without getting antagonistic. If that doesn't work, go see your department chair, but only as a last resort.

You are in a bit of a tenuous position since your advisor could refuse to sign off on your dissertation (or let you defend, or drag his feet on revisions, etc) if he becomes scared by feelings of abandonment in your desire to leave. Bringing in higher authorities could make this worse. It would be best to convince him with the power of good arguments than to make the situation adversarial.

The timing of this can be tricky. He's probably going to find out that you applied for postdocs with out his recommendation and blessing, and given the usual schedule for postdoc recruiting, I'm assuming you will have to apply before you defend. I think it's probably better to be open with him that you are definitely going to apply, find a postdoc, and leave than to do so behind his back. Maybe when he sees your resolve to do so, he will change his mind about writing you a good letter.


What can happen if a recommendation letter falsifies information? For applications of virtually any kind, it is stipulated that an offer may be rescinded or even during a course, a student may be taken off, if any false information is discovered in their application.

However, suppose for a graduate program a student asks a professor to write a recommendation, and whether knowingly or unknowingly the professor includes false information in that letter of recommendation which has a bearing on the application, what are the consequences of that?

The onus of selecting the recommender is on the student/applicant, but I do not see how they can suffer consequences since recommendation letters are often not shown to the applicant.

To help answer the question, assume I am referring to universities in the U.S.

Few cases can happen (probability will decrease as we go from case to case).

(They don't find out) nothing happens.
(They find out) they'll remember the professor and his recommendations will be considered of no value

The reader of this recommendation can have the professor marked as a dishonest person within the facility or keep it for himself

They contact the professor ask him about it. Then they contact the current professor's employer and he gets in 'trouble' - some people get aware of it.
They contact current professors employer, he get's fired for dishonest behavior
They make a lot of people aware (Including his colleagues and newspapers/media?) he gets fire and it's going to be hard for him to find another job, highly unlikely.

It really comes down to the credibility, you're not going to jail because of that. It can only really hurt your trustworthiness in the academic and human sense. If you're going to lie it should be something small like if someone worked in your company for a year you can say he worked there one and a half years.

If the one recommending someone isn't aware of something chances of this affecting him are very low ~0. This is in the case of something that common sense dictates, he shouldn't be aware of I don't know, Like does he have a dog, and on the other side, one can't say he's was not aware of his e.g. effort or performance.


Using other people's data for dissertation: ethical or not? It was recently shared with me that a professor in my department (and if anyone saw my question about the verbally abusive ex-advisor...yeah, same guy) offered one of his PhD students his own corpus of data for writing her dissertation, and apparently made this offer in response to her deciding to quit the PhD program. As I understand it, she accepted this offer and decided to stay in the PhD program because of it; I also believe that this corpus -while used in a number of publications - as a whole is not publicly available or anything.

Because I am admittedly biased (see the aforementioned question for context) against this professor, I don't entirely trust my judgement. Is it just me, or is this a ridiculously unethical offer?

Next question, if it is unethical, do I say anything about it to anyone? The person who told me did so in confidence, and I don't want to betray that. I'm hoping he reports it (he said he's thinking of talking to the graduate director in our department about it, as he thinks it's shady too) but if he doesn't - should I say something or just let it go? Because I already have a bad relationship with this professor and have complained about him, I feel like me complaining yet again about something else will just make me look bad and not be taken seriously, not to mention there is the whole matter of this not being any of my business.

My heart and soul are all riled up because I just want to see this professor be held accountable for something (I'm pretty sure he's going to get away with how he treated me. See linked post), but my self-interested brain is telling me to let it go and stay out of it. Thoughts?

Unless the student claims that they collects the data himself/herself. I do not see any scientific misconduct in using other people's data with their permission.

Of course collecting good data is a contribution. However, even if the student collects data themselves, I would be very surprised if that is more than 30% of the contribution in their thesis.

TL;DR: No big deal. That might be a bad professor, but it doesn't mean everything he does is wrong.


How can a Master degree lead to 300 ECTS? http://emjd-dc.eu/files/2011/11/emjd-dc.pdf

Here, one of the admission requirements is, A Master's degree corresponding to 300 ECTS.

How is that possible?

A Masters degree is at most of 2 years. 2 years = 4 semesters.

1 semester = 5 courses = 5 * 6 = 30 ECTS.

Then, 4 semesters = 30 * 4 = 120 ECTS.

Where does 300 ECTS come from?

I'm guessing ECTS is the European Credit Transfer and Accumulation System. From that page, a bachelor's degree is worth 180-240 ECTS credits, and the master's is worth 60-120.

It sounds as though the institution you're interested in wants a master's degree and at least 300 ECTS credits. From the linked page, it's possible that you could have a master's but still only have 240 ECTS.


Is participating in professional meetings helpful from a CV point of view? My professional society (a physical sciences one), arrange an annual meeting where almost 10,000 people attend and almost one third of them present. The benefits of participating are overwhelming, but I was thinking whether or not such participation is useful on a CV, especially that what you present is not going to be published (although normally you present your work which is to be published or has just been published).

Note that this is a meeting, not a conference.

EDIT: by participating I mean presenting.

The key factors here are that it's a contributed presentation (not invited) and it's in a huge meeting with many presentations of differing quality.  It sounds like you may be talking about the APS March meeting, but similar things are true in many other cases, such as the AMS/MAA joint meetings in January.

How valuable such a presentation would be on your CV depends on how far along you are in your career.  If you are coming up for tenure, then you'd better have far more impressive things to list on your CV, and presentations like this would be inconsequential.  (The only value on your CV would be in demonstrating continuing scholarly engagement if your job is almost entirely focused on teaching.)  If you are a college sophomore, then presenting at a meeting like this would be noteworthy.

To a first approximation, if you're an undergraduate then these presentations are worth highlighting on your CV (unless you are lucky enough to have something more impressive to emphasize), while if you're a grad student they are worth listing but probably won't be very important.  However, it's worth asking a mentor for personalized advice.


If I interview a professor, should I pay him or her? As part of my Toastmasters club, I am preparing a speech where I have to research a topic I am not familiar with. One suggestion is that I could interview an expert (e.g. a professor) in a field related to the topic I choose. If I do interview a professor, should I compensate the professor for his or her time? What's the protocol for this? Does the answer change depending on whether I use the interview for commercial gains or not?

Unless you're giving a veeeery long speech or speaking about something highly technical to a group of experts in the field, there is no need to interview a professor. What you're most likely trying to do is give a layman's introduction to a fairly broad field. By contrast, researchers are highly specialised in very narrow fields. A short speech is unlikely to get to any details that you need to speak to an expert to learn about.

You mention that you're supposed to speak about a topic you're not familiar with. That means you don't have the background knowledge about the field that makes speaking to an expert useful. You would most likely get more useful information from Wikipedia, blogs (possibly by professors) or finding an introductory textbook in the library. Asking a professor to give you an introduction to an area you're unfamiliar with (outside their teaching duties) is kind of a waste of time for them. If you want to waste their time, then you should certainly offer to pay them, or at least offer to take them out to a lunch you pay for while they talk to you.

Like @cag51 metioned in the comments, you'll probably have more luck with a grad student. We're still new enough to the whole "expert" thing to be flattered that you would ask, tend to have a bit more time than professors, and never say no to free food.


Leaving an Area of Specialization (AOS) off of my CV? So with the job market being as it is, I'm considering the prospect of leaving academia after my PhD. The problem that I have is that the name of one of my Areas of Specialization has been co-opted by some new age mystics and if you search "X" after seeing that I specialized in "X", you're more likely to think I specialized in some arcane form of crystal healing than the work I actually did.

My other AOSs sound fine, even semi-impressive to the layman, and so don't really concern me. This one, however....

So, two quick and related questions:

Am I right to think that my AOSs at least would still remain when listing my PhD on a non-academic CV/resume? Or just "PhD in field X"? (The question on CV for leaving academia didn't provide too much specific guidance here.)
Is it ethical to leave one of my AOSs off of the CV, assuming I leave the others untouched? In a sense it is misrepresenting what I did during my PhD, since I really did a lot of work in all three of these areas. On the other hand, listing this troublesome AOS might misrepresent what I did even more--- crystal healing and such.

This seems like an obvious opportunity to briefly explain yourself on your CV by listing the formal names but then stating what that actually means in parentheses. As an example:

PhD, Some Named Institution (2007-Present)
Areas of Concentration:
 - Science thing 1
 - Science thing 2
 - Crystal healing sounding thing (Chemical Engineering)


Why am I getting rejection in PhD admission after interview? When I was in my bachelor's program, I applied to three universities in Europe for masters. My two first choices accepted me and offered me funding for my masters studies which is competitive (2 students in my field got it). The third university which is not as well known as the others in my field, but still very good, accepted me but did not offer me funding. They interviewed me in this university and then rejected me. For the other two universities, I also had interviews and they both accepted me.
Now I am applying to PhD programs again in Europe. I did my masters in one of those universities in which I was accepted. Again, I have applied to three universities. This morning, the one that was not my first choice and again is not as well-known as the other two, after an interview, rejected me. This position had 5-6 vacancies.
I am confused about this, to be honest. Because I do not know if I should interpret it as that I will be rejected in the other two as well, or just assume it depends on my match with their programs. If the latter is the case, why did they even interview me? The thing that confuses me is this: if they shortlisted me, it means they were considering me. After the interview, they rejected me. I did not have the impression that I could not answer their technical questions. My question is this: should I interpret that the same thing will happen with those well-known universities? Why do you think that they rejected me while I feel I am qualified enough to the other two as well?

In late 2019, I had funding to employ a single PhD student at my European university. So I opened up a vacancy, and I received about 140 applications. By sheer necessity, I had to reject 139 candidates, and that included several very good ones indeed.
The main difference you're experiencing is that European Master programmes can accept scores* of students every year, but many European PhD positions are job vacancies that can only be awarded to a single person. So you're suddenly dealing with significantly more serious competition for the available positions. Rejection merely means that at least one candidate was even stronger than you.
*exact numbers depend on country, university, programme, but it's typically much much more than one student per programme.


If I accept a PhD offer but change my mind about attending, do I have an obligation to attend for some number of years before dropping out? I know there's alot of questions on S.E. about dropping out of graduate school after having started.  My position is similar, but also different:

I was accepted into a prestigious university's program for a PhD in Computer Science earlier this year.  I am expecting to be fully funded for up to 5 years, the school and program are great and well known, etc.

This summer I have been working at this same school as a Research Associate, doing very similar work to the kind of work I understand that a PhD student would be doing in order to work towards their completion of their Thesis and I've come to realize several things:

Upon class signups I realized that I didn't have a particular yearning to take any of the graduate school's offered courses.  I've come to a late realization that I'm not looking forward to any future course work.
Having been working 60+ hour weeks since early May, I've come to the conclusion that I'm not capable/willing to work this many hours.  I would like a life outside of my work/schooling.
The geographic area in which the school is in (and by extension, I am living in) is not one I am used to.  I am finding it extremely difficult to adjust to these new living conditions (Large city, deep south, etc).
This is exacerbated by my perception of the fact that my graduate school is highly composed of work-oriented and often culturally different individuals that I am finding it extremely hard to relate to.  I'm discovering a lack of anyone willing to "hang out" outside of lab or classes.
Personal and family issues are calling me home most weekends, and the school is a bit further from family than I'd like.

That being said, I think all indications point towards me dropping out of the program as soon as my work contract is finished (just before the start of fall classes).  However, I would like to do this as gracefully as possible without burning any bridges, but am unsure of a few things.

Due to the April 15th resolution, am I obligated to spend any amount of time at this university as a graduate student? (I'm technically employed now, not a grad student). If so, how long?
If above obligation is not present, should I try and remain to attend classes for an amount of time before dropping out to make an effort for the graduate school?  I'm fairly certain at this point nothing short of a miracle change in many factors would be enough to change my mind about wanting to stay for a 3-5 year period.
If I choose to leave in either case, what is the best way to professionally explain the situation?  Who should I explain it to?  My graduate school does not assign advisors until the end of the first year, so there isn't a sole advisor to ask.

The April 15 resolution is a commitment that you won't accept another PhD offer without the OK of the school whose offer you accepted:

  However, an acceptance given or left in force after April 15 commits the student not to accept another offer without first obtaining a written release from the institution to which a commitment has been made.

and also a commitment not to accept an offer you don't expect to honor:

  Acceptance of an offer of financial support* (such as a graduate scholarship, fellowship, traineeship, or assistantship) for the
  next academic year by a prospective or enrolled graduate student completes an agreement that both student and graduate
  school expect to honor.

It doesn't obligate you to go to grad school if you decided you don't want to, after all.

If you are really sure you don't want to do a PhD, the department will be much happier if you don't start (rather than starting and dropping out), so that they can offer your spot to someone else. In the first part of a PhD, the department is investing (time, money, teaching and supervision) in you with an expectation of future returns. You're not doing them any favors by letting them invest those resources in you when you don't plan to really use them.

You can politely inform the person responsible for the program (e.g. director of graduate studies) that you don't plan to attend after all.


Which factors in PostDoc opportunities choice? Many of you probably have already lived these career turning point: your PhD program is going to end, and you have to choose an university research group to apply for a postdoc position.

Which factors do you consider as more important in this choice?

Take research group X at university Y.
Which factors you consider to decide if it's worth to write to them for a postdoc opportunity?

Research group project's affinity with your PhD research work?
Research group's excellence, and international ranking of its team
leader researchers?
Research group members' human affinity with your personality (if perceptible)?
Research group project's scientific novelty and genius?
University excellence, and its international
ranking?
Distance from your hometown? Proximity to your hometown?
Salary?
Going abroad?
The university city/country way of life?
Other elements?

Please tell which of these (and other) elements you consider the most important (or by giving a percentage to each, if you want).

Many thanks! :-)

Actually, I think the frame of this question isn't quite right. I would argue that these are criteria that I would use if I were choosing between multiple postdoc offers, but these are not necessarily appropriate when deciding where to apply.

What I would do is decide what my "deal-breakers" are: that is, what are the criteria that would prevent me from accepting an offer, regardless of how good it is? For instance, if you need to take care of an ill family member that lives in a specific location, then you're probably not going to want to consider international programs. Similarly, if you're determined to go into industry, you're not going to be inclined to take a purely theoretical postdoc project.

However, once you've decided upon those deal-breakers, if you then see a project for which those criteria do not apply, then you should go ahead and submit an application. You don't have much to lose by doing so.

Once you have the offers, the challenge is tougher. All of the criteria you've listed are valid, and it's hard to say which of those might be the most important—it all depends on your own personal circumstances. One hopes that research concerns are the most important of all, but as I've mentioned above, there are valid reasons why that might not be the case. The only thing that I would make sure of is that whatever option you decide for in the end, it helps you in moving on with your career beyond your postdoc. There's nothing worse than getting stuck in "PD purgatory," where you can't really stay as a postdoc any longer, but are having problems moving to a permanent position afterward.


Is there a tool to visualize the academic citation network around a researcher? I'm looking for a PhD position. Of course I'm reading and following the papers of the field to get to know the community. Is there a tool to visualize a citation/co-author network (or at least a database I could visualize myself)? I have looked into tools like CitNetExplorer and VosViewer. Csauthors.net is also a nice tool, but it is limited to showing only a path between two researchers instead of a full graph.

Essentially, I would like to map all collaborations of the researchers to get a feeling for where the hot spots are and where the niches are.

You might want to have a look at the Web of Science (formerly known as ISI Web of Knowledge). When I started my PhD back in 2008, I used it particularly for visualizing citation networks relevant to my research. I think some time later it became a subscription based service, so the access is not as easy anymore, but a lot of scientific institutions or libraries may provide you the access. I haven't used the Web of Science any more in recent time, so I am not really aware of their capabilities today -- but the description still reads similar to what I remember.


Is it unethical to access journal articles from Torrent websites? Getting access to journal articles can be quite expensive, in particular for those not affiliated with some University (even then, it's still expensive, it's just the uni paying the cost...).

A question asked on this site Why are most scientific articles locked behind a paywall?
ponders why this is so. The answer is not convincing at all, it essentially says "that's just the way it is, pay up".

Well, if that is the way it is gonna by, then I am just going to torrent-download the articles. How could this possibly be unethical, if you guys yourselves, for no good reason and for the detriment of scientific inquiry, help support the monopoly that these journals have?

Ethics is (by definition) personal or at least culture-dependent.

Personally, I think it is unethical to have publicly funded research results behind a paywall. That would make the answer to your question: No, it is not unethical to use websites like sci-hub. But that's just me and others may disagree.


Can I use my university email to contact professors in other university? Shall I use my university address to contact professors in other universities who are specialized in the field of my dissertation?

That is actually a fair question. (Some commenters here have possibly missed the point that for the beginner in academia even the most obvious things may cause confusion).

And the answer is: yes, you can.


Is it acceptable to contact senior people suggested literature? I saw a postdoc at a small workshop, and heard him state his research interests. I didn't speak to him in person, but I later contacted him via email, asking whether he has suggested literature on those topics. I haven't yet received a response after a while.

Is it considered unacceptable to contact someone like this, immediately asking for suggestions on literature?

It is perfectly acceptable to ask for information. His lack of a response could be due to a couple of things. One (most likely) is that he is just busy and this has low priority for him. The other, of course, is that he feels you should be able to find the answers yourself based on the phrasing of the question you asked.

If it has been less than a couple of weeks, I think you can still expect an answer. You can always follow up, of course, but not too soon.

You might also be able to get an answer you need from anything published at the workshop. It might be good to start that in any case.

And, BTW, a post-doc is probably chuckling a bit to be considered a "senior" person. They feel pretty far down the pecking order, actually. But even full professors can be asked, and will often reply.


Reference software patch in paper In algorithms papers, how common is it to reference accepted software patches based on the algorithm presented in the paper? Is it appropriate to even mention it?

Yes, it is common and fairly reasonable.

So say you've implemented a new method for X.
And you submitted it as a PR on say github, as a new feature for
"SuperXdoerLibrary", and it was accepted.
Then you would, say something at the end of the Section where you describe your algorithm something like:

  This method for doing X is now available in SuperXdoerLibrary (V1.23)1.

And then in a footnote put a link to the SuperXdoerLibrary website, or github page. And probably also put a link on your website

It is very common to refer to what implementations of your algorithm referred to in your paper. And a "good thing".

As to if it is a stand alone implementation, or as a component in a larger library, I don't think it matters.
I would in-fact suggest it is even better if it is in a larger library as that will generally mean it is in a more usable state.


Google Scholar vs other academic search engines How is Google Scholar compared to other academic search engines and catalogues such as ScienceDirect, Scopus, and universities' own online catalogues--in terms of the following?

comprehensiveness of search (i.e. can fetch all the ever published relevant titles, whether the user have access to full-texts or not)
accuracy and precision of results
advanced search features
usability

Are there good reasons for (or against) using Google Scholar as the only literature search tool for PhD research?
Does the answer of (2) depend on the research discipline?

There has already been much scholarship on the comparison of different academic search databases. I leave it to you to ascertain the usefulness of Google Scholar versus all the other usual suspects. Here, here, here, here and here are some of the prime literature on this topic.

The real answer of course, to all your sub points is, it depends.


Website for professorship positions in Germany? Is there any website for professorship positions in Germany? I find few websites, but they don't cover most of the universities. There are more up-to-date advertisements on the website of universities, but it is very time consuming to check them one by one.

I have covered this very recently in the answer to a related question.

Firstly, there is is Academics.com. It is a free service that should have you covered to a large extend. As a bonus, it is not strictly for offers in Germany, but also has some professorships in neighbouring countries (although coverage for those is rather spotty).

The most complete list is the newsletter sent out monthly by the "deutschen Hochschulverband", which is the union of German university teachers. This list is pretty much complete for Germany, but it does not have any info on professorships anywhere else. You need to be a member to receive this newsletter, and one can only become a member by having been employed in an academic post at a German university before. If you currently work in Germany (e.g, as a PhD student or postdoc), you are either already a member or can easily become one.


Is copyright transferred to IEEE upon submission? In the IEEE policy on Electronic Information Dissemination (Section 8.1.9 of the PSPB Operations Manual), it says:

A.2.a. An author-submitted article is the version originally submitted by the author to an IEEE publication. An author includes a completed IEEE Copyright Form during submission of the article to an IEEE publication and thereby transfers the copyright of the article to IEEE.

and then later,

D. E-PRINTS
Before submitting an article to an IEEE publication, authors frequently post preprints of their articles to their own Web site, their employer’s site, or to another server that invites constructive comment from colleagues and provides a publication time stamp. Upon submission of an article to IEEE, an author is required to transfer copyright in the article to IEEE, and the author must update any previously posted version of the article with a prominently displayed IEEE copyright notice (as shown in 8.1.9.B). [...]

This seems to have changed with respect to previous policy. In the past, copyright was only transferred upon acceptance, not upon submission. Transferring copyright upon submission seems to have implications that are negative for the author and for the scientific community: it means that IEEE owns the article even if it is rejected, and that the author cannot submit it to another journal if it is rejected.
However, in my last submission to IEEE, the submission process did not include any IEEE Copyright Form. I was not required to explicitly transfer copyright, nor did I receive any document that states that this has been done.
My questions are then:

if the submission process did not include any copyright transfer, does the copyright anyway belong to IEEE now?

if the copyright belongs to IEEE, am I right that this disallows me from submitting to another non-IEEE journal if the article is rejected in this journal?

Copyright is only transferred during submission if:

  An author includes a completed IEEE Copyright Form during submission

Without the copyright form, there is no transfer of copyright. Even if the form is complete, transfer only occurs under terms defined by the form. For instance, the form might define transfer upon acceptance.


Should I decline unrelated work assigned by PhD advisor? During the past years of my PhD program in biology, my advisor has developed a habit of lending my service to other labs/groups for potential collaborating opportunities. In addition to helping fellow students in the lab with their projects, I've helped a handful of other labs/groups with various data analysis and statistical testing tasks that were totally unrelated to my PhD project; I rarely got anything in return other than practicing my relevant skills.

There is a lab in our department that I helped with data analysis in June. I've submitted my PhD thesis in August. This lab now came back to my advisor asking for a further work involving testing the correlation between the expressions of 200ish genes and different phenotype in 20ish RNA-seq datasets. My advisor has handed the job to me again.

It is not a small task to me, and since the submission of my PhD thesis my scholarship has stopped so I have to work to pay the bills. Also, I feel unappreciated because the other lab doesn't even know I am the person doing the job, and they will probably list my advisor as a co-author should there be a paper.

I'd like to know if I should turn down the request, even if it will potentially result in my advisor rejecting a recommendation letter? My advisor once jokingly mentioned that they are holding their recommendation letters hostage so I have to continue working for them (for free). I've done tons of unrelated and unpaid works for them and this project feels like the last straw.

Very politely notify them your scholarship and RA position (or whatever it is called that requires you to do work in return for money) has ended, and offer a consulting rate to continue. Make sure there's an agreed-upon number of hours for each task, so they aren't thinking they can give you one hour of work at a time, when the emails alone take longer than that. Research in most fields doesn't happen unless there is a fountain of money behind it, so this is not as beyond the pale as it may seem from your perspective. Just be careful to make clear it is simply the economic situation of the real world (which apparently they forgot they live in) that is the issue, not that you are making these demands to be unhelpful and make them go away.

If they can't pay you, then you can offer to help someone else take over the work, for example by giving them a list of steps and answering their questions via email.

Or you can offer to help in exchange for co-authorship, but then make sure you get into the loop so it is clear to all that they are violating journal terms by not including you as a co-author. If they are dependent on your analysis for their paper at this point, they may put in a position where you are compelled by professionalism to help them finish, but of course this needs to be out in the open with a promise of at least co-authorship in return.

Everyone with valuable skills has to deal with this kind of thing. People will push until you push back. The overwhelming majority aren't necessarily as cutthroat as the occasional bad joke might imply; they just convinced themselves your time is near-worthless while theirs is precious. Clarify to them this is not the case anymore.


Writing sample requirement for PhD application - submit something you assisted in writing? I'm applying to PhD programs and some require writing samples with a reminder of prioritizing works that are related to the phd program or to my research proposal. The only related writing I have is the paper I'm working on now as a research assistant.
The research topic is my professor's of course, and I'm sure I will not be listed as a co-author. I did write the paper from scratch, but the professor has constantly reviewed its structure and content, and provided comments on things that need to be changed. I did the literature review (research, reading, synthesis, writing), the data collection, statistical analysis, and discussion of results.
I would say that for the current version of the paper, content is 80% mine. Of course, the seed idea was the professor's, but the concept of the paper has changed based on my input after I did the literature review. Would it be okay to submit a portion of this as a writing sample for my phd applications? Or is this not allowed since I'm just a research assistant and not a co-author? Also, the paper is meant to be submitted to a journal for publication so will it be illegal for me to submit a portion of it as a writing sample? I will definitely not send the results sections.
Thanks!

Would it be okay to submit a portion of this as a writing sample for my phd applications?

Yes. (Personally, I'd submit the whole paper.)

Or is this not allowed since I'm just a research assistant and not a
co-author?

You should make the circumstances clear, e.g., the seed idea was the professor's, the literature review is yours, your literature review influenced the concept of the paper, you wrote 80% of the material, and anything else that's relevant.

Also, the paper is meant to be submitted to a journal for publication so will it be illegal for me to submit a portion of it as a writing sample?

Sharing preprints is fine.

I will definitely not send the results sections.

You can send the results section. If there's concern over IP theft, just make the entire paper available as a technical report.


How to respond to an e-mail asking me to suggest a doctoral research topic? With networks like ResearchGate and Academia.edu, it's easy to connect with and follow researchers from a variety of different nations and backgrounds.  I personally think this is great, and I hope such networks can help reduce redundancy in research.

Every now and then, though, I get a request from someone whose English is poor enough that it obscures meaning, and they are usually from a non-Western country with limited access to research materials.  Recently, I received an e-mail from a PhD student wanting me to suggest a thesis topic.

I'm all for helping people, especially if they are bright and eager and trying to work their way out of a crappy situation.  But I honestly have no idea how to respond to such an e-mail.  I intend to ask for more information about who the student's advisor is, what people in their group work on, etc.  But are there are other things I should keep in mind?  Is there anything I should be wary of?

P.S. I'm trying to choose my words carefully-- I don't want to play "Western savior," but I also acknowledge I have a real advantage as a Westerner and don't want to lightly dismiss a request for help when it could have a real impact on the student.

I would suggest, unfortunately, that you refrain from giving students research topics. That is, unless you are able to continue to guide them through their degrees remotely. I doubt that you are able to do that, hence my recommendation.

It would be different, of course, if the request were coming from the advisor of such a student. In that case, you can examine what it might be that the advisor is most capable of doing for the student.

As a positive response to the student, and a general one that requires minimal tailoring in each case, is to ask the student to connect with a local advisor and, if the advisor is unable to come up with something, to have that advisor contact you.

But I think that local advice will be needed for nearly every student. In the very rare exceptions, the initial letter will probably make that clear.


Repository or university working paper series I am from the field of economics and preprints are ok with econ journals. I just cannot understand what is the difference between repository (like ArXiv) and publishing results in some working paper series?

I read somewhere that repository assigns DOI and working paper does not. Also, it is possible to update the repository's version, and I am not sure about working papers. From another point of view, working papers might be registered to more databases and make one's research more visible to the public....

So what are the main pros/cons in publishing preliminary results in a repository and in working papers (or discussion papers series??)? What are the differences?

People actively follow arXiv. They subscribe to the RSS feeds, mailing lists, Twitter bots, etc. that inform them about recent relevant preprints that appear on arXiv. Google Scholar finds new papers on arXiv quickly, and this way the authors will get quick notifications when something that cites their work appears on arXiv. ArXiv papers are also indexed in other widely-used databases (e.g. DBLP in computer science).

I don't see any reason to use a local working paper series. In terms of visibility, it doesn't sound much better than e.g. simply hiding the paper somewhere on your personal home page and hoping that Google will eventually index it and someone will accidentally find it that way.


Is there a need to mention page numbers from a book in APA 6? I am citing some books in me work. Normally there referenced from google scholar are without page numbers, see below. My question is with the APA-6  method should I add the page number to this kind of quote?

Makhlouf, A. S. H., & Aliofkhazraei, M. (2015). Handbook of Materials Failure Analysis with Case Studies from the Oil and Gas Industry: Butterworth-Heinemann.

APA 6 seems clear on this: you should include the page numbers if it is relevant to a paragraph or chapter or you are directly quoting text, see the image (source https://libguides.library.usyd.edu.au/c.php?g=508212&p=3476096):


Are there good reasons to avoid using color in research papers? I do scientific research, and I noticed for a lot of plots, the different curves are represented with different styles, but they are all black.  For instance, one curve may be a solid line, one may be a dashed line, one may be a dotted line with triangular markers, etc.

However, this makes it hard for me to differentiate between the curves.  Color is much more effective for helping people distinguish between data (and I’m taking a data visualization class that has research to prove it).

So... can I do this in my research article?  I imagine most people are keeping their plots black and white because of printing restrictions on color, but at the same time they include colors in all kinds of other figures in their document.  Also, how many people actually read printed articles anymore?  For scientific work, I look all of it up online.

Are there good reasons for me to stick with this backwards black-and-white scheme?

Hail to Colorbrewer
I use Cynthia Brewer's website Colorbrewer to pick color schemes. It's also embedded in ggplot2 which is a common choice of graphing package in R. It allows users to specify colorblind-safe and photocopy-able color schemes. It's meant to be for map making, but the idea works for visualization all across the broad.

Other color specialists
For graphs that are used in more eye-catching media such as reports, posters or infographics, you may consider taking some advice from fashion and interior designers (See the graph below proposed by Japanese Shigenobu Kobayashi). Each combination can conjure a certain type of feeling, color schemes that seem absurd may work in other settings.

Works on data visualizations
You mention there is research backing up the use of color, which I do believe there must be. Though for that, I'd just like to share another point of view. Bill Cleveland, whom I consider the guru of visualization in science, advises that color should actually be avoided. In his book, he lays out this hierarchy:

I may not go thus far to suggest color is worse than area and volume, but I do agree that positioning along non-aligned scales is much better than color. In other words, if I have two curves to show, I'd opt for paneling them onto to their own coordinate then put the graphs side by side, or plotting them together using line with different styles or grey scales over using colored lines.
The baseline for me is, the added colors should have their dimension (aka variable) to represent. If there is anything that does the same job, remove the colors because now the colors are "non-informative ink," as described by Tufte.
Human eyes are prone to visual tricks
I do agree that colors catch attention, but just because it gets attention does not mean people can distinguish them well and can isolate the information well. Particularly, colors interact; just by pairing with some different colors, the same color can look different. For instance, here is an example borrowed elsewhere. The brown and the orange tiles pointed by an white arrow are actually of the same color.

Why care about black and white?
And you asked "how many people actually read print articles anymore?" I would think that there are a lot. Schools in developing countries may not have color printer, and not every student has access to computer and the Internet. Their only way to learn about a journal article may just be through photocopies. Even in the US, with the rapid adoption of tablets, I still see a lot of journal clubs and meetings relying on B&W photocopies.
Now when I go to deliver any workshops in other countries, I always photocopy a few sample pages of my handout to make sure they are still legible. And Brewer's work has been a lifesaver for me.
Closing remark
In a nutshell, I embrace data visualization and the increasing acceptance of colors thrills me. Though in the process I believe we should remind ourselves to be humble and do not create works that very disproportionally benefit people who are riding high at the technology tide. John Tukey laid the groundwork of some graphical exploratory data analysis, Charles Minard made a visual with rich amount of variables like 150 years ago and yet still considered to be pretty bad-ass by today's standard. How many colors did they use? Just one.
At the end of the day, I would probably argue that design trumps all. It's not about color or non-color, it's about if they are used efficiently to maximize information transfer and minimize noises. At this moment, for me, lines, dots, shades along grey scale, and empty spaces are my staples; colors are my spices.


Is it ethical to force graduate applicants to decide before they hear back from all schools? I have applied to and been offered admissions to a masters program in a U.S. university, but I'm still waiting to hear back from some other places. The deadline to accept is before the 4/15 national deadline for funded graduate programs (as the program I've been accepted to is not funded).

I've expressed my situation and my concerns, and my intent to enroll in the program unless I am offered admission to a funded program. However, the admissions staff claims that what I'm suggesting (withdrawing my acceptance at a later date) is unethical, and that I must commit to or decline the offer from their program by their deadline. There were also unwilling to give an extension.

While I understand that it's not good to cancel on anyone in any case, I feel that I am not acting unethically this way, and that actually they're acting unethically on their part! If I understand correctly, they likely do have a waitlist of some kind and still can offer my place to another students even if I withdraw. However, if I decline their offer, there is no way for me to change my mind!

So, is it ethical to make students make a decision before they've even heard back from all places they have applied to? If the admissions staff are not willing to change their mind, what can I do besides withdrawing from their acceptance at a later date anyway?

The April 15 Resolution technically applies only to offers of financial support, not to offers of admission. There’s no clear-cut rule saying a school can’t require an early answer for admissions, saying it’s unethical to do so is a difficult claim to make. To my mind, it’s definitely poor form and suggests that the program is either (a) quite prestigious and doesn’t need to worry too much about yield or (b) rather noncompetitive and desperate for enrollees, but they’re risking rejections as well with the hardline approach they’re taking. (Funny how extreme cases in different directions can take the same approach!)

However, given that the program in question is unfunded, it's completely unreasonable for them to expect you to commit irrevocably to an offer of admission, particularly since they are effectively not committing any additional resources to offer you admission. I would thus feel no moral qualms whatsoever in withdrawing my acceptance if another, funded program were to make an offer before the April 15 deadline.


Invited to a meeting where I will receive a postdoc offer, what should I discuss/prepare the meeting? I had a postdoc (field is computer science) interview 2 weeks ago. The HR team told me that the panel is willing to offer me the position and want to discuss the details in a 30mins Zoom meeting. This is a first one for me, I really don't know what can I expect during this meeting and what can I bring into the discussion. I am also a coming from outside the UK (need a visa).

Salary negotiation
Benefits
other elements?

Since I need a visa sponsorship

Visa procedure
Will the university cover immigration fees?

Basically, what are the key elements that form the typical start-up package for a postdoc job offer?
PS: I am having the meeting with one HR member and not the PIs.

Read the agreement between your university and the union (presumably UCU) if applicable.  It's boring.  This defines what you can request.
Read benefits information on the HR website.
Read visa rules on the government website.
Figure out your preferred start date.
Estimate your relocation costs.
Find out what local taxes are.
Find out local housing costs from a regional housing website.  (In the UK they are often unreasonably high.)
Make a list of questions to ask.  Questions should demonstrate that you are genuinely interested in the position. They are not negotiation.
Reread the job ad.  Some places will try to offer you a job you didn't apply for.

For a postdoc, it is not called a startup package.  If you ask for "startup", people will think you don't understand what a postdoc is.
Unless you are an experienced negotiator, do not try to negotiate during a meeting.  Negotiate by email.  Get everything in writing.


Graduate Program Director Congratulating Me on Failing Comprehensive This was a few years ago now. My PhD program had two exams. The first I passed with high marks the second I failed.

I did not really know who to talk with about this. It is common in my program for people taking their exams to fail on the first attempt. However, the nature of the way this news was conveyed by the graduate program director and other passive aggressive tenancies by another closely related senior member, really shook my confidence.

Unfortunately, I did not recover and ended up switching departments and programs, which has cost me time and money. I won't blame my failures on this professor, though I believe he seems to have abused his power in order to act out a personal vendetta.

Here is the email:

  Dear XXXXX,

  I just received the results of the XXXX comprehensive exam
  in XXXX.  I will follow up with a more formal
  letter shortly, but I wanted you to  know the basic results as soon as
  possible.

  I'm pleased to relay that you received a Fail.

  This is disappointing news.  With my formal memo, I will be sending
  feedback on individual questions to assist you with further study.

  Best regards,

So here is my question:

Is there anything to be done about this? Or is it better to keep my head down and not complain?

No one writes these letters "by hand," but rather cuts-and-pastes names to avoid writing the same thing dozens of times. It seems extremely likely to me that this person copied a standard "I'm pleased to relay ...", used to tell students they passed, into the letter telling you you failed, and then didn't notice this. There isn't anything else in the letter that seems at all disagreeable. Seeking legal recourse, etc., without even finding out whether this is a typo seems like a severe over-reaction.


Paid temporary job as research assistant I'm a master's degree student. A professor of mine offered me work on some parts of his paper that I have good knowledge about, because of my background. He said he'll pay me in return, and acknowledge me in his paper. I accepted and suggested a 10 EU/h work and he accepted. I suggested that rate mainly because this is my first experience of this kind (and hence, I don't know the average payment rate) and I thought it would at least take 40 hours and the final money will be enough for me to minimally live where I live. Now it turns out that (I guess, unfortunately?) I was faster than I thought and the work was done in around 12 hours. At the same time, of course, I'm not going to lie about my work hours just for the money. What do you think I should do? I had counted on that money, and it seems that my speed is turning against me!

PS 1: He's friendly with me; I'm just thinking bringing this up might make him feel I'm overstepping my friendship with him, and that's the last thing I need him to think.

PS 2: The paper that he's working on is part of a big university project that he's here for. Accordingly, the payment will be done from the budget of the project, not his pocket (or maybe they're the same?)

PS 3: The contract will be prepared by the university in a few days. If I ask him to raise the money and he accepts, he'll probably be able to convince the university for that.

He will almost certainly agree to use your talents for the remaining time, and pay you the full sum. Take some additional time to check your work; speed and quality will matter. Then talk to him about your predicament, and request to be kept on for the agreed upon hours doing whatever it is you agree upon. He should be impressed that you do good work quickly. Do more, you may acquire an ongoing arrangement.

Note that this outcome is not guaranteed: humans can be strange creatures sometimes. That said, it is virtually guaranteed. If you have a good relationship, I suspect you can proceed without fear.


"Excellent foreign scholar" from Chinese National Science Foundation I am reading a colleague's CV which lists an "Excellent Foreign Scholar" scholarship from the National Science Foundation of China.  I am not familiar with this program, nor is google particularly helpful for me as a complete non-speaker of Chinese.  Is anyone familiar with this program, and what it would entail?

Preamble: I am one of a few Chinese active participants on this site. There have been some questions about Chinese academics here. I always tried to not to answer them. For example, there was a question about the role of correspondence author in Chinese academia(the OP even offered a bounty for it). I did not answer them for two reasons: I am not an insider and I do not wish to give out information I am not absolutely certain about. However, I feel that I need to give some answer for this question because I just see some un-useful answer. Hopefully some Chinese scholars will answer them after they see this one.

According to this document, "The Joint Research Fund for Overseas Chinese Scholars and Scholars in Hong Kong and Macao is established by Natural Science Foundation of China (NSFC) to encourage excellent overseas Chinese scholars (including those with foreign nationalities) under the age of 50 to conduct high-level joint research with researchers and organizations in mainland China."

I suspect your colleague received this fund. Please note that the qualification is oversea Chinese scholar. "Foreign" here means he could be born in oversea but at least one of his parents is a Chinese.


Supervisor wants my paper in another conference, but I have paid for travel for the current one My supervisor wants the paper at another huge conference where all the funding are given and it's more valid than the current accepted one. But I have paid all my air fares and hotel fares for the current travel. Refunding is not possible it seems. Can I go to a conference and just present without publishing?

I can't waste my money by just avoiding the conference. I have to take something out of it.

There is only one solution:

The paper has been accepted on first conference.
You paid for going there
You go there and present the paper.
Withdraw from second conference ASAP (like Monday morning after notifying your adrvisor).
Search for new advisor, because him a) advising double (or multiple) submission of the same paper and b) pay travel costs from your own pocket for first conference, shows he knows nothing about how academia works.


Self studied courses during my PhD. How to fill the relevant courses section in the CV? My PhD thesis is on numerical modeling using finite element methods and non-linear continuum mechanics. My university did not offer these courses during the first two years of my PhD. So, I had to self study them from different books to the best of my ability. As I got completely engrossed in my research after my second year, I decided to not take the courses which were then being reintroduced.

I am finishing up with my PhD thesis and have started writing a CV for postdoc applications. In many sample postdoc CV's, I have seen people mention about the relevant courseworks carried out. I think that my lack of relevant coursework will be a huge negative in my applications. Is there a way, I can address the self-studied courses in my CV?

Additionally, since in the future, I will be applying for tenure track positions, do courses taken during graduate school carry weightage in shortlisting a candidate for a position if they are expected to teach exactly those courses too? Like, I might be required to teach finite element methods and non-linear continuum mechanics at the university, won't it be an issue as I have not done the courses in a structured manner myself?

I think that my lack of relevant coursework will be a huge negative in my applications.

I seriously doubt this. While I cannot speak to all cultures and fields, I find it hard to imagine that anyone will doubt your ability to understand and teach underwater basket weaving if you have published original research in underwater basket weaving.

So, I would not give this undue weight in your mind, and certainly not in your application. In particular, I really recommend against raising this issue in your application, and certainly not in a prominent place such as your introductory paragraph. Your application should focus almost entirely on your research. A rule of thumb is that successful post-docs act like faculty members while unsuccessful post-docs act like students -- and giving undue weight to coursework risks placing yourself in the latter group.


Adding the full text of the articles that I manually added to Google Scholar How can I add the abstracts and/or the full text of the articles that I manually added to my Google Scholar account?

The question is somewhat unclear, it seems like you want either abstracts/PDFs to appear in Google Scholar results or guidelines on how to add a missing citation. I'll address both below.

Help Google Scholar find full texts and PDFs

You should upload your paper to your website (e.g., e.g., www.example.edu/~professor/jpdr2009.pdf) and link to it from your publications page (e.g., www.example.edu/~professor/publications.html). Make sure you follow Google guidelines:

  the full text of your paper is in a PDF file that ends with ".pdf",
  the title of the paper appears in a large font on top of the first page,
  the authors of the paper are listed right below the title on a separate line, and
  there's a bibliography section titled, e.g., "References" or "Bibliography" at the end.

Source: https://scholar.google.com/intl/en/scholar/inclusion.html

Manually add a missing citation

From your Google Scholar profile page, select "add"

Then select "add article manually" and enter your publication details.

Source: http://www.technocrazed.com/manually-add-your-publicationarticle-to-google-scholar-step-by-step-guide


Should I abandon any further higher education knowing that I was dishonest as an undergraduate? This feels uncomfortable to ask, because I know my actions have undermined what I've worked toward.

A little background: I graduated with a bachelors degree, and then went on to get a masters degree in a different field from a different school. I did well in both programs, including a few years of research during my undergrad. That was a few years ago, and since then I have been working professionally outside of academia. My goal has been to eventually go back and earn a PhD.

That is still my goal, and although I didn't behave unethically during my masters, I am troubled by academically dishonest actions I took as an undergrad and I'm not sure how to reconcile them. There are two specific incidents that particularly bother me.

In the first incident, I gave a class presentation that kind of followed a secondary source while only citing the primary sources. I now understand that is also plagiarism. In the second incident, I was panicked because I was struggling in a class. Another student had evidently found the solutions manual to the homework. He approached me, and I ended up giving him a small sum of cash in exchange. This is especially bad.

I have a few questions. Although it could certainly never happen, If I faced sanctions from the undergraduate university, would they revoke my degree? Would sanctions prompt the other universities to revoke my other degrees, including my masters and a PhD if I had earned it? How should I move forward? Would it be wrong for me to enter a PhD program?

Sounds like you have had some insights to your past behavior, and understand what you did was wrong - that could serve you will in future situations where you might be tempted to game the system. That experience could be a positive rather than a negative.

You escaped any consequences, and I don't think it's productive to think about hypothetical situations where you didn't, especially for something that is at least a few years in the past.

There are lots of good reasons to not enter a PhD program. I don't think you've found one here, but you should think about what goals you would have as a PhD student since a PhD is unlikely to advance your career unless you want to enter academia. You'll need a lot of internal motivation to get it done. Focus on those things rather than dwelling on your past indiscretions.


How to find suitable PhD programs in Computational Social Science? I recently graduated from a master's program in Information Science in the U.S. and want to get into a Ph.D. program in the near future. I am pretty interested in computational social science, specifically, I love doing research about social media and understand online communities and social behaviors.
I'm wondering how to find some suitable Computational Social Science programs I can possible get into. I looked up some network science and social dynamics labs. They are pretty cool. But my concern is a lot of hubs of CSS are in CS/EE departments and the competitions are way much bigger than i-schools (where I finished my degree), and I do not very interested in getting too technical or engineering. A good blend of social focus and DS would be ideal for me.
Any suggestions on how I can make the best of the school searching in this specific filed and how to find some inner information are appreciated. Thanks in advance.

There are several/many programs in Communication (which may sometimes refer to itself as Mass Communication and some related terms) that would be good places to study social media, online behavior, etc. using computational methods. Just going off the top of my head, I'd look at the PhD programs at University of North Carolina, University of California at Santa Barbara, Ohio State, University of Wisconsin at Madison, Northeastern University. I also know that Northeastern has an interdisciplinary network science program.
Basically every Communication program that I know of is actively trying to enhance their capacities in this area and would probably be attracted to prospective students with such interests as well. You should also know that competition for faculty jobs in this field is also much less fierce than in most other fields that I know about (there are typically more open positions than new PhDs in a given year). Of course, COVID-19 will cause a hopefully temporary downturn in available jobs in all fields.


How to cite a book that has appeared in multiple versions/editions over the years? I would like to cite a book that has first appeared in 1976 and has since seen three editions.

Book on Google Scholar

I need to cite the book in a paper I am writing that will (hopefully) be published by Springer. What version do I cite or do I cite the first but indicate I used the third edition?

It seems there are multiple choices but I can't find a concrete answer in Springer's guidelines nor can I answer this to my satisfaction with my prior experience.

You cite precisely the version that you use and add something like "5th edition" (that is what the "edition"-entry is there for in BibTeX). Be careful to use the correct year!


What is a suitable job title for someone responsible for data and software in a research project? My PI has just asked me what she should call me when introducing me to visiting researchers. I couldn't give her a definite answer.

I work in a research project where I supervise its research data in terms of versioning, formats, conversion, storage, etc. In this function I've, e.g., written a data management plan. I also (and this is the gros of my work) develop software which is used within the project but is also generic enough to target other researchers. And finally, I work on my PhD thesis, albeit not in a structured PhD programme (in my neck of the woods you can write a thesis as long as you have one or more supervisors with the right to supervise PhD theses.

As of now, I've usually been introduced as the "project's programmer", which my PI finds is somewhat dismissive of my actual work and responsibilities.

What would be a good title then, one that could also be printed on business cards?

This sounds essentially like my position: research programmer

It encompasses a lot, but perhaps 80% of it is helping researchers who know what they want to accomplish but have no idea how to get there.  It can include things like web scraping or cleaning up very ugly code, or translating a project to a different codebase, or writing simulations, or running models.  Version control often comes into play, along with data storage - I'm often teaching researchers about GitHub or S3, for example.  It also tends to involve data vis and data presentation (like on the web).

It also has an element of data science, where a researcher gets access to some data that has what they want but is too big for them to know how to work with or manage.  But I wouldn't call yourself a data scientist; it's a whole separate field with its own methods that often diverge from traditional research.

It sounds like "research programmer" encompasses everything you're doing, but sound a bit more grand and more accurate than what you're using now.  It's also one that is in official use elsewhere (in my case, the policy and think tank world), so that's a bonus.


Admitting candidates from a no-name college? How many times have you really seen Graduate Admissions Office of top universities in the US and the UK admitting students for Masters Program from no-name colleges in South Asia? For example, they might know the university but the college is unknown to them because there hasn't been any student of previous batches who went to that particular university?
If a student is stuck in such a case, what could he/she do to improve their chances?

Every student, whether they come from a well known or an obscure university has to make his or her own case for admission. While it is easier to accept that the education from a well known place is adequate it isn't impossible to evaluate the record from someplace not yet represented in the student population. Some colleges have people who will do this as a matter of course.

Perhaps one or more of your professors can help. Sometimes the web of academic personal reach in a given field is quite broad.

But the case is still yours to make. You should demonstrate in your materials that you not only have taken courses at your university, but that you have learned the essential things needed to advance further. The presumption that MIT, for example, turns out skilled students is, for the most part, justified, but it doesn't imply that NOT-MIT cannot also do so.

But you need to make your case.


What is the difference between Ph. D programs with coursework and those without it? I have been looking into PhD programs in the Engineering field, and I have found different types of programs, such as some with coursework, and others without any coursework.

What is the practical difference between them? (Besides the obvious coursework) What kind of student is expected for each of them?

EDIT: To be more specific, I have been looking into Robotics PhD programs, such as:

CMU Robotics PhD (Coursework + Research).
KCL Robotics PhD (Only research).

It seems to me that there are several advantages; none of these are suitable for every student. It's up to you whether enough of them apply to you, to make it worth doing a taught PhD:

A PhD with a bit of coursework in the first year will help those who
are crossing over into a discipline that they're not already deeply
embedded in: it will give you some hand-holding through the things
you'll need to know but don't yet;
it should (if taught well) also teach you some extra research skills;
it will give you some indication as you progress as to how well you're doing, compared to how well you should be doing if you're going to finish
it will allow you to explore different aspects of the field, to help you finalise your thesis topic
it may, depending on the country and institution, give you an intermediate degree at the end of the taught section, such as an MRes, which will count for something even if you then don't go on to do the full PhD
it lessens the culture-shock for those going straight from fully-taught study to a research degree.


Is it useful for a student trying to get an undergraduate research position to have a personal website? I'm studying a Bachelor in Engineering Physics undergraduate program and I know that most of the people that does research or that teaches have his/her personal website with their publications and their curriculum. I even know a friend of mine that has his own personal website. This made me think about creating one for myself. However, I don't really know if it really matters to have one now. I don't know if it is important to give my undergrad curriculum via personal website.

The things I'm including in the website will be:

CV

Portfolio

Contact Information

Research Interests

About me (section where I can talk about me in an extracurricular way)

So, will it matter if I do my website and include it in my signature whenever I send a mail to a professor looking to have a research stay or a research project with him?

As just going through a round of interviews for hiring students to a research lab, I would say it is beneficial for you to have a website, on the condition that it is informative of your work.  Out of your list, the only one that I would view as beneficial is a portfolio.  Without the portfolio section, I would say it is not beneficial.

When people apply to my lab, they send their CV.  This usually includes some bullet points of work, school, extra curricular, etc.  The hardest part to extract from a CV is the type of work or actual capabilities of a student.  When receiving multiple applications, the ones that had a website were taken positively.   I was able to see not just the bullet points, but what type of work the student has previously done (Just be careful to be honest and full disclosure, if it was a group project, specify your role).

On the other hand, if your website gives no extra information than the CV, I would be a bit annoyed if I was directed to the website only to learn nothing more about the applicant.


How do you verify facts claimed by a deceased author? The question is not a arising in my capacity as an academic.  I was recently reading a book, and I came across a claim that seemed dubious; so I wanted to find out whether it was accurate.  I thought of contacting the author, but then I disovered that the author had been dead for a few years.

My question is, what is the appropriate thing to do in such a case, where the author is the only one who has the information necessary to verify a claim, and yet the author is deceased?  Assuming you cared about it enough, would you contact the family of the author, to see if they had notes the author had used in writing the book, or is that impolite?  What else can be done?

Assuming you cared about it enough, would you contact the family of the author, to see if they had notes the author had used in writing the book, or is that impolite?

It's implausible that the author's files are well-organized and clear enough that a non-expert family member could easily answer your question.  And unless the answer is dreadfully important, it seems inappropriate to ask whether you could fly into town and spend hours/days searching through any files the family possesses.  (One can accumulate a large number of boxes of papers over the course of a career.)  That could make sense if you were working on a major project about the author and the family was eager to help, but for an isolated question it feels like far too much of an imposition on the family.

If the family felt the files were likely to be of continuing academic or historical interest, then they may have donated them to a university library or archive (most likely at the university the author worked at, if any).  I'd start by doing web searches to try to find out.  If you can't find out online, you could enquire at the most likely university library.

Before trying to track down the author's files, it's worth convincing yourself that there's no other way to get an answer.  For example, maybe the author is alluding to something well known among a certain community, or maybe the author supplied more details in a different publication.  You could try ask online (e.g., on a suitable stack exchange site) and see what happens.

If the author worked with a collaborator or had a student who specialized in this topic, then they would be natural people to ask.  You could also try asking another expert (e-mailing someone out of the blue will come across best if you give an explanation of how you have tried and failed to find the answer).

If nobody else knows and the author's files weren't formally archived anywhere, then I'm not sure how much more you can do.  The author's information may simply be lost and will have to be reconstructed from scratch.


How do I come up with a dissertation topic early on in my degree? I'm currently 2 units into my MSc degree (6 units over 2 semesters left).I know this is rather early, But I would like to start work on my dissertation as soon as I can, to give myself enough time and preparation to do "distinction level" work.

How do I come up with a topic I'll stick with? I've had tons of advise from different sources telling me to choose from an area of interest. Considering I still have the bulk of my degree work ahead, this wasn't too useful for me. Do I read all areas ahead of the units to "fast forward" the process?. Any advice is welcome.

This is a classic example where talking to your advisor is of the utmost importance.  Some advisors want their students to choose a topic as early as possible, and others don't mind if their students take their time. As for the topic, hopefully, your advisor should be able to point you in a direction if you don't already have one.

While I understand the rush to get started on something concrete, you really don't want to do a lot of work on a topic that ends up being (1) uninteresting, and (2) unfruitful.  Talk to as many other faculty and students as you'd like, and there isn't anything wrong with reading ahead, with the exception that you might not understand something well enough to make a good decision about whether you should do research in the subject.

My bottom-line suggestion is to take your time picking a topic, because you really do want it to be a good one.


How do grad schools design courses for potential students? For graduate schools in STEM which take students with a Bachelor's degree (BS/BE/BTech etc.) and graduate them with an MS and/or PhD, what do they assume about the student's prerequisite knowledge when designing courses, their difficulty and overall dynamics?

My question is pointed towards knowledge and not what is on the student's transcripts. For instance, a student might have "Linear Algebra" on his transcripts but might not remember Singular Value Decomposition very well.

Do they:

assume that student knows all the courses he has taken very well and build from there? (What happens to people who had a BS in allied fields? For instance a student may have a BS in Pure Math but enrol for a MS/PhD in Computational Math with little idea about a "compiler".)
assume he knows nothing and take him to proficiency?
anything in between?

I agree with @aeismail's and @dmckee's answers, but let me add a different spin:

Students are admitted to strong PhD programs not on the basis of how much or what they know, but rather on their potential for successful research.  Every program admits students from all over the world, who may or may not have undergraduate degrees in exactly the same field.  Beyond a few fundamental concepts, it is not reasonable to assume that incoming graduate students have any specific prior knowledge.

That said, most courses for PhD students are generally taught as if the students have a strong undergraduate background in the same field.  The definition of "strong undergraduate background" depends strongly on the graduate program; the expectations at the top PhD programs are generally extremely high.  More importantly, PhD students in top departments are expected to have the intellectual maturity to recognize and correct weaknesses in their background, even if the missing material is not normally covered in a strong undergraduate program.

Also: Courses are arguably the least important part of any PhD program.


What are some examples of negative effects on a career for boycotting Elsevier journals? I fully support the Elsevier boycott, and came from mathematics (BS and MS) into my current PhD program in an engineering subdiscipline. I'm finishing up my PhD now and starting a post-doc soon.

I've already refused to review an article a few years ago for an Elsevier journal, and the editor seemed quite angry about it.

Once again I have been asked to review an article for an Elsevier journal, only this time the journal editorial board has a prominent researcher who I have had personal contact with, is a recently retired Emeritus Professor from my department, and if he became angry about my refusal he could potentially harm my career.

Does anyone have any specific examples of, or even better statistical data showing that boycotts of Elsevier journals had negative career impacts on early career/junior scientists?

People decline to serve as editors or reviewers for all sorts of reasons. "Too busy" and "conflict of interest" are two common ones that are easily applicable to your case.

All junior faculty have too much on their plate and no one knows what your chair or mentor has told you that you need to focus on. So "unavailable/too busy to take this on" is an unprovable and thus good excuse. It's also impossible to know who you've had a fling or a spat with and so "conflict of interest" (and you don't have to give the reason for a CoI or for why you're unavailable) is perhaps less apt in this situation but also a valid excuse.

  Example: These are the three options I was given when I received my last reviewer assignment email. If I clicked on decline due to COI or unavailable, I'd be taken
  to a webform that asked me for alternate reviewer names, but that was
  entirely optional on my part. I would not be asked for a reason or justification for my response.

As to negative effects, I think it's fine to have principles, but when you're junior faculty, you're also vulnerable. You can choose not to buy products made in China (for example) or to decline to provide free work to Elsevier, but you also don't have to tell any and everyone that you've made that decision for yourself. It's fine to decline with a vague reason if that will protect you from the  possibility of retribution.

When you are in a position where you can speak your mind without fear of retribution(which is what tenure is designed to ensure), then do so.

As an aside: Especially in well-established journals, editors and editorial boards tend be composed of people known for their expertise as well as their dedication to the field of study. These people also tend to be very, very busy. Your response to the 'board' will likely be entered by a junior editorial assistant and it's highly unlikely that the editorial board will even get involved -- except perhaps to solicit names of other reviewers. Quite simply, it's too small of an issue and people are far too busy to get worked up over this. While I've heard of editors being angry at junior scholars for not publishing in their venues, I've never heard of anyone being angry because someone didn't serve as an article reviewer. A declination then is risk-free. But going out of your way to declare "I'm not reviewing because of my political position against ____" is making a statement (which is what you want, right?) and thus carries the risk that that statement is offensive to some.


What is the significance of the corresponding author? In your field of research, what is the significance of the corresponding author?

Does the title "corresponding" imply that the person is the expert out of the list of all authors, or that the person is responsible for communicating with the journal / reviewers?

When should the PhD student, if she/he is set as the first author, also be the corresponding author?

As Faheem pointed out there are other questions that deal with what a corresponding author is. You second question is not covered by those questions though.

The corresponding author should be an author that will be easy to find again after a few years. Ph.D students are not great choices since they are almost by definition not going to have the same contact information by the time most people read the article. In mathematics this is a serious concern because the backlog in articles can be multiple years and the student can already have graduated and moved across the world by the time the article is officially published.

As the other questions point out in some fields corresponding author is used to indicate contribution to some degree. But the old fashioned use of "the author you can find an address for" is still a worthwhile thing.


How to explain to college that religious observance precludes me from living on campus, as required? I am planning to attend a college that requires students to live on campus, in a coed setting. As an observant Muslim, I cannot do that.

The college asked me to write a letter explaining why I cannot live on campus. I also have to explain why I can't eat the cafeteria food.

I'm asking how I should start the letter, and what I should say in the letter.

This kind of letter should typically be brief and straightforward. Unless they have told you specifically what should be in the letter, you can write:

To whom it may concern:
Please be advised that, as a Muslim, my religious observance precludes me from living on a coeducational campus. As per the advice of [person or office who told you to write the letter], I am writing this letter to request an exemption from the on-campus living policy.
Thanks for your consideration,
Nimbra

If you want, you can also include contact information for a member of the clergy (i.e., a religious leader) who knows you and can vouch that you do, in fact, have such a requirement. (Sometimes this is required as a matter of policy; for example, those who cannot take the SAT on Saturday due to religious observance must provide a letter from clergy attesting to this.)


What are the publisher's obligations when a research paper's term of copyright ends? When a research paper's term of copyright ends, say, N years after publication, does the publication house have to make it freely (i.e. no cost) available for use by general public?  Assume that currently it's charging some money to download papers.

No, why should it? Running out of copyright explicitly means a loss of a right. It does not mean the beginning of any additional obligation.

Running out of copyright, however, means that anybody who already owns a copy may duplicate it and make it available under any conditions he chooses (including making it available free of charge). Many university libraries do this.


Publishing papers in pure vs applied machine learning research As far as I understand, in pure Artificial Intelligence (AI) research one is required to come up with a new/improved  algorithm and show that the  algorithm has competitive performance across a set of toy or real data. Thus, I find this  a well specified target for pure AI research. Such research would be usually published in journals such as: Journal of Artificial Intelligence Reseach, Journal of Machine Learning Research.
I wonder how the target differs in applied AI research, such as machine learning (ML) applications in some domain, for instance,  Health or Finance. Some example of such journals include: Artificial Intelligence in Agriculture, Journal of Machine Learning in Finance, Artificial Intelligence in Medicine, Expert Systems with Applications.

Do you have to come up with new/modified learning algorithms in order to publish in applied AI/ML journals?
If the answer to the above is no, then what is the nature of the contribution? Would it suffice to apply existing ML methods to new domain data?
Suppose some existing methods are applied to new domain data. Considering  the fact (model = algorithm + data).. would it be acceptable to state "this paper proposes a new model" instead of "a new learning algorithm"?
What is the effective learning path that enables people to  publish to some hypothetical journal "Artificial Intelligence in X" (where X is some other domain e.g. Finance or Medicine)? Are the same people supposed to hold BSc/MSc in both AI and X? Finally, are they supposed to already have published papers in either pure AI journals or X journals, before starting interdisciplinary research?

There are several questions in your post and it is really difficult to give a pin-pointed answer. So, I would go ahead and break your post into multiple segments and answer likewise:

... In pure Artificial Intelligence (AI) research one is required to come up with a new/improved algorithm and show that the algorithm has competitive performance across a set of toy or real data.

This premise is not entirely true. I work in AI (mostly in Machine Learning and Deep Learning) and we don't use the word like "pure" AI. It is just AI. If you really study history or inception of AI, it is more applied in some fashion. It is the fields like mathematics, probability and statistics that have helped in studies to be more focused around "purity" of it as such. In AI, you can come up with unique problems that cannot be solved using the present tools and techniques. That too is a great contribution. You don't always have to develop new algorithms.

Thus, I find this a well-specified target for pure AI research. Such research would be usually published in journals such as the Journal of Artificial Intelligence Research, Journal of Machine Learning Research.

These journals also publish applied research article, tools including software, and surveys. Of course, these journals and along with Machine Learning Journal by Springer are very well-known and oldest of their kinds and don't entertain papers which say "Here is the dataset, here is the method we used, and here are the findings"-type works. The contribution must be significant in so many different ways (be it a problem, a solution or a theory) that could be hugely contributing to the AI community.

I wonder how the target differs in applied AI research, such as machine learning (ML) applications in some domain, for instance, Health or Finance. Some example of such journals include Artificial Intelligence in Agriculture, Journal of Machine Learning in Finance, Artificial Intelligence in Medicine, Expert Systems with Applications.

The said journals are mainly problem or application-specific and they would like to see novel applications in their own fields. I don't have much experience with these journals. But, I certainly have reviewed papers for a few of these.

Do you have to come up with new/modified learning algorithms in order to publish in applied AI/ML journals?

As said earlier, not always.

If the answer to the above is no, then what is the nature of the contribution? Would it suffice to apply existing ML methods to new domain data?

My advice for you would be to read (and re-read) some papers from each of these journals and see what kind of works are valued there.

Suppose some existing methods are applied to new domain data. Considering the fact (model = algorithm + data) would it be acceptable to state "this paper proposes a new model" instead of "a new learning algorithm"?

"Model = Algorithm + Data" --- This is WRONG and whoever said this (even if it's not you) is WRONG!!! So your question does not stand. For your information, "Model = Structure + Parameters" (for starters, refer: Some papers from Bayesian ML)

What is the effective learning path that enables people to publish to some hypothetical journal "Artificial Intelligence in X" (where X is some other domain e.g. Finance or Medicine)? Are the same people supposed to hold BSc/MSc in both AI and X? Finally, are they supposed to already have published papers in either pure AI journals or X journals, before starting interdisciplinary research?

There are so many questions to answer. Please take my words with a bucket of salt: "You need to do some basic and then some moderately advanced courses in ML to make your base adequately strong. Alternatively, get your hands dirty by solving problems in a platform such as Kaggle. In parallel, you could read some easy papers from the journals that you are interested in. Also, find a mentor who could guide you in these directions.


Can a failed research become the object of research? I am working on a paper on social conditions during the pandemic, and have been using mixed methods. Unfortunately, the qualitative data collection process has been a disaster as I was unable to conduct any interviews. The reasons given for declining interviews were mostly due to pandemic disruptions. As such, I am now wondering if it's possible to do a reflective analysis instead, by arguing that the failure to collect qualitative data is in fact an indication of the real-time state of affairs?
I haven't quite been able to find relevant precedence and am unsure if there's an established methodology for this sort of "reflective analysis"? If anyone could point me in the right direction, that would be greatly appreciated!

Meta-science/meta-research is the discipline that deals with studies that use the research methods to study research itself. Its currently quite en vogue, I don't know if you could make your study fit into this category.
Personally my two most successful papers are about what would have been quite mundane studies but anomalies in the analysis lead me to identify problems with the way data was commonly analysed across the whole field.


How to pay for or avoid publishing cost without research funding and without limiting journal choice I am wondering how can someone publish a manuscript without having any money to pay for the publication costs. I am aware that there are some journals that do not require a publishing fee, however by limiting the choice to only these journals it leaves very few options given the specificity of most journals.

Can the cost be shared among co-authors? Is it common for the first author to ask money to the co-authors to pay for the publishing costs? A previous answer to this did not explain if this is a common practice.
Are there certain journals that might waive the publication fee given the financial circumstances? There was a previous question regarding unaffiliated researchers, but what if someone is affiliated but is publishing research from done at the previous institution which does not have money to cover the publication cost.

My field is biology and I am from a developed country, so the option of applying for a publication fee waiver for developing countries is out of the question.

Can the cost be shared among co-authors? Is it common for the first author to ask money to the co-authors to pay for the publishing costs?

It is not common to share the fee of one publication. However it is common to ask for a collaborator to pay the full fee if he has a funded project and then you pay for other publication in the future.

  Are there certain journals that might waive the publication fee given the financial circumstances?

Yes. I am from a country which suffered several cuts in science due to the 2008 crisis and my research center was left without funding for several years. Due to the lack of fundings my supervisor started to ask for fee waiver and he got several waivers from Open Access journals, such as: PlosOne, Plos Computational Biology, Nature Scientific Reports, etc.

In the PLOS journals he is used to get 50% of discount and in the Scientific Reports he got 100%. The Sci.Rep. staff asked for the research center budget in order to deliberate if they would give a discount or not.

Usually you can find the waiver policy in the website of each journal.


Papers written with the sole purpose of finding flaws in someone else's paper This question is based on a paper I came across a couple of years ago written by a famous professor who had developed a method to solve a certain problem. His method was not the first or the only method but it has some advantages and it is widely used in industry.

The paper I came across was written with sole purpose of finding flaws in a method for solving the same problem that someone else had published 15 years later.

Regardless of who was right, is this the proper way to deal with a flawed paper? This seems a bit weird to me. Do journals even normally publish such papers? Aside from citing the (presumably) flawed method, he also specifically named the authors in the abstract.

This worries me a bit because I plan to publish another method of solving the same problem soon, and although I have confidence in my work I don't think it's bullet-proof. I feel that if such a paper was written about my research it could have a significant negative impact on my future career if that was what popped up when you googled my name.

Whether papers like this will be published depends on the journal and the editor. It usually is preferable to show how a problem can be solved correctly. However, it might be well justified to solely point out weaknesses in existing work.

Keep in mind that very few things are actually "bullet-proof". The more you know about a method (new or old) the more this will become obvious. Most methods have their limitations. Newton's laws are still "pretty good" although Einstein and others have shown their limitations.

If you have confidence in your new method, you will probably highlight the advantages it has over existing methods in your paper. However, you should also be open about the limitations of your own contribution. Be clear about what your method can and cannot do and where and when it is applicable. In being honest about your own work you are making a true contribution to science. However, if you’re starting to have severe second thoughts about your method, it might be better to double check what you're doing. Talk to other people in your field and openly discuss your concerns before publishing.

As long as you don't over-egg your own contribution you will be close to bullet-proof. It won't be bad for your reputation or career if somebody were to find a weakness in your work and improve your method or the knowledge of the field. That's part of how science works. You can only make contributions to the best of your current knowledge and move on when you have new information. The only thing negative for your career would be to ignore new evidence and trying to hide past mistakes.