If a journal publishing an article about a software tool requires the software to be freely available, must the article be open access? I am interesting in publishing a Bioinformatics software as a paid access article in a journal where they have open access as well as paid access options (Oxford's Bioinformatics).

But it stated at the journal's website that

  Software If the manuscript describes new software tools or the implementation of novel algorithms the software must be freely available to non-commercial users at the time of submission, and appropriate test data should be made available. Availability must be clearly stated in the article. Authors must also ensure that the software and test data is available for a full TWO YEARS following publication. The editors of Bioinformatics encourage authors to make their source code available and, if possible, to provide access through an open source license (see www.opensource.org for examples). Authors should make every effort to use URLs that will remain stable. At the minimum, authors must provide one of: webserver, source code or binary. The name of the software should be included in the title of the paper wherever possible.

Does that mean the article publishing that software must be an open access article?  or can it be a paid access article?

The two are entirely independent.

The journal does not require you to make the software open source. It merely requires you to make it free for non-commercial use for at least two full years from the day of submission of the article.
It however recommends that you make the source available, preferably via an open source license. But it states that it is even acceptable to simply provide the compiled binary to the editors. (Presumably to verify that the software does what you report it to do.)

The requirement is only applied to a software if you wish to publish a paper describing a new software tool or a new implementation or algorithm. (Which seems to be your case as you want to write about a new bioinformatics software.)

The OA publishing option is something else entirely. The default publishing format in the journal is subscriber pays. With payment of additional fees you can purchase the option to make your paper open access, but that is not a requirement.

I note that the condition described in point 1 would be evaluated at the time of submission by the editorial board, whereas the possibility of publishing the article open access will not generally be discussed at all until after the paper is accepted.


European student trying to get a clear picture of US PhD system I am born and educated in a northern European country.

After I graduate I want to continue doing research within the topics I am passionate about. Much of the research I am interested in happens in the States. So, I am trying to get a clear picture of the PhD programs in the US.

I have tried to find answers on my question online, but the university webpages something leaves me confused.  I would be very grateful if any of you can answer my questions or provide me with useful references.

Questions:

How does the application process work?
Do I apply directly to the university and the later if accepted look for a professor?
Do I have to take courses before I can start doing research despite having a master and highly relevant skills for the topic in question? And if so usually how long?
How does research funding and salary work?

To answer your questions in order:

For academic graduate programs (that is, not a professional program like an MBA or JD), either at master's or doctoral level, you apply to the department via a central administrative unit which is usually called the university's "Graduate School" or something similar. The department website will probably have details. The contact person within the department/program is called the "director of graduate studies" or "graduate director." It's a good idea, but not necessary, to contact potential advisors first if you have a clear idea of what you want to work on. Most American students do not do serious research-level work prior to grad school and do not have specific research directions in mind when they enter a grad program.
In addition to your academic credentials, you will almost certainly need GRE scores, and also TOEFL scores if you are not a native English speaker. Check with the program's grad director.

See 1.

Usually, but you can often place out of coursework by taking exams. It is unlikely that you will be able to avoid taking exams in the US system, regardless of your credentials. Check with the grad director.

PhD programs, especially in the sciences, generally admit students with a package of free tuition and a living stipend, which usually requires serving as a lab assistant or instructional assistant. Sometimes there is research fellowship money available through the school or through the advisor's grant which does not have these obligations. There are also some fellowships funded by government agencies, but these are generally reserved for US citizens. Master's programs may or may not offer funding. Check with the grad director and/or the university's Graduate School.


Should I report a labmate who is into drugs? I am a second-year PhD student in the US. I work in my lab during the night-time. I find that one of the senior PhD students in my lab is into drugs big league. I would not mind that if it were not to affect me, but it does in two ways - sometimes the smell in the lab during the late hours is horrible, and he moans incongruously and loudly at times without taking others' presence into consideration.

Talking to the supervisor may not be of use, because he takes it coolly and I have heard the two joke about drug use in casual conversations. The fellow PhDs also take fun in his eerie ways, and him being an excellent and helpful chap, they do not want to fuss about his habits.

If at all, should I raise this issue with my advisor, the department or the police? Sometimes I feel I should be silent about it all, bite my teeth and bear it for a year as he will graduate then. But at other times, I am so heckled about being disturbed during my hours of concentration. Is there a discreet way for me to handle this tricky situation?

Are you just talking about marijuana? This is (mostly) legal in Washington and Colorado currently, decriminalized in New York (in practice it's similar to  a parking ticket), and on ballot measures in many other states (so give it two weeks). In short, the American public (or more than half of it) has shown signs of moving past marijuana as a moral issue.

Here you write:

  I find that one of the senior PhD students in my lab is into drugs big league.

Which makes me think he's running a meth lab out of your school. But here:

  sometimes the smell in the lab during the late hours is horrible, and he moans incongruously and loudly at times without taking others' presence into consideration

That sounds more like marijuana. (Not sure what you mean by moaning though).

And here:

  Talking to the supervisor may not be of use, because he takes it coolly and I have heard the two joke about drug use in casual conversations.

It makes me think it's a drug that's just actually accepted for use. Which raises the question: Is it possible you are being very judgmental here and are in the wrong?

Normally I would discuss the smell and "moaning" in their own right. You generally have a right to an odor-free work environment. But I also don't know if these are grievances you only have because you have a vendetta against his marijuana use in the first place, and yes, there is a pretty realistic chance that anyone you raise this grievance to will have the same thought. If you portray recreational drug use to his supervisor or anyone else the way you did in your post, you're going to be laughed at and lose trust.

You probably want to entirely let this go. See if you can lessen the vendetta against the drug. It's possible the student has some awful behavior but I don't even have enough information in your OP to seriously advise on this.


Masters or 2nd Bachelors? Should I attend a likely lesser university, PSU in Pittsburg, Kansas, for a graduate degree in history, or should I attend the University of Minnesota for a second bachelors degree in psychology? All of this is aimed at eventual graduate work in philosophical counseling and the history of philosophy. I want to take the time to read and study ancient philosophy in depth so that I can teach it, but I'm also pretty sure that I have the ability to become a decent philosophical counselor and have spent a good deal of my time thinking and reading about it. The U is a stretch financially at the moment, but I might be able to make it work. Financial aid is sparse for a second bachelors degree. This is why there is even a question. I can definitely afford to live in Pittsburg, KS and I do like it there and I can go to PSU and sort of revive my rusty study habits (3.5 yrs since graduation) in a slightly less rigorous setting, most likely, that I should be able to receive adequate loans for. If I can manage to pay for 13 credits at the U, the rest are free. That is one semester, with tuition around 18k. Living in Minneapolis is very expensive too, all the amenities are higher and rent averages 600 just for a room. I have a lot of history there and friends, but haven't lived there in some time. I also have friends and history in Pittsburg whom I've seen more recently. I have no idea what to do at this point. Looking at both acceptance letters, reading them back to back, over and over, and feeling paralyzed. School starts in January.

This really depends on your personal factors; there's no one-size-fits all answer to your question. Thus, your question is likely to be closed. Still, I'll take a stab at it.

Disclaimer: my background is physics and CS, so I'm completely unqualified to answer your question. Feel free to disregard everything I say.

Nonetheless...

I don't think a master's degree in history from Pittsburg State (not to be confused with the University of Pittsburgh) will get you very far on the academic job market. Of course, good work speaks for itself, and PSU may be better regarded if you want to stay in/near Kansas long term. But jobs teaching history (particularly at the college level) are very competitive and not terribly well paying. $18K per semester seems very high given that reality.

But, I don't like your other option much better. Minnesota is a well-regarded school, but this is even more expensive and gives you a lower degree in another field with high supply and low demand. I do not know what the job market for "philosophical counseling" may be, but I suspect that it's also competitive and not very well paying. You could well end up spending $100K (or, worse, taking out $100K in student loans) to get this bachelor's and then a master's, only to end up with the same job you have now.

My advice is to calculate the full cost between now and graduation for both of these options, and weigh that against the (realistic) job prospects that these will open for you. You may well want to consider other options altogether. It is admirable that you want to go back to school, but I would really hate to see you invest so much time/money and end up without a viable path to a job.


How to present in lecture a paper that students have read (or should I not have them read it)? I would like to present some classic computer science papers in a class I am teaching.  I know teachers usually assign papers before the lecture, but I can't figure out how to present material they've already read and likely understood.  In the case of a highly technical paper, I'd go over the more technical portions, perhaps letting them know beforehand not to struggle with the proofs, programming examples, etc., but I'm thinking of less technical papers, such as:

Reflections on Trusting Trust by Ken Thompson
The Cathedral and the Bazaar by Eric S. Raymond
No Silver Bullet by Fred Brooks

While I don't need to use pure lecture format, I am not sure that discussion would work well, since some of the papers (such as "Reflections on Trusting Trust") aren't really discussable, and my students lack the experience to discuss others (such as "No Silver Bullet").

EDIT: I was hoping not to task the students with extra prep, since they already have a lot of assignments to do, but, as some of you suggest, that may be the best way.

I recommend the discussion format. The two downsides of it you list can be overcome by using a guided discussion. When you assign the paper, also include a list of questions that you expect the students to be able to answer after having read the paper. When the class meets:

Select students at random (or through a random permutation).
Have the student answer an assigned question as a discussion seed.
Open up the floor to other students to make comments and pitch in their ideas (thus starting a discussion).
When the topic dies down, move to the next question on the assigned list and repeat from step 1.

This format has several advantages:

It ensures that the students have read the paper (since they might get randomly selected)
It encourages them to think of their own answers and participate in discussions.
It eliminates the intimidating factor of the professor having tight control of the discussion (since you only moderate who speaks)
It lets you address the key points of the paper (through your initial selection of questions) without having to go over the whole paper in class.

I have experienced this format in upper level undergrad/grad courses during my undergrad and enjoyed it greatly. It really encouraged me to read papers and reflect on them carefully.


Is a letter of recommendation from a suicide line worth anything in academic career in STEM? I'm finishing grad school in STEM. I have a postdoc offer already, but will be applying for more. During grad school I volunteered at a suicide line taking phone calls. If you volunteer a certain number of hours (I have) they will write you a letter of recommendation.
I chose to volunteer just to volunteer. It has been helpful training in other areas though. Learning how to listen, empathize, etc. has been really helpful and surprisingly relevant to other areas of life.
Is there anything I can use that letter for as I go from grad school/postdoc to TT and beyond? If not that's fine, I was just volunteering to volunteer.

If you have a PhD, a letter that does not describe your teaching and research ability is not helpful for applying for academic jobs.
So no.


Emailing professor too early has any impact? I was just wondering when should we start contacting professor of grad school for admission. Does contacting professor too early cause any impact? like, professor gets irritated and never reply back again, blocks forever and things?

Any sensible professor would be happy to reply to a talented student with A+ results; and be more than happy to supervise one.

The only issue with the time is, sometimes the good professors at a university can't take more students to supervise; because they are supervising 5-8 students for their final year projects. So, as soon as you can contact the professor, the better.


Are there any resources to find modern (or effective) assignment types, knowledge control techniques? I'm participating in creating blended (online/offline) courses. Faced a problem of inventing well-designed assignments/assessments. There are already quizzes, essays valuated by teacher, webinars/live lessons. But they are usual, they don't involve students.

So I started searching for teachers' experiences in more unusual ways to control students' knowledge, gather information about each student. But it is very scattered.

Can anyone advice some resources (sites, publications, works, magazines) about this topic? I'm absolutely new in education, so any help will be appreciated.

A bit more information about courses:

oriented on graduate, under-graduate levels and professional development
2 levels of audience: medium (60-100 members in a moment) and big (close to MOOCs: 100-thousands).
technical difficult is not limited

The number of students in each blended course is definitely a consideration when creating effective assignments and assessments of student learning, however, the most important consideration is the student learning outcomes (SLOs) - what are students expected to do, think, or know by the end of your course?  The SLOs will direct the design of the assignments, as well as the assessments of student learning, for your course. Here is a very short training to help you learn to create assignments and assessments from student learning outcomes: http://jeandowns.weebly.com/  There are additional resources and references at the end of the training.


Нow to start an academic career if you got your PhD five years ago and didn't do science for these five years? I think that it's too late for postdoc. Also, I think that my PhD thesis is weak and not many people would be interested. What is the way to start academic or near-academic career, if not teaching? Thesis is on CS and applied mathematics. I live in Ukraine and could move if it's needed. Volunteering or studying for some period is also acceptable.

I don't know what might be available in or near Ukraine, but can offer two possibilities that might be open to you.
The first is a long-term plan that assumes you have sufficient resources (job, money, time) to start some research. To do this efficiently, you might need to be in a place that has one or more local universities where you could make some contacts and start some collaborative activities. But a professor (maybe one you know) might be interested in working with you on some projects of mutual interest. If you can establish yourself as an effective researcher, you might find a way back in to a university. Your old thesis advisor might be able to offer some possibilities for collaboration. But you wouldn't/needn't be either an employee or student to do this. Your status as an "independent researcher" is enough.
The second idea would work in the US and possibly elsewhere, but requires the ability/desire to teach. Here we have a large number of Colleges that are not focused primarily on research but, rather, on undergraduate education. People are expected to do some research, but are expected to excel at teaching. Moving around might raise language issues, of course, for this type of position. If you were teaching at such a college and it were located in a place with other, more research focused, universities, you might be able to establish some collaborations as suggested above. And, the life of a teaching professor can be pretty nice in the right place in any case.
In the internet/covid age, however, things are a bit weird. The internet provides a way to do remote collaboration, but the pandemic makes it harder to make contacts. Attendance at conferences is often a good way to do that.


How to obtain average and total impact factor of publications for an academic? For a while ResearchGate provided something called impact points. It was calculated as the sum of the impact factors of all the publications an academic had. For example, if an author had been an author on four papers with impact factors 0, 2, 4, and 3. They would have 0 + 2 + 4 + 3 = 9 impact points. They've recently stopped reporting this value because supposedly they no longer believe impact factors are valid indicators of an individual article (of course, as a side note, they continue to report their own mysterious ResearchGate points which in addition to publications also weights things largely irrelevant to the research community, but relevant to encouraging behaviour on the site that they desire).

If you also knew the number of publications someone had, you could also quickly determine their average impact factor per publication.

I found the combination of average impact factor and the sum of impact factors to be a really useful metric when getting a quick feel for an academic's publication track record. In addition, I think that impact points seemed to provide a reasonable starting point for discussing some of the trade-offs in publication strategies between quality/significance and quantity.

Given that this site includes many who are mindful of the problems with metrics for evaluating academic output, allow me to justify why I like the combination of average impact factor per paper and the sum of impact factors (i.e., impact points):

Person-specific citation based metrics (e.g., h-index, total citations, and so on), which are often cited as preferable, are heavily influenced by time. Citations accumulate over time. Thus, a young researcher a couple of years out of their PhD may have been publishing high quality work in top journals, but may have very few citations. In contrast, a researcher may have been publishing lots of publication at the mid-tier level for many years, and may have a lot of citations. This connection with time is more than the linear increase in publication output you might see given a research with consistent output each year. Instead, In a simplistic model, it is a multiplicative effect of average number of publications per year, time since first started publishing at that level, and average time between publications and now.
While journal impact factor is field dependent, you can start to adjust for this mentally, if you know your field. For example, I'm in psychology, and it tends to have lower impact factors than psychiatry due to various citation practices. As an aside, it would also be useful to use other journal impact metrics to form the average or sum that are less field dependent (e.g., the SNIP or SJR).

Probably the biggest issue with impact points is that some authors have publications with many more co-authors, or have more or less first-author papers, although this is less of an issue if you focus on average impact factor per paper.

So my question is, given that ResearchGate has stopped reporting impact points, is there an alternative provider where you can quickly obtain the sum or average impact factor of the publications of a given academic?

I'm not aware of any specific tools like ResearchGate which provide an average impact factor for a researcher - maybe others know of something? However, you could fairly painlessly generate the average SJR/SNIP value for a researcher through SciVal in Scopus.

If you add a researcher in SciVal, then click on the benchmarking tab, and then click on View list of Scopus Sources for the selected Researchers and Groups this will bring up a list of journals the researcher has published in. You can then click on Export and download the list of journals, with their SJR/SNIP values into excel, where you can then just use the =AVERAGE formula to calculate the average. I just did this and it took me 3-4 mins max.

Back to your specific question, you could use InCites to follow a similar process as above to calculate a researchers average Journal Impact Factor (Thompson Reuters) however it's not as straightforward as SciVal. As far as I know, you can't generate an XLS list of journals a researcher has published in within InCites (so you would need to get this list somewhere else). You can however export a list of journals from InCites with their impact factors but you would then need to link your researchers list of journals with the incites list to collate the relevant impact factors. you could use excel VLOOKUP to do this and then calculate the average. This is a lot more effort though, so it would depend why you want this average measure of research impact in the first place and whether it might be enough to just use the scopus impact metrics.


How do you cite an image no longer found on the internet I have been working on this report and I saved and downloaded certain images off the internet to put in my paper. When I was going back to cite them later, I reverse google searched the images by uploading the images to have the search engine find them on the internet. Some of these images could no longer be found. How do I cite the images I can no longer find the sources for? Or should I just find different images?

If you can't find the source at all, you should choose a different image. You can't simply put a citation like:

  Image. Found on the internet, source unknown.

Even though it would be nice to be able to do that, that defeats the purpose of having a citation at all, which is so that people can see where you got it.

You might find the following questions useful:

This question that was pointed out in the comments seems to be a case similar to yours, with good advice. Basically you need to somehow track down the source; once you have tracked it down, the specific citation text is not such a big deal, as long as you are listing the source.
This question is also relevant. Unfortunately or not, the culture is extremely pervasive in academia to just go pasting images from the internet without citations (especially Google images, and especially in presentations rather than published papers). This is not completely ethical, but it is common practice.


How to deal with radically different prerequisite preparation? Let's say there is a core sequence of classes for an undergraduate STEM program, starting with what we'll call STEM 101 and STEM 102. The STEM 101 course is predominantly taught by two instructors: Professors A and B.

Now, in STEM 102 the performance of students coming from those two instructors is radically different. In STEM 102, Prof. A's students have an 86% pass rate, and an average GPA of about 3.0; Prof. B's students have a 33% pass rate, and an average GPA of about 1.0. Qualitatively, Prof. B's students appear bewildered by expectations on the first few days of class in STEM 102; they mostly cannot perform the expected basic skills; and they don't seem to get better over the course of the semester, either (still making the same basic-skills mistakes on the last day of STEM 102).

What are the best practices for dealing with this situation?

This is a problem which is very, very common and unfortunately has no good solution.. Let me write just a few hints here. (I will assume that "GPA" is some kind of grade.)

1) First of all, please make sure that Class B is "worse than avarage" and not that Class A is "better than avarage". I want to say that if it is the case that by the syllabus, after course 1, students are expected to have level B, you should teach for level B (even if teacher A was especially motivated/good and did more than expected). This is especially important if you are both teacher A and the teacher of the second course.

2) If your insitution has meetings about teaching quality, mention this problem here. (Try to be diplomatic: do say "A and B teach different topics" instead of "B's students are unprepared." (In fact, it could be that B teaches different things than A and your course is about A's topics.) Try to find a solution together: Maybe one teacher can teach all three courses? Or all can follow one book and cover the same topics? Or at least all teachers teaching those courses can come from the same "group"?

3) Use the first course hours to make a recap of the first course and to determine student's levels. Give them material to study the first course on their own, tell them which topics are especially important. If time permits, make addditional sessions/additional homework for students of level B to bring them to a good niveau.

4) Be as transparent as possible about what you expect. Create a syllabus and, if possible, a course homepage. Make them accessible as early as possible to the students so that they have more time to learn the material.

(I implied here that if (1) does not hold, really teach for niveau A. I think you have an obligation that your student have learned after the course what the syllabus says.)

Ultimately, it is the student's responsibility to learn. (At least where I come from) students know this and will be angry against teacher B rather then against you. From my experience, there are many bad teachers/useless classes in university - students usually learn soon that they have to learn by themselves. Sometimes, they take other courses before and just take course 1 again next year - but this time with teacher A instead of B.


Why is the city of publication important in most bibliography format? Most bibliography formats require the city of publication for books. Why? In this digital era, ISBN would be way more important. But even before the digitalization of everything, why was the city of publication important?

I can imagine some purposes:

to distinguish potential same names of different publishers, and
to help book-seekers find the publisher and the book by actually visiting the city or contacting libraries in the city.

I want to know better stories about the 'city of publication'.

Mentioning the city in the bibliography is important because sometimes the same edition published in different cities would have different pagination, and occasionally even redacted content. Therefore when someone wants to look up the original source, they need to have this additional information available to them.

Another important reason to keep the bibliographic information on place of publication is for reasons of style. Many of us might have bibliographies stretching a century or more, and it would look odd to mention place for some and not for others.

But naturally changes in citation styles are continual, and another element of the citation that is of lessening importance is the page number for journal articles. For one of my publications, I was actually required to remove the page numbers in the in text citation, because the relevant information is easier to find using a search engine rather than by leafing to the correct page in a printed copy.


How to phrase the title in a presentation at an academic interview? When delivering a presentation at an academic interview, what are some keywords which should be included in the title of the presentation? Should the title be in the first person? What are some good examples?

The position I am considering is assistant professor / lecturer

I imagine some choices to be:

The interview presentation for JACK JAY
The presentation for lecturer at Uni Awesome by JACK JAY
JACK JAY'S presentation as candidate lecturer at Uni Awesome

Just throw it out here. Perhaps others can upload their suggested topic slide as well? That would be fun.

I don't like to appear to be overly kissing-up, so I'll opt for toning down the university. My talk would have been broadcasted and posted for a while at the institute so the audience should know why they are here. So I'll just focus on up-playing my topic and who I am.

It'd be prudent to clarify with the hiring committee chair on the format and topics to be covered. But beyond that, just be at ease with the format stuff; focus on the contents. Be very, very certain that you cover just enough background to show you can think in breadth and depth, explain what your research questions are, and present your methods and results in alignment with your questions, and state briefly the implication. For job talk, leave a few minutes to elaborate how your work can grow into your career path, and highlight potential synergistic collaboration with some hot areas that your target institute is good at (e.g. "I'll also love to collaborate with the specialists at your Marine Dietary Assessment Center to cast a more critical look at the diet-obesity association.") You'll need to read their website/reports up on that. Find some friends, colleagues, and mentors to sit in your practice sessions.

Best of luck!


How does Semantic Scholar count influential citations? On Semantic Scholar, each author has a count of "Highly Influential Citations", see for example https://www.semanticscholar.org/author/Onur-Mutlu/1734461.
This information is also present in the API (field influentialCitationCount).
How are those "Highly Influential Citations" identified and counted?

Semantic Scholar's algorithm for counting "Highly Influential Citations" is described in this paper:
Identifying Meaningful Citations (Marco Valenzuela, Vu Ha, Oren Etzion)
https://www.semanticscholar.org/paper/Identifying-Meaningful-Citations-Valenzuela-Ha/1c7be3fc28296a97607d426f9168ad4836407e4b


How do you deal with trolling students? This is inspired by the other question about dealing with stupid questions. The popular answers all seemed to assume that the student really wants to hear an answer. While this is a reasonable assumption, and the answers are very good, they don't cover trolls.

Imagine that you are teaching a computer science lab and a student asks you why our noses run and our feet smell. I agree that you should act professionally no matter what the student does - but what behavior would be considered "professional" in such a situation?

There isn't One Right Way, any more than there is one right way to teach or manage a class room as a whole. I've most taken note of a few styles:

"Old-school" academic style. They state clearly in the rules/syllabus they will treat everyone professionally, with respect, and they expect the same from all students. They will be more than happy to call you out, right then and there, for inappropriate behavior, and they will call a spade a spade without hesitation. They will, if necessary, be so clear and blunt that it will make you cringe, and if the person will not take direction then they will be shown the door - no one is required to be in their class.
Humorist. My dad always use to say, "ask a silly question, get a silly answer." Sometimes its just a fun invitation for a little ad lib comedy. Real smart asses find, if they push it too far, they will quickly end up the focus of the joke in a rather uncomfortable way (some people's version of humor gets very cutting in a hurry). These sorts tend to deal with such people like comics deal with hecklers.
Redirection - judo master. This sort of style will take any question, no matter how assinine, and turn it into a good question that relates to the task at hand. "Why do feet smell? Well, neurobiologists studying sensation often utilize specialized applications of neural networks to improve their understanding, but first we'll need to have a good hold on the fundamentals - which brings me to the next slide on genetic algorithms...any other questions on this slide before we continue?"
Sweet and simple, KISS. This style would just say, "that's not within the scope of this class, or course. Any other questions about this slide/class/topic?"
Tangential. Maybe you just have extra time or enjoy talking about what they asked about. It has nothing to do with the course, or maybe even anything important, but go ahead and answer the question fully, in depth, with citations, if you know it. Go nuts. Have fun with it, and sometimes you can over-load them with so much knowledge and facts about something they didn't actually care about that they will simply reply with a nod and feel sorry they asked. I'm sufficiently good with this that someone once remarked, "never trifle with someone who has a vastly longer attention span than you do." But obviously you'd better not be pressed for time!
Troll right back (thanks to Shion). Tell them you'll be happy to cover his question next class if he'd like, you think it would make some nice variety to add to the mid-term and comprehensive final. Tell the student you aren't sure of the answer, but you love to learn something new every semester - why don't they look up the answer and prepare a 5-10 minute presentation? You'll even give them a bonus point! You can ask them to email you after class if they'd be interested in the bonus point. If they take you up on it, schedule it for an office hour.

The thing is, most of the time you just really must assume good intent, because otherwise you will - especially if you are not in a fantastic mood - bite someone who genuinely wasn't trying to be unpleasant, or just wanted to be a touch playful. Anything you do to that student will ring much more loudly in the ears of the other students than the one you are addressing.

So be careful to promote a positive environment that encourages other students, rather than one that gets locked in on the one wise-acre who might just be playing a clown for the day.


In what order should existing inter-related research be cited in a journal paper? In a given field, the initial breakthroughs were made by A in 1951. This was developed by B in 1960, further developed by C in 1965. I am, in 2018, using equations from C's 1965 paper. In that paper, C cites A and B as having developed the method.

My question is, should I:

(a) Cite only C,

(b) Cite A,B,C in that order (historical order of finding),

or (c) Cite C,B,A in that order (decreasing relevance to present work)?

Would the answer change if these papers were newer or if there was a greater number of them?

Edit:
This pertains to the text of the body, not the reference list. The purpose is to use results from C, not to extend their work. The sentence would be something like:

'C [] tackled this problem by considering..., based on previous work by A[] and B[].

I think you should cite them in the order how they appear in your text and not the year which it was published.


Looking for Mathematics Subject Classification I'm writing a math paper for submission to some journal or other and section 2.1.10 of https://www.ams.org/publications/authors/AMS-StyleGuide-online.pdf says I need a Subject Classification number in the top material of my paper.

The paper is about an original formula I developed for generating Pythagorean triples and then goes on to show how to find such triples "on demand" given criteria such as side length, perimeter, area/perimeter ratio, area, product, and side differences. Indeed, the title is "On Finding Pythagorean Triples".
I have looked here https://zbmath.org/classification/ and my best guess is that the number I'm looking for would begin with 11 (number theory) but that's as far as I can figure out. I don't even know the proper tag(s) for this question. Can anyone help me in my search?

(originally this was a couple of comments, but perhaps it should be an answer)

Section 11: Number Theory is on pp. 4-6 of this current Mathematics Subject Classification (MSC) document. Besides just looking for what seems to be appropriate there (often, however, this requires a much broader knowledge than the specific topic you're looking for), you can look for similar papers and see how they're classified. For example, you can try a google scholar search for "Pythagorean triples", pick a possibly similar paper such as Height and excess of Pythagorean triples, and if you don't have access to it and you don't see any MSC's for it, you can look it up at MR Lookup (freely available), click on the MR number to get MR2126355, at which point you can see "11D09 (20M99)" (11D09 is the primary classification, 20M99 is a secondary classification). Repeat with other papers you find. Thus, in the case of Clifford algebras and Euclid’s parametrization of Pythagorean triples I get 11D09 (11E25 15A66 20H20). It appears (but do some more checks of this nature) that Nate Eldredge (in a comment) was correct -- 11D09 seems an appropriate classification, probably the primary classification.


How to tell a hiring committee that my family lives in the city How can a job applicant tactfully tell a hiring committee that they particularly want to live in the location where the school is located?

I am applying for a faculty job in the city where my wife's family lives. I would love to move there to be close to her family when she and I have kids.

The school might be concerned that I would take another offer over theirs. I want to communicate that I would be particularly likely to accept their offer if they made one.

What is an appropriate way to communicate this? I want to avoid inserting unnecessary personal information, like my marital status or sexual orientation.

I'm thinking of something like this toward the end of the cover letter:
"I am particularly excited about this position for both personal and professional reasons. Most of my family lives in [city] and I would be thrilled to live there."

"I am particularly excited about this position for both personal and professional reasons. Most of my family lives in [city] and I would be thrilled to live there."

That'll do.

And this may indeed matter - from being on recruitment committees in several places that have trouble getting people to move there, signs of interest in the area are helpful.


Should I include test scores and recommender information given elsewhere in my application in my CV for graduate admissions? All of the universities I am applying to require a CV as part of the application process.

As I am requesting the recommender from the on-line application and also giving the test scores there, is it necessary to add these in the CV?

Do you mean references? Occasionally you will see a CV that lists references or it will say "References available on request." I myself have always just left them off.

As far as test scores go, it is typical to leave off them off since you have to send the official scores separately anyway.


How does one find an advisor for an online graduate program? I'm in an online part-time graduate program at a well-established state university in the U.S.. I'm having a hard time getting responses from professors when it comes to asking about potential research topics for a final project that is required for my degree and asking for them to be my advisor. I imagine it's a mix of things causing this:

My e-mail messages might be too long. Although they are direct, I haven't met these people before, and I usually give them a 2-3 paragraph message introducing myself and the goal. No more than this.
I'm in a M.S. online program. I'm not a Ph.D. student who is on-site, and thus cannot contribute more to whatever research they are doing as much as I could.

I've read advice online and haven't found anything about this particular situation.

How do people go about finding an advisor if they're in an online program? What can I do to maximize the chances of having a professor at least respond to an e-mail I send?

If this question is too broad, I can delete it.

I think it depends on the nature of the particular online graduate program. Unfortunately, for the reason RoboKaren suggests in her comment, I think that many faculty don't care for online education. Which faculty members recruited you to come? Which of them answered your questions when you applied? Which are teaching your classes, or other online classes available through the same program? These are the faculty members that have made some investment in this program, and I think they are the ones most likely to be willing to supervise you.

Three more pieces of advice:

I strongly second RoboKaren's office to travel to the campus and meet with as many professors as you can. Let them know that you're an online enrolled student and that you're travelling 6 hours each way and hope to meet with them. Knowing that you're going to such an effort will probably lead some of them to take you more seriously.
Don't ask anyone to be your advisor on the spot, or over an initial e-mail. It is a major commitment, which most people wouldn't make to a stranger (whether online or not). Wait until you know each other well and the professor is somewhat familiar with the quality of your work. In the meantime, start smaller. For example, if one professor recommends a particular paper for you to read, read it and ask some thoughtful questions. This has the chance to make a very positive impression.
If this goes poorly, you might consider withdrawing and enrolling in an in-person graduate program, if at all possible.

Good luck to you.


Asking an external professor for a feedback on my BSc. thesis In my senior year. I have put so much effort in writing my thesis and my supervisor didn't even read what I have done or even bothered to do his work, I wrote my thesis in a topic in mathematical analysis. I think it is interesting to read, no new results but, there are many undergraduate publications that are just interesting to read and contains no new mathematics! so I think my thesis is interesting to read.
All undergraduate journals I found requires a letter from the supervisor, I can't get a letter from him because:
1. He didn't read it and he won't
2. My relationship with him is not good

I thought maybe I should ask an external professor to give me a feedback but, who would do that!
I am even embarrassed to ask for such a favour. I just want to learn even if my thesis is not as good as I think it is, it is okay but at least I would then know why and learn something!

If I had it published. It would then help me when I try to apply for scholarships and stuff.

Can someone suggest me a solution or something?
Do other professors normally agree to review other student's work?

Thank you.

Look for other magazines that don't require such a letter.  (Do they all?)
Find a professor that you can talk to. Or a postdoc.  Or a visiting scholar.  Some won't give you time of day, but some will be OK for a conversation.  Then maybe talk about what you've done that was interesting.  (Make some notecards and then be able to show/talk about the topics on the board.)  Keep it a little lighter than "read my manuscript".  That's a little leaden to be expected to read amateur work.  But a meeting where you are able to say interesting things like

"lots of people want to have geometric interpretations of analysis and say that is novel, but they most likely think in areas or volumes.  I like to think in decision trees and nodes.  It's not really novel, as Russian authors from the 50s like Guestanovitch have written this way.  But it's kind of rarely seen nowadays."

[Made up example...I don't know analysis...but you get the drift.


PhD: what happens if I quit? Here's my story. I moved from my home country to the UK in October to start a PhD in the UK with lots of excitement and positive expectations. However, what I discovered once I started was that the division I am in had never funded an Academic PhD project before (they focus on professional doctorates), the environment is not a research one (I share the office with lecturers and tutors, apart from another PhD student who won my same scholarship). My main supervisor, although supportive, is only at the university for for 3 days per week, has never supervised a PhD and has not an Academic PhD (but has the professional doctorate). My second supervisor does have a PhD, but follows me very occasionally, since only taking care of the 20% of the supervision.

Therefore, since the beginning the experience has been very isolating and not really stimulating. In addition, for various reasons, I have changed the theme of my original project and since then I have the sensation that my main supervisor is not really interested in this, even though saying otherwise. Also,  has no particular expertise in the specific subject I am doing research on, but has to supervise many people from the professional doctorate as well and is generally very busy (and yet doesn't even check emails during the whole weekend).

Moreover, I am doing clinical research and I have to face many logistical difficulties, such as the fact that the hospital in which I should work in is quite distant from the university (at least hours roundtrip), the collaboration from the staff and patients is hard to get and basically my PhD depends on lots of people whose sudden disappearance may lead to very big problems.

As a result, I am now approaching the 10th month and I haven't done anything yet, apart from having started the literature review the draft for a survey. I feel as this project is going nowhere and even if I managed to fix some of the logistical issues, the isolation, the lack of expertise of my supervisor and the lack of a research environment really bother me. My supervisor actually said my PhD is a "pilot" for the division to see if they should fund any other PhD in the future, but the problem is that the pilot is not going well.

I find myself thinking about quitting quite often in this period, but I am terribly concerned about the possible consequences: even if I quit I still would like to pursue a PhD somewhere else, but what are the odds of getting any other scholarship after having quit one? Also, I obviously can't apply somewhere else without quitting here, because I need updated cover letters, so this means that I would have to move back to my home country just to restart submitting applications. And without any money, of course.

I haven't spoken about it  because I think that once I disclose my reservations  with my supervisor would definitely lose interest in the project, so I am taking some time to think before doing anything. The problem is that I really don't know what to do. I moved to the UK because I thought I could have better opportunities compared to my home country, but I think I ended up in a quite peculiar and difficult doctoral experience; I am afraid that the fact of having already obtained funding is going to prevent me from having any other opportunity if I quit. Also quitting would have a very big impact on my psychological well-being, since I do not see myself as a quitter and I would totally feel it as a personal failure, despite all the variables that I have told you.

What do you think?

If the program is really a pilot, then there are likely some people somewhere in the department who would like it to succeed. I would definitely recommend finding those people and seeing whether they can assist with any of your issues, both logistical and advisor-related.

Past that, though, I would definitely also seek other options. For many PhD graduates, their advisor plays an important individual at the start of their career, and not having that resource can make things very difficult for you. Given that you are already in an academic vacuum, you probably don't want to have that kind of handicap. Take care to make sure you're giving yourself the highest likelihood of success.


Weightage of a review paper on an undergraduate CV Background: CS Undergraduate applying to CS PhD (USA)
I am involved in a review paper as a 2nd author. The review paper is of a very high quality and most likely will get accepted in a journal with a high impact factor. There will be 2 other authors who are both Co P.I. s of the project.
Question:
Does that hold any weightage in front of a PhD Admit Panel?
Note: The paper length is around 30 double columned pages so ample research is covered and future prospects are suggested in depth.

Yes, it holds a weight.
How much? it depends on the sensibility of the Panel, if no hard-rules are set.
Maybe 0.5 times the weight of a regular paper, because it is missing the novelty? Or maybe 1.5 times the weight of a regular paper, because if you took part in the review, then you already are updated about the State-of-Art on the topic and it can be very relevant to your PhD?
In absence of hard rules, it depends strongly on how you frame it. Be smart.
Then of course it has not much weight in the CV, if it is a 10 years old review paper: in 10 years the SoA changed a lot ... and if did not change much, you can publish an update of the same review paper, updating the content.


Choosing between PhD students or postdocs as a lecturer I have been appointed as a lecturer in a UK university. For establishing my lab, the department head offered two fully-funded PhD students (research programme) or two postdocs. I am struggling with what to choose. I consulted with some colleagues but received contradictory advice.

Postdocs are more experienced for a starting lab but successful PhD students are better points for my promotion. On the other hand, PhD students have lots of official responsibility and paperwork while postdocs have no direct interaction with the university/department.

It obviously depends dramatically on your discipline and what you want to do with those positions.

That being said, in most cases I would assume that the decision should either be to hire 2 students, or 1 student and 1 postdoc. Here are some advantages of hiring students in your case:

As a new faculty member, you need to develop a profile for your team. PhD students are often largely a blank slate with not many preconceived ideas for what they will be working on in the next years - it's much easier to steer a team of 2 students into a coherent direction than 2 postdocs, who pretty much by definition already have a research agenda.
Similarly, postdocs should and will develop their research direction independently of you, which should also include letting them work on their own projects and publishing their outcomes without you. Mentoring postdocs to be fully independent is great and very fulfilling once you yourself are fully established, but in the beginning you may want to use your scarce startup funds in a way that better maximises them for your own career progression.
PhD students will stay on longer. You have a better chance to develop them and publish extensively with them before they graduate. With a postdoc, it's easily possible that they are gone on to their own faculty position before you have really started to hit it off.
In many fields where some amount of manual labor is required, a team of 3 PhD holders but no students will be highly dysfunctional, with lots of talking heads and nobody doing the grunt work.
As you say, successfully mentoring PhD students will reflect positively on you in, or will even be required for, your promotion case. I don't think that having had postdocs usually really counts for anything in this regard.
You may simply not need a postdoc at this point. In my experience, postdocs are most productive in a large lab where the PI is stretched too thin to supervise all students effectively. This will not (yet) be the case for you.

Not all of those factors are true everywhere, but you should be able to decide for yourself what of the above is accurate for you. However, what I suggest avoiding is hiring postdocs in the hope that they will be some sort of pre-trained super-student, who will do as told with no real benefit to his own career. The few times I have seen young faculty take such a stance, it always ended with very little outcomes and a postdoc who quit after a short time.


What incentives do professors have to increase the PhD completion rate in their department? In other words:

  How do professors profit if a larger (rather than smaller) proportion of entering PhD students in their department complete their degree?

(At my department at least, it seems like the only benefit is "warm-glow altruism". A professor gains no more from having more students at her department complete their PhDs than I do by having fewer stray dogs in my town getting killed by traffic. A professor's career prospects does not seem in any way affected by whether 80% rather than just 50% of PhD students complete their degree. Not surprisingly, the completion rate, at least at my department, is closer to the latter.)

Note:  I am not asking whether it is a good idea to give professors stronger incentives to increase PhD completion rate. Neither am I asking for suggestions as to how PhD completion rates can be increased. Rather, I am asking what the incentives at present are (granting of course that this varies from place to place).

In the United States, the National Research Council (http://www.nap.edu/rdp/) regularly ranks university departments. One of the criteria by which departments (and thus universities) are ranked is the "Average of Median Time to Degree" with the presumption that lower is better.

In my university, this results in the provost's office putting pressure on us to reduce our time to degree through a number of measures, some coercive and punitive. Most of the time, the coercion and punishment is directed towards the graduate students (i.e., after the sixth year they lose their rights to certain fellowships, they have to pay more for their gym and library memberships, etc.).

But the department as a whole gets some attention. Our chair has been regularly sending out lists of our orphaned and missing ABD candidates (some now in their 12th year) and asking us to find and terminate them (either through graduating them, or formally asking them to leave the program).

I've also been putting some pressure on my peers through the admissions system by suggesting (since they are my colleagues, I have no power) that people with many students on the books should refrain from taking on new students until they clear their backlog more a bit.

I should note that I'm in anthropology where: 1) students tend to go into the field and disappear for quite sometime; 2) doctoral students are mostly useless to faculty for slave labor as most of us work individually and not in labs (with the exception of some of our archaeological / biological colleagues).


Tools for PDF presentations commenting that respect slides For my problem-solving classes I prepare presentations which include a reminder on the theoretical parts, statements of the problems to be solved, some (partial) solutions, tips and so on. These presentations are then displayed to the students by means of the screen sharing. Then we discuss the problems, try various approaches and do the usual stuff one would do in an offline class with a black- or whiteboard.

We mostly use Zoom which includes commenting tools which we actively use in the process. The comments and the drawings stay where they are when I go over the pages of the PDF, so when we switch to another slide, I have to clear the comments. It is mostly okay, but there are two issues:

When one of the students asks to get back to one of the previous slides, all the comments are gone (this is even more relevant for the research seminars).
The comments are not saved, meaning that the presentation I would share after the class contains no comments we made during the session (in particular, the solutions to the problems we solved in class). We record the video, sure, but the students told me that the slides themselves are more convenient for later use.

Now Adobe Reader and other PDF reading programs also contain the commenting and drawing tools, and all the comments can be saved in the document, but the comments are attached to the pages of the PDF and not to the slides, so I cannot combine drawing on top of the slide while also turning the pages of a single slide (in order to reveal something I prepared in advance).

  Q: Is there a way to combine these features, so that the comments are not lost, while also not tied to specific pages, but rather to the blocks of pages (say, for the sections of the PDF)?

If you use webex at least one part of your problem is solved. In Webex the comments I do stay with the slides.

Zoom is somewhat funny regarding the defaults: A scribble on one page of a presentation is rarely relevant to the next page. But that's zooms default behaviour. And yes it's rather annoying to erase each time you change slides.


Is there a more user-friendly way to download multiple articles from arXiv? I am subscribed to the arXiv daily digests for my subject area. I find myself, every day, doing the following, when I get to work:

1) Browsing through the arXiv email and right-clicking on the articles of interest to me (to open each of the pages in a different tab in my browser)

2) For each of these pages, downloading the pdf by clicking on the link, re-naming it <article-title> by <author name(s)>.pdf, and saving the pdf in a directory on my PC

[3) the directory is then automatically synched to my tablet during the day]

4) Looking at the articles on my commute home on my tablet.

I am bored of doing (2). It only takes 10-20 seconds per article (depending on things like how many carriage returns or inappropriate characters I have to remove from the cut-and-pasted article title and author names -- e.g. math characters (I am a mathematician and symbols in titles do not cut and paste well)) but when I'm interested in 5 articles and one has a lengthy title with carriage returns and symbols in, my mind wanders and I start thinking about whether this has already been automated by someone, because it seems to me that there would be no obstruction to doing so in theory, but I would not be capable of doing it myself.
Does such an automation exist?

You can use JabRef for this. More precisely, there are plugins by Christoph Lehner that do the job:

arxiv-rss to browse the list of new preprints and import the ones you want;
localcopy for downloading the PDF and automatically renaming it (according to a pattern you can define).

This isn't 100% automated (you still need to manually click "download arXiv PDF" once you've imported the entry in your bib file), but this is still much better than doing it all by hand.


How to know whether my submission to a mathematics journal is significant enough? I have received the following referee comment:

  This paper is well-written and the results appear to be correct. But I don't think the research is significant enough to warrant publication in ....(math journal name). Perhaps it would fit better with ......(another math journal name)?

How could I know that my article is significant enough?

"Good enough for journal X" is not a mathematical claim.  Operationally speaking, it is precisely a matter of collective opinion.  Math journals group themselves into rough, approximate equivalence classes (which is also entirely a matter of collective opinion), and you should take this negative referee result as one data point that your paper is not good enough for a journal of that class.  If your prior belief was that the paper was roughly equal or better in quality to other papers published in journals of the same class, you should try at least once more at a different journal of about the same level.

A good referee report reveals something about why the referee thinks the quality of the paper is not sufficient, either in absolute or relative terms.  This may give you something to improve: either actual mathematical improvements or improvements in the exposition to make referees believe your work is more valuable.

In summary: it doesn't necessarily mean much on its own.  Revise if applicable and resubmit.  Good luck.


Is it stupid to quit graduate program after one year? As the title says, I'm thinking about quitting. Everyone I've spoken to seems to think this is a dumb idea (quitting after one year, at least), but I haven't talked to anyone who's actually gone through grad school and been in this position before. I've been having second thoughts about grad school since the month or two before I started, and now that I'm here I know it's not where I want to be at all. I'm in a philosophy PhD program, and I could take a master's degree and leave after two years in the program, but I'm deciding whether I even want to do that, or just leave after this year. I am a teaching assistant, which is why I can't quit before the end of the year.

Last year I had the chance to work abroad for a few months, and I could have prolonged that, but I went ahead and returned to my country because grad school was just what I had been expecting to do long-term. But now I really have no interest in getting an academic job. I don't really have a long-term plan now, I just want to go back abroad while I'm still young, become fluent in the language there, work on my own writing projects, and get broader experience. So that's the plan whether I stick around for a second year to get the master's or not. My classes are interesting enough (I still love philosophy), and the teaching is easy enough. So the issue isn't that I'm too stressed out because of the workload or anything. It's just because I know what I would rather be doing, so I feel stupid for being in this program at all. (When I say that, I always hear "If you weren't smart, you wouldn't have gotten into the program." Sure, but I've made a stupid decision starting this program.) So I am still anxious all the time, and for the last couple of weeks I've had an awful time trying to focus on anything. I'm working on getting help for that, but I'm still worried that being anxious and miserable while I'm here might keep me from learning as much as I otherwise could, even if I did stay.

So, my question is whether leaving after a year (rather than staying another for the MA) for reasons like these is a horrible idea, or how common it is. Since I don't plan on pursuing an academic job, the degree would just be a piece of paper; it's not like the philosophy MA is a hard requirement for anything else I plan to do (and it wouldn't be from one of the top ranked universities anyway), and I think the experience working abroad will be valuable in the long term too. I just really don't want to feel dumb and like I'm stuck in this program while I'm still young (in my early twenties), especially when I know what I would rather be doing.

Are you paying for this MA programme yourself (e.g. with student loans) or do you have a scholarship that pays for it? If you are about to walk away with debt but no degree, you should strongly consider sticking it out for the second year, especially if the issue isn't academic and you feel that you can continue to do well in your studies. Even if you are not going to be walking away with debt, consider staying on.

While you may feel that you do not need a master's now and that it is just a piece of paper, you can't quite predict where your future will bring you. You might find yourself in a position where a master's degree (any master's degree!) will allow you to progress in you career in a way that is vastly more beneficial than if you only have a BA. To go a bit sociological on you and to whip out the Pierre Bourdieu, you are proposing you bank on your embodied cultural capital and are wanting to forgo the objectified manifestation of it; you are wanting to head off into the world without the degree. Yet this world likes degrees and may not always believe in you when you don't have them. In 10 years time, when you are somewhere in life that you can't predict now, how would you feel if not having the master's holds you back?

If you stick it out one more year you will be, at most, in you mid twenties if not still in your early twenties. You will still be young. Mid twenties abroad is just as good as early twenties abroad, and one year is not very much time to wait. Everything is the same, nothing is going anywhere, you'll just have a master's degree when you get back to it.


How to make my papers accessible to other researchers? I have published some papers in some conferences, but the problem is that the people in charge put them in bibliographic repositories, such as DBLP, and they take too much time to do that.

I would like to know how I can allow more people access to my publications, so they would be able to review them, use them if they want, maybe bring more ideas or even suggest that I correct something.

Initially, I was putting them in a personal webpage that I have created, but I took them off because I also got some papers accepted by ACM and IEEE and they require a payment to see them. In this last case, if I upload them for free (on my personal webpage) could I be charged with something by these institutions?

From the context of your question, I assume you are a computer scientist graduate student.  (Computer scientist because you mention DBLP, and graduate student because you're worried about people finding your research quickly.) My answer is specific to computer science, especially the first two points.

Just post your papers on your web page already.   Among other things, posting your own papers will allow Google Scholar to find and index them after only a few days. Despite scary legal language to the contrary, neither ACM nor IEEE (or SIAM, or AMS, or Springer, or Elsevier, or...) has any interest in suing individual researchers for providing copies of their own papers.
Post preprints of your work to the ArXiv and/or your institutional preprint server.  Again, despite scary language to the contrary, granting a license to the ArXiv to publish your papers does not deprive ACM or IEEE (or SIAM, or AMS, or Springer, or Elsevier, or even ACS) the right to later publish peer-reviewed version of your papers later.  Many publishers explicitly allow you to publish post-reviewed but pre-copy-edited preprints on the ArXiv and similar servers.  Posting camera-ready versions is technically illegal, but neither ACM nor IEEE has any interest in suing individual users for such violations.
Post publication announcements on Facebook/Google+/Twitter/your blog.  Yes, this works.  Really.
Give lots of talks.  At a minimum, you should give talks about your results in an appropriate local seminar.  But especially for really strong results, you (or your advisor) should also arrange to have yourself invited to a few other institutions to give a talk.
Send copies of your work directly to a few colleagues.  Just send them email with a link to your web page.  (Don't blindly send papers as attachments; remember that some people read email over the phone and pay by the byte.)  But don't just spam the whole world.  Limit your email to the small handful of influential people that you are sure will be interested — other researchers working on the same problem, people whose results you directly improve or extend, your advisor, and—if you're nearing a point like graduation or tenure where you need letters—a few potential letter-writers.
Take the long view.  It really is not important that see your results RIGHT NOW THIS MINUTE ZOMG NOW NOW NOW !!!!111¡¡¡CXI.  Relax.  Yes, DBLP and other indexing services operate with a delay of several months.  (Although my impression is DBLP has gotten faster, thanks to some outside funding that allowed them to hire more than one human being.)  And yeah, that's frustrating.  But in the long run, those few months of publication delay are not going to make a bit of difference.


What makes a Bachelor's thesis different from Master's and PhD theses? All the three types of research revolve around an argument, a thesis. They of course differ in terms of student level, that is complexity.

But, what makes a bachelor's thesis different from master's and PhD theses in terms of procedures of researching given that all of them may follow the same process of research, questions or hypotheses, review of the literature, methodology, results and discussion?

The PhD thesis should be on a much higher level than the Honours/Masters thesis, offering a contribution to human knowledge that is of a sufficient level of "significance" to warrant publication in a respected journal.

Significance is highly subjective, and you also do not necessarily have to publish to be awarded the PhD (sometimes the peer-review delay means that they come out afterwards, or there may be some intellectual property issues that make it beneficial to refrain from publication). It is awarded based on your supervisors consent and a review of academics in your field. So the "significance" would probably be judged by them in terms of how much original work they see as a reasonable expectation at that stage of your development (first 3 years of serious/committed research). Unfortunately it also means that some people who probably do not deserve PhD's are awarded them anyway for fulfilling grunt work for their easy-going supervisors.

It is possible that some Honours/Masters thesis might even be more significant/higher quality than a PhD thesis. Unfortunately, this does not mean that the submission of the thesis will award the degree that they deserve. The university may have a policy to upgrade the student's enrolment if the supervisor senses that such progress is being made. However, it is impossible to upgrade to a PhD without completing Honours and I believe nearly every single university has a policy of a minimum period of enrolment before submission is allowed. A subsequent question that you may have is how to gain a PhD without enrolling in one, which is another level of achievement completely.

As for the difference between Honours/Bachelor and Masters it would depend on your university, but both have no requirement for publication quality research and are usually small tasks/ideas that are not worth the supervisors time to think about alone, or involve a lot of labor. In fact, in my school, many Honours thesis are of a higher level than the Masters, because the smart Honours students will either graduate into the work force or go straight into a PhD. The Masters students are usually those who cannot find a job and are not suited to research. However, I believe some other universities may require a mandatory Masters degree to start the PhD.

You may get a better idea by looking at some titles/abstracts of completed theses. The PhD level will be something like a new method/observation/application whereas the Masters/Honours will be an application specific set of measurements/simulations or even simply a literature review to gauge the needs of future work. The word limits are also typically different (although note that quality is NOT proportional to the number of words), with PhD at 100K, Masters at 50K and Honours at 30K at my university.


Does securing a supervisor basically guarantee acceptance? I received an email from a prospective supervisor telling me he'd like me to join his lab and that he'll forward my name to the grad office. Assuming my entire application is strong, does this mean an official acceptance is very likely? Or is there a chance I could still get rejected by the admissions committee? This is for a funded PhD program.

It depends on where the funding comes from. If the money comes from the professor's own grants, then you're extremely likely to get a formal admission. If the money comes from the department the professor now has to convince the admissions committee that you should get the position. Why not send an email to the potential supervisor and ask what the next step is? That should let you know where you stand.


Can industry experience make up for undergrad courses? I am an undergraduate applied math and statistics major and plan on applying to PhD programs after graduation. My research interests are in machine learning, cv, etc.. And do research in the stats and CS department in ML/DL. I am thinking of applying to PhD CS programs, but have only taken 4 CS classes in undergrad, but I have had two internships with Amazon as a software engineer.  Can my experience in industry make up for the lack of CS classes as an undergrad?
I obviously want to get into the best program possible, but worried that my lack of CS classes might hinder my chances of getting accepted.

edit: Not a duplicate. Not worried about weak grades, gre, research, etc.. I am just wondering from a graduate admissions perspective will they look negatively on less CS classes even though I have research and industry experience in CS.

While not every place will respond positively, I don't see a huge problem in the US. But you will need to write your application materials so that people look at your "special case" positively and find strong evidence that you will likely succeed. You will be facing a lot of stiff competition at good places by people with a more standard and easy to judge set of qualifications, so you need to find a way to stand out.

Your current majors are useful in your proposed study, of course, even if you are missing some CS things.

So, don't stress the lack of additional courses in CS but the possession of skills related to the program that you want to join. Your academic record is what it is, though you may have time for some additional courses, but your other activities may, in the eyes of a reviewer, compensate for that and even give you an advantage. It is all, or at least a lot, about how you present yourself and your skills.

It might depend, of course, on which particular CS courses you took and on the kind of things you did in the internships. But like anyone, you have to make it easy to answer the main question: "Is it highly likely this person will succeed?". If you make it obvious that the answer is yes, then you have a shot. It will also be helpful if you have some ideas, even if only partly formed, on the kind of thing you want to study. Fairly specific. Fairly detailed.


Statement of purpose: how important is correctness of grammar and punctuation? English is not my first language, and I am concerned that my statement of purpose might contain some grammatical and punctuation mistakes that neither Microsoft word nor I can see. What is the best way to overcome this problem, and to what degree does this affect the admissions committee decision putting into consideration that English isn't my first language?

P.S. I don't have any native English-speaking friends and I don't trust companies or online sites to see my statement of purpose to check its correctness.

If the written question above is a genuine reflection of your English spelling and grammar abilities, then I strongly suggest you seek professional services to assist if you are in any way concerned about your abilities having an adverse impact on your application.

This application is clearly a very important step in determining your future, and if it is so important and you have concerns, it is not worth leaving it to chance. If you have no suitable friends, use a professional service. Plenty of other native-English speaking applicants who are competing for spaces with you will have done so.

I can't say for certain how a selection committee will factor your English as a second language. It is likely to depend on the institution and the course you are applying for.


What if the lead author disagrees with the coauthors on manuscript content and target journals? The lead author has conceived the initial idea, developed the methods, the experiments, the analysis, and has written the draft. Coauthors have contributed to that draft mainly by rephrasing and restructuring it, in a way that lead author disagrees.

Additionally, coauthors insist on submitting to a journal which lead author disagrees with, but also the coauthors do not agree for submission on journals which the lead author prefers.

Lead author wants to stop collaborating with the coauthors, but doesn't want to leave this work unpublished (coauthors say they will ask for retraction if work is submitted, since they believe they contributed considerably). Would it be possible for the lead author to omit the coauthors' contributions by rewriting the manuscript, and submit it as the only author?

Given that the solution of negotiating and finding a middle way is excluded, do you have any other solutions to propose?

It seems to me that choosing where to submit is within the responsabilities of the first author. Even though the acceptance of the co-authors is encouraged and desired in order to maintain a healthy relation, I think the last word is his.

I also think that there's a lack of empathy in this matter. Co-authors should be asking themselves how would they feel in the author's position. How would they feel if they had an idea, developed methods, analysis and drafts and kept being undermined by the rest of the team?

For closure, keep in mind that a work is best if published, regardless of place. Spending all the effort taken because of such disagreement seems petty and dull to me. It is better to let it go and focus on the next project.


Is it unethical to use a published code in my PhD thesis work? I have used a code published in a published Masters thesis into my PhD work. I have modified just 10% of the code to suit my research requirement. However, most of the code is as developed by the original researcher. I had to use the code from the literature because I currently don't have the time, the resources or the motivation to write the code from scratch.

However, I am in a dilemma whether I am doing something unethical by using the code developed by someone else for my research. I will cite the original thesis in my papers and thesis. I will cite it in the following manner:

The code used in this thesis has been developed based on the work published by John Doe at the University of Agartha [1].

[1] Doe, J. Implementation of a code. University of Agartha, 2008.

Also, I am not going to add the code in my thesis or my paper. Will this be unethical and violation of the original author's copyright?

There are three issues:

Is it a copyright violation? This depends on the license under which the original code was released.  You'll have to read it.

Is it plagiarism?  No, you have credited the original author.  However, you may want to make it more clear that it is really a relatively minor modification of their code.  Your current wording, "developed based on work...", could be interpreted as "I got some ideas from their work but then wrote all my code from scratch", which would misrepresent the real contribution of the other authors.

Is it adequate for your PhD thesis? You could write an entire thesis that just used the work of others, appropriately cited, with minor tweaks.  It wouldn't be plagiarism, but it also wouldn't get you a PhD, because it doesn't demonstrate an ability to do independent research.  So, you need to make sure that your advisor and committee are fully aware of what parts are your own work, and what parts are the work of others, so that they can evaluate your research accomplishment based on what you did.  If they don't feel it's adequate, then you may have to do more work in order to complete a thesis that will pass.
The same applies when you publish a paper.  Here, the editors and reviewers need to evaluate your paper based on its novelty - what part of it is new work, versus what simply makes use of existing work?


What is the process for retroactively (post completion) reviewing plagiarism on a dissertation? I am currently at a community college so I am not privy to the inner workings of the big university world but I am curious how this works.

Recently it has become headline news that a student from a prestigious Ivy League school apparently completed their PhD back in 2000 with a dissertation that contains significant amounts of plagiarism. The university has supposedly initiated a review (though they are officially taking the standard "no comment" position and also the more extreme position of not even confirming if they are conducting any investigation).

  Note: Here is a link to the news article for those interested in the details but I do not want to make this Question all about the politics involved, I am interested the academia processes.

At first glance I was rather stunned that a school as prestigious as this one could have possibly accepted such extremely poor work and provided a PhD based on it but I guess even the best of us can make errors. What I want to know now is how such "fixing past mistakes" issues are typically handled.

Specifically I would like to know the following (based on your experience at your institutions):

(1) Would such a review process be limited to the dissertation itself or would all the work of the student be reviewed?

(2) Would such a review involve questioning the academic advisor/research supervisor? What about the thesis committee?

(2a) On a sidenote: Would the thesis committee for a doctorate degree be obligated to check the research in detail or are they allowed to rely on the research supervisor for that task?

(3) Would such a review look at the theses of other PhD graduates who were under the same supervisor?

(4) What happens if such a review finds a doctorate is academically or ethically flawed? What, if any, penalties can be invoked against the student?

(5) If the outcome is to void the degree would the student be offered a chance to comment/defend or would the degree be revoked without warning?

(6) How long would such a review typically take to complete?

Because this Question is prompted by a high-profile incident I am not sure if any of the process used by Columbia University in this particular case will be "typical". For instance I can easily envision that some eager beaver investigative reporter will pull copies of all the theses with the same supervisor and look for more instances of plagiarism. If I can predict this I am just as sure that Columbia will do the same and want to get ahead of any exposé by both expediting the initial review and being comprehensive to prevent any further "unexpected" embarrassments.

That said, I would like to know what is/has been typical in such review processes before today.

The scenario of an investigation for suspected plagiarism in a PhD thesis is so rare and unusual that I'm pretty sure there is no "typical" recipe for how it would unfold. However, I'm familiar with one such case that happened some years ago at my institution, and I'll take that case as my definition of what "typically" happens.

  (1) Would such a review process be limited to the dissertation itself or would all the work of the student be reviewed?

It might, if the student's other work was available to be inspected (which I think is doubtful since the student will have already graduated), and if there was some concrete basis for suspecting plagiarism in that work, and (which IMO is the least likely condition to be satisfied) if the people involved in the investiation had enough time on their hands and were energetic enough to pursue such secondary investigation leads.

  (2) Would such a review involve questioning the academic advisor/research supervisor? What about the thesis committee?

This would be highly embarrassing to the people you are mentioning, so I expect they would only be questioned if there was a strong basis for believing that the information they could provide would materially affect the outcome of the investigation. Thus, the advisor might be questioned to get some background information on what took place when the student was writing the dissertation; the thesis committee members, almost certainly not.

  (2a) On a sidenote: Would the thesis committee for a doctorate degree be obligated to check the research in detail or are they allowed to rely on the research supervisor for that task?

See the comment by BrianDHall. The thesis committee never "checks the research in detail", and in all except a rare handful of cases, neither does the research supervisor.

  (3) Would such a review look at the theses of other PhD graduates who were under the same supervisor?

This question suggests to me that you have watched one too many episodes of late-night TV crime shows. Unlike such shows, universities aren't populated by dogged investigators (with checkered pasts and colorful personalities, usually divorced and heavy drinkers) who work day and night, dedicating their lives to exposing all instances of wrongdoing and then bringing the perpetrators to justice.

In other words, the answer is no.

  (4) What happens if such a review finds a doctorate is academically or ethically flawed? What, if any, penalties can be invoked against the student?

Given that the student has already graduated and is no longer a member of the campus community, the only punishment the university can actually impose is to revoke the degree. The only real question to debate would be whether the student would be allowed to come back and rewrite the dissertation if they wished to. Moreover, given the severity of the offense, and the risk posed to the university's reputation and credibility by PhD degrees it grants that are based on plagiarism, revoking the degree seems like a completely appopriate and logical response.

  (5) If the outcome is to void the degree would the student be offered a chance to comment/defend or would the degree be revoked without warning?

Undoubtedly the student would be given a chance to defend themselves against such an accusation before any action such as revoking the degree is taken. They would likely be entitled to ask for the case to be reviewed by a committee, and to have a panel convened where they could present evidence in their defense. Given the high stakes involved, if they wished to contest the accusation they would likely hire an attorney.

  (6) How long would such a review typically take to complete?

Probably a few months, but I assume it can vary a lot and take longer in some cases or be completed quite quickly in other cases.


Grades and Predoctoral NIH Grants I am applying for an F31 Diversity Grant for Predoctoral studies to support my 3-5 year of PhD studies. There is no mention of needing to submit transcript of grade with the application. Is this true? Does the NIH not require transcripts for F31 applications? Are applications solely graded on the merit of the proposal or do student grades also considered?

Each NIH grant comes with extensive guidance. For the Ruth L. Kirschstein National Research Service Award Individual Predoctoral Fellowship to Promote Diversity in Health-Related Research the guidance says

  Note that scores for standardized exams (e.g., MCAT, GRE) as well as a listing of the applicant’s courses and grades must be included in the Fellowship Applicant Biographical Sketch, and NOT in this attachment.

The guidance also says

  Follow the instructions in the SF424 (R&R) Individual Fellowship Application Guide to ensure you complete all appropriate “optional” forms.

SF424 (R&R) refers you back to PA-14-148.

In general, it is advisable to talk to the Program Officer at the NIH whenever you are considering applying for a grant/fellowship. They are more than happy to help navigate you through the submission process and generally can provide you with invaluable insight about how to improve your application. Each institute at the NIH and each funding mechanism has a different Program Officer, but they are generally pretty easy to find online.


IRB guidelines for secure online data storage, backup, and syncing? I am asking to get people's success stories in presenting a data management case for secure data backup using remote online services, rather than the antiquated "server in a locked room" model of security.

In general, I have gotten the impression that most IRB's think that a server on-campus in a locked room is safer than a cloud server in a mysterious data center.  It's an argument that doesn't hold much water to me.  In the business world, vital data is stored in cloud data centers all the time. However, given that IRB boards tend to not have many data-security specialists (if any), I am not sure what kinds of guarantees are typically requested.

For those who have gone down this road, what kinds of services and guarantees were required to meet the requirements of an IRB panel (and for what level of vulnerability of subjects and disclosure risks)?  For example, for medical data, I would assume that a HIPAA-compliant data service (e.g., Carbonite's Pro version) would usually be sufficient (but possibly not always).  I am most interested in slightly lower-risk data (e.g., sociological or cognitive), but would be interested in any reports on reasonable and IRB-approved service requirements for storing, syncing, and sharing data on a project.  Is a HIPAA-compliant storage usually sufficient?  Is it sometimes sufficient to have a non-HIPAA-compliant one, but with some other types of certification or privacy guarantees?  How important are guarantees that data will be fully-stored in a same-country (e.g., US) data center or on a discrete server?  In short, I'm hoping to figure out the guidelines that are generally used for matching a remote data service to an IRB data management plan.

While this solution will likely be only a drop in the bucket for your request, I did write a paper covering security issues related to health information and HIPAA while finishing up my Master's. Section 6 has a case study on Amazon Web Services as a "HIPAA-compliant" cloud storage solution, including both its positives and its negatives.

Since this was a review paper, I feel the need to point out that I don't have any personal experience with Amazon Web Services or with setting it up for HIPAA compliance, so don't take it as an endorsement either for or against its use.

It's important to evaluate exactly what any proposed service you select actually provides. AWS, for example, supports basically the creation of the HIPAA-compliant environment. That being said, that's the creation of one, not one provided out of box. You'd have to implement a variety of features normally associated with data storage such as backing up data, auditing all changes, and so on.

Basically, you're asking what you need to do to satisfy the IRB, I guess. What you should probably be asking is what you can do to satisfy HIPAA regulations, and using that, justify that it is a viable solution to the IRB.

I can't really provide you a concrete example of an actual cloud data storage plan (the one I was involved in is non-disclosure and I'm also not an IS guy) but I might be able to answer some more conceptual questions.


Why do I have access to Springer articles/books using a laptop when I am not logged in? I have several laptops and I noted that with one laptop (and only this one laptop, and no access at all with other laptops) I have access to all Springer articles (at least in mathematics) and seemingly even to all math books (such as this series of books) in the Springer website without even being logged in any account.
How is that possible?
I have access to the journals in my university computer, but even there I do not have access to the books.
When I go to a journal website like this one, I see on the right of the page "You have access to our articles". I am not logged in there (at the end of the page, above the copyright, it even says "Not logged in") or have ever tried to log in. When I click "My account" on the top right of the page, I'm told to login and thus I assume I'm not logged in in any kind of form. (I only log into Springer journal sites when submitting or checking the status of an article and then logout, but that is not via any university system that grants access).

It looks like Springer does this using cookies.
I also observed what you described in the question. I was able to access articles that had a paywall when I was neither in my university's IP range nor logged in. However, at the footer of the page, near the copyright notice, it showed name of my university and a mention that this was what gave me access to that particular page.
This did not work while browsing incognito, which suggested the use of cookies. I was then able to verify this by clearing cookies from link.springer.com in my browser, after which I lost access.
I suspect the cookie was stored at some point when you were in the institutional IP range, and had a sufficiently long validity that you continue to have access, and will probably do so for as long as it is valid or until you remove it.
Edit: I was able to verify this as well, accessing Springer from my institution's VPN resulted in me getting access again, which persisted even after leaving the network. A further check showed that the cookie is a session cookie, valid till the end of the session. The duration of storage of such cookies varies by browser and operating system, but should generally persist for at least as long as you keep the browser open (which on a laptop could potentially be a long time), and often even beyond system restarts (e.g. Firefox, Chrome).


What do they mean when say “the French equivalent of a Ph.D.”? I read the biography of a French-born scientist-turned-entrepreneur Philippe Kahn. It says that Philippe Kahn received the “French equivalent of a Ph.D. certified by the French Academy of Sciences”.

I discovered an article about Kahn which says that he earned the equivalent of a doctorate, but not the degree. In yet another article, I read that he holds an agregation de mathematiques, and this is the French equivalent of a doctorate. I am rather baffled at all this, since Wikipedia clearly indicates that agregation has nothing to do with the equivalent of a doctorate. Can you explain what Kahn's biographers mean by “the French equivalent of a Ph.D.”? And if this is the degree then why should it be certified by the academy? So far I have come to conclusion that by the equivalent they mean the D.E.A. degree

According to a 1985 biography in PC Magazine:

  During his college days, Kahn played saxophone in Paris jazz clubs while earning an Agrégation de mathématique, equivalent to a Ph.D. in math.

Another 1985 PC Magazine biography states:

  Kahn, who received the French equivalent of a Ph.D. in mathematics from the French Academy of Sciences, taught mathematics at the university level in Nice and Grenoble before coming to the United States.

Both Wikipedia and Kahn's LinkedIn page state only that he received a master's degree in mathematics from Université Nice Sophia Antipolis in 1975.  This is not the equivalent of a Ph.D., and Sophia Antipolis is nowhere near Paris.

The agrégation de mathématiques is a competitive civil service exam used to recruit high school and university mathematics teachers.  While the exam is extremely rigorous, and agrégés are qualified to teach at universities, the agrégation is not a research degree.  French doctorates underwent a major reform in 1974 and again in 1984, but I believe the closest French equivalent of a Ph.D that Kahn could have earned in the late 1970s was the Doctorat du 3ème cycle.