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Tools for creating and managing a Data Dictionary
I'm looking for tools to create a data dictionary for my project's data.  We have a large database of many variables, and I would like to create a data dictionary that describes what each variable means so that I can share it with collaborators and other researchers (including on the Open Science Framework).  I'd like other researchers to be able to use the data dictionary to understand the data we have, find the variables they need, etc.  I'm not sure what tools/software/systems are available for this purpose, and whether I should just create a large spreadsheet to do this, or whether there are more specialized tools that people like for this purpose.
For a sense of what my data dictionary might include, here are suggested guidelines for what a data dictionary should include according to the Open Science Framework (https://help.osf.io/hc/en-us/articles/360019739054-How-to-Make-a-Data-Dictionary):

Variable name
Human-readable variable name
Variable type (string, numeric, integer, etc.)
Measurement unit
Allowed values
Definition and description of the variable

Note that "shopping questions" do not include recommendations for software solutions: https://academia.meta.stackexchange.com/a/3658/17886. As noted here (https://academia.meta.stackexchange.com/a/4679/17886), "Softwarerecs.se is a bad idea for specialized needs". I posted my question here rather than on Softwarerecs.se because my question deals with a specialized need.

How is this question different from "How do I make a database?"

A data dictionary is a specialized database in academic research.  The needs will differ from other types of databases.

I would keep things simple and write a small script in Python (or your preferred language) to read and write entries with the desired fields to a JSON file. You could also do .csv, but JSON is nice a readable. Then place the script alongside the database in a shared repository so that you can grant access to anyone who needs to query or edit the database, and you have version control too :).
Even if you do not have any programming experience, I would be surprised if you didn't have a collaborator who could help you set up such a thing.

There are indeed some tools available for such 'metadata management'. You can find a list here: https://library.stanford.edu/research/data-management-services/data-best-practices/creating-metadata/metadata-tools


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How should an undergrad pick a journal to submit to?
I am an undergraduate who has been doing research in a lab since my freshmen year, and I have usually just worked on projects with a PhD student. That being said, as of now I have co-authored two papers (both accepted) with said PhD student.
The professor has entrusted me to do my own research and he is really pushing that we publish a letter as soon as possible on the research I was doing, since no one in our (relatively new) subfield has even touched on this method. The first journal he said was Physical Review Letters (which made my eyes light up). Now though, he is leaning more to Applied Physics Letters or a much more specified journal.
I am looking to go into a PhD program in physics; should I submit to whatever journal my professor says to? He is very open and I think I could convince him to let me send it to Physical Review Letters but maybe he knows something I don't (like that it would be a waste of time - autorejection). Are there any other physics-based letters for broad and novel physics research?

maybe he knows something I don't - have you asked him why he suggested a more specified journal?

He has suggested more and more journals each time the topic comes up, is the thing. He doesn't often speak candidly, but maybe that is what needs to happen to get a concise answer.

Your advisor is almost certainly the best person to talk to about this, since (unlike everybody on this site) he is familiar with the field and with your work.

Assuming your professor is not new at advising, he would have the best opinion on the matter since it is surely something he has dealt with before. If you are really unsure about this, express your concern and ask him why he would suggest one over the other, and then make your decision from there.
Additionally, can you get input from the PhD student you are working with?
If all else fails, you may be able to talk to another professor in the same field to get a second opinion on this.

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Collection and return of homework and exams
I am about to teach a class with about 100 students.  The class has weekly take-home exams, and multiple in-class exams.  I have TA's, but still the task of collecting and returning the students' write-up is non-trivial, and if not done well can take significant time away from the class (including because of people not always coming to class, reportedly missing write-ups, etc).
What system (electronic or not) is better for collection, grading, and return of take-home homework and in-class exams?
Specific starter points: I heard some people use Blackboard for electronic submission, grading, and return of homework.  Is it good?  I also heard of Watson.  Is anyone using these?
What about in-class exams?  Is there anyone who scans them and returns them electronically?
What about paper-based systems?  Do you have a submission box?  Do you leave write-ups for the students to pick at each class?

Many universities now have a central online system for this, e.g. Moodle, Blackboard, etc. Check what your colleagues use, and stick to it - it will be much easier for you and your students.

From personal experience, I strongly recommend avoiding your university's central online system like the plague and using Gradescope instead.

@JeffE A potential problem with that is that most students will be familiar with the institution's LMS, and perhaps not with Gradescope.  (In my own institution, Brightspace is required; I wouldn't be allowed to use Gradescope.)

@JeffE It would be very helpful if you explain your workflow with Gradescope.  Such as: students do exam in class, TA scans them (?), Gradescope automatically splits the scan in multiple documents corresponding to the students (??), ...

@EmanueleViola So far I've only used Gradescope for homework, which students submit electronically (except some students submit scans of hand-written paper).  Everything is done online with simple interfaces, especially for setting/changing rubrics and for regrade requests.  Gradescope does some support bulk-scanning paper exams, but I haven't tried it yet, primarily because exams have to be associated with students manually.  I'm thinking of trying it this semester; ask me again in a few months.

To my mind, the biggest problem, after actually grading so much work, is the possibility of a student claiming that work was turned in but later lost by you or the TA.  You allude to this in your question.
You don't say where you are, but it is likely your university has a "learning management system," such as Blackboard, Brightspace, or Moodle,that can be used to collect take-home work.  For multiple-choice assessments, the learning management system can probably grade them, too.  The huge advantage of this is that there's no possibility of "lost" work; either the student submits the work or not.
For in-class exams, have a letter tray similar to the "inbox" one might have on a desk.  Require each student to deposit his own exam into the letter tray and, at the end of class, put a binder clip on the stack.  (For 100 students, you'll probably need four stacks of 25.)  Grade the exams on a completely clear desk and there's no possibility of lost work there, either.  If a Scantron machine is available and multiple-choice exams will work for you, use that for grading.  I have smaller classes, and I take each paper directly from the student's hand and mark the student's name on the class list.  Students observe me to do this, and I don't get complaints that I "lost" their work.
Work graded through the learning management system is returned electronically.  If you use Scantron forms for in-class testing, it may be possible to get the results electronically and return them via the LMS.  Your testing center can probably tell whether that's possible.  I have returned in-class paper tests through the LMS by scanning and uploading them.  We have a copier that can serve as a scanner, and that work can be performed by a TA or student assistant.  If you must return paper exams in class, have them sorted alphabetically and return them at the end of class so that students may leave when they've picked up their graded work.

As a student, I couldn't agree more.  My college currently uses Canvas, previously Blackboard.  Neither work particularly well, but that is more a function of Administration forcing all departments to work on a centralized server than anything else.  Have had the pleasure of submitting an assignment, having it recorded as being submitted, having a record of files uploaded on the schools servers......but having the server somehow delete my files on it's own without user input.   The only drawback to physically handing in work, is when the exam is writing a program, hard to compile paper.

@NZKshatriya Hmmm... I made the assumption that the LMS server was administered competently.  If that's not the case, it is not only not useful, it's a detriment to teaching and learning.  (The major LMSs all seem to work more-or-less like the documentation says, so lost files are quite likely a problem of incompetent administration.)

I'll address the "Blackboard" part of your question, since this is what my university uses. And I must say, I'm quite happy with it!
A short (non-exhaustive) overview of its features with respect to homework and exams:

Basic assignment features: starting date, deadline, description of the assignment, attaching extra documents...

Different "shown" deadline and "actual" deadline. When making an electronic assignment or test, you can choose 2 dates: the deadline as shown to students, and the deadline where it becomes impossible to hand in the assignment/test.
This second deadline allows students to hand in their work late, which you may want to allow - if not, just make both deadlines the same. Note that this second deadline is invisible to students.

There is a grade center providing a spreadsheet overview of all students and their assignments, tests, grades, etc. It allows you to grade assignments, to weigh the grades, but also to send mails by selecting students on this spreadsheet.
If students had handed in homework past the deadline, there will be a notification saying "too late" next to the relevant assignments.

In case of the assignment being a recognised document (e.g. pdf), you can make annotations on the document itself and, if desired, add these to the feedback the student receives.

Students have a my grades menu where they can read their grades, together with any comments and annotations you have added.

TurnItIn integration: this automatically compares uploaded documents to other documents found online; with the goal of detecting plagiarism.

And I must say, I'm quite happy with it! — Huh.  This is literally the first time I have heard anybody say that they actually like Blackboard.

@JeffE To be honest, I have the same experience. Nearly all of my colleagues dislike it.
My main annoyance is that, when making a new course in Blackboard, there are a bazillion of unnecessary things enabled (wiki, achievements, ...) while many of the extremely useful tools are quite hidden and hence rarely ever used! I'll admit, it can take a lot of time and effort to make a good course on blackboard that is useful to both teacher and student - but it's definitely possible!

Re: Blackboard: Yes, it works perfectly fine this purpose. I use it for weekly multiple-choice quizzes in all my classes and find that it benefits my class management a lot. It's automatically and instantaneously graded, provides immediate feedback to students, a 24/7 grade center that students can check on at any time, and copious statistical reporting on the back end which I use to drive future updates in all of my classes. There are lots of options now that you may want to investigate. A few pointers:
One: How you make Blackboard tests in the first place is a bit of a question; I find the web interface a bit slow and inelegant. Personally, I find it more efficient to make my quizzes locally in Pearson TestGen, and then export them to Blackboard as a separate step. TestGen looks like this:

Two: While the most familiar use-case is for multiple-choice questions, Blackboard has many other formats of questions you can use. Just one example: For quantitative questions, you can require numerical input that gets scored as correct if it matches a certain number within a certain tolerance ("Calculated Numeric"). You can even include variable questions, so different students have different questions, with a formula under the hood that determines the correct answer ("Calculated Formula"). Limitation: The answer must be a decimal-notation number; fractions and algebraic expressions cannot be constructed/graded automatically in this way. (Also, my Pearson TestGen process doesn't work for more than simple multiple-choice items.) List from the Blackboard interface:

Three: The back-end statistics are so fascinating that I find some amount of risk in being a bit personally addicted to checking them on a daily basis. You can also export all of the individual responses to an item and run statistical tests (in, say, a spreadsheet or SPSS) looking for what important factors correlate with entry diagnostics, final exam scores, etc. Here are some samples of reports from within Blackboard:

Finally, if you don't want automatic grading of tests, then that's supported as well (e.g., for essay, coding, or other subjective questions); tests come in and then the instructor gives grades and feedback via the interface later. Also there are "assignments" in which students can upload documents and then the instructor grades them likewise (including possibly use of a "rubric" which allows grading by selecting from among several radio-button options).

Wow, so that's what the instructor sees in Blackboard.  How thick is the manual?

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Why would my teacher's dean care when I took the final?
The class was scheduled to take the final next week.  I wanted to take the test this week, because there's some place I was planning to be on the day of the final. My teacher said that doesn't count as an extenuating circumstance, and that his dean wouldn't like it.  His dean isn't even administering the exam, so why would she even care?

Mentioning the dean may just have been an easy to avoid saying: "No, I don't allow you to do this".

In most situations you are not entitled to make alternate plans on the day of the final.

Anecdote: I used to be pretty liberal about allowing students to take finals early so they could travel.  Until someone requested to take an exam early, failed it big time, and then complained to the dean that he would have done well if he'd been given as much study time as the rest of the class.  Now everyone takes the exam on the scheduled date at the scheduled time.

"because there's some place I was planning to be" - that excuse doesn't fly, or else everyone would be asking to re-arrange exams to their convenience. At many universities, you are expected by the University, upon enrolment, to be available during the entire exam period.

Many professors allowed us to take the exams early. No-one would dare to complain if he failed. But we also had the minimum of three exam dates guaranteed by the faculty laws. You have only one date for the exam possible?

A dean of academic affairs is responsible for overseeing all exams, even if she isn’t directly administering them. Ensuring standards are uniformly upheld is part of her job.

Allowing students to take finals at other than the scheduled time could cause the following problems:

Complaints from other students (in other courses under other professors) that they weren't allowed to take their final exam at a nonstandard time.  "My friend Johnny got to take Professor Smith's final early, why can't I take Prof Jones's final early."
If the same final exam is used for all students, then students who take the exam early can leak information about the questions to other students.
To avoid the problem in point 2, we often give a different final exam to students who must take the exam at a non-standard time.  However, this can lead to complaints that the alternate exam is unfair.  At the very least, it means extra work for the professor in writing the exam.

There are certainly circumstances where a student can't take a final exam at the scheduled time.  For example, a student in one of my classes is ill, so we've arranged for a makeup final exam to be given in January at the start of the spring semester.

Ok, this point has some validity, but the dean/professor could always reply that Professor Jones simply did not mind letting Johnny take the exam early.  If the professor won't take travel plans as an excuse, then that could be made clear from the beginning (an "I won't allow alternate arrangements unless you have a dentist or doctor appointment or are too ill and have a doctor's note" in the syllabus and/or said in class would do)

At my university it is clear policy that students have to take final exams at the scheduled time and that travel plans are no excuse.  Thus there is no need to include this in the syllabus.

If there is a scheduled time when exams are given, the dean is often the person who receives complaints about exams that are given at the wrong time (e.g. if the professor unilaterally moves the exam).  The dean cares because he or she has to deal with the complaints!
To keep things organized, the dean may have told the faculty (perhaps through their department chairs) only to reschedule exams if there are extenuating circumstances. That would not be an unreasonable or surprising request, in my experience.
The professor might (depending on the institution, their tenure status, and their own sense of agency) be able to move your exam anyway. But the answer you received should be viewed as a polite "no".
Personally, I am only sometimes able to move the exams in that way. It depends, for me, on whether I have the exam written, what day and time the student wants to take the exam, how many students I anticipate will want an alternate time, etc.   Of course, if there is a serious circumstance I will schedule a make up. But just wanting to be somewhere else is not much of an extenuating circumstance - taking the final is an expected part of taking the class.

The professor would not require everyone else to take the exam on the same day I wanted to take it on, so I think the other students would likely have complained regardless of whether or not I took the exam on a different date.

It is not uncommon for students to complain when other students get to take the exam at a different time!

"Someplace where I was planning to be" doesn't tell the full story. By itself, that's a reason for denying a request for a different test time.
"Someplace" (at a particular time) is a lot more excusable for an emergency. If there is an illness or potential death in the family, and you need to get there before, say, one of your parents die, or for a scheduled funeral, that would be an adequate reason for rescheduling your test. So might a (legal) "court" date; possibly even another "court date" at the invitation, of say, Queen Elizabeth II.
But barring a "good reason," professors and deans are supposed to deny requests for rescheduling a test.

Here is a perspective people don't usually consider...accreditation. Each student is required to meet a certain amount of instructional hours per class. The accreditation committee sets the required hours and audits school records to make sure these requirements are being met.
If a student takes the final early, it implies they are going to miss a class. By allowing this, the teacher has tacitly agreed to violate the accreditation requirements of the class.

That applies only in the case where an exam is directly after the week of the last class, and only accessible to students that attended the respective class right before the exam (instead of, say, one or two semesters earlier, which case the student may well not have missed any class).

As O. R. Mapper suggests, a rescheduled exam does not necessarily imply missing a class.

I now have 2 students who want to reschedule their final exams - both for valid reasons, but both in reasonably high level courses - calc 2 and a programming class.  The final for Calc 2 requires significant preparation time, and time setting the rubric.  The programming exam is easier to write but harder to grade when there is just one person taking it.  Both require an addition of about 8 hours (each) to write, proctor and grade these finals.  I don't want to stand in the way of my students who have excellent opportunities - but I have a policy in place that requires exams to be taken at exam time - barring extreme (i.e. hospitalized emergencies). Part of the problem is the schedule of the college I teach at - spring semester runs into June.  The other problem is guilt - other professors are doing it so I should to... peer pressure maybe.  There should be one clear campus wide policy requiring students to take the final on the day scheduled. I shouldn't be spending any time worrying about this.  :-/

I’ve never heard of a US university that doesn’t have such a policy that includes the regulations under which an exam must be rescheduled.

Welcome to Academia SE. Note that we follow a strict question-and-answer format. While parts of your post may be intended to address the question, most of it reads like a separate story. Please [edit] your post to focus on answering the question (or delete it).

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Received a less-than-great grade due to bad instructions. Should I appeal?
Last week, I did a computer lab for a class. At the end of the instructions was a script that would verify that everything in the lab was done correctly. At the end of the lab, I knew I had done everything correctly; however, the verification script wouldn't show that everything was done correctly.
The instructor didn't mention that some additional changes would have to be made to all the lab files for the verification script to pass. I found that out by going to the TAs. I have proof that the professor took notice of this error last week only after I had brought it up, and that I submitted the lab on the same day he did so - albeit a few hours later.
However, I forgot to make the necessary change for one of the lab files, for which I was docked 3 points (out of 20).
The professor has thus far refused to give me those points back.
Assuming the evidence I have of the professor's oversight and of my same-day submission of the lab satisfies the standard of evidence at the department/university level for a grade dispute/appeal, should I appeal the grade or just let it go?

Can you make the case that you forgot to change because of their error?

@CaptainEmacs: I believe so, although the fact that I forgot regardless of the TA's instructions now creates doubt in my mind.

Your best strategy might be normally to operate by goodwill rather than demand, in this case. However, you seem to already have tried to fix it, so I see little chances to improve upon that, especially if the TA instructed you about what to do.

Just wanted to add a brief update - the professor received my phone call from this morning (just FYI, I'd also e-mailed him earlier in the week) and he said he would fix my grade.

If you have already submitted the request for a regrade to the TA and instructor, then, for now, you've already done everything you can do at this time.
The real question here is how much this will matter at the end of the semester. Unless those points will take you across a "transition" point where the letter grade will change, it doesn't matter in the long run whether you get those points or not. So, ultimately, the need to fight for them depends on what weight those three points have. If the total basis is 1000 points, you're arguing about 0.3% of the total grade, and it's not likely to make a difference this year. But if it's 100 total, those 3 points become 3 percent of the total, and it's much more likely to matter.

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Waiting times and hurdles between inclusion in ESCI and getting an impact factor?
In two cases recently, my co-authors are considering/decided to submit joint work to some young journals which I think are a good match. However those journals happen to be only indexed in the Emerging Sources Citation Index and thus not having an impact factor. Unfortunately, my academic employer cares literally only about impact factors (sad, I know). I would like to make a rough guess how likely are those journals to get an impact factor in the near future and conversely, how likely is supporting those journals by sending them our work to be an issue career-wise. My results are currently not stellar metric-wise, so those publications could plausibly really make a (small-ish) difference at some point.
Did someone publish data on how long journals spend in ESCI and how much citations/publications/... they need to gather before "moving up"? I understand this will be field-specific, but really I just want to be able to make a rough guess...
The journals in question are:

Research Integrity and Peer Review (by BMC),

in ESCI since 2018
48 publications in ESCI total
130 citations (without self) according to Clarivate, including 4 citations from Nature

Statistics surveys (this one is non-profit, open access without publication fees and I really like it!)

in ESCI since 2015
22 publications in ESCI total
112 citations (without self), also including a bunch of reputable journals.

No hard and fast rules here but the answer is about a few years.
The publisher is the only one who can make the application (see this page, "Submitting your journal for evaluation"). Of course they are heavily incentivized to do so, but they will only do so if there's a reasonable chance of success, since failure means they can't submit for evaluation again for at least two years. So that's the approximate time frame: about a few years, depending on whether the publisher judges they have a chance of success and when they apply.

Just to understand this better: the "few years" is based on your personal experience? Or on something else? Would you go as far as saying that the two journals I posted are "ripe for inclusion"? Thanks!

@MartinModrák it's based on how there's an embargo period of 2 years if the evaluation fails. I have not personally handled a journal that made the jump from ESCI to SCI. As for whether these two journals are ripe for inclusion, I can't rightly say without knowing what exactly the citations are. For example you write that the 2nd journal has "112 citations (without self)". How many of these citations are by SCI journals?

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Value of my prior publications when changing fields
I am finishing my PhD and strongly considering changing my field (Artificial intelligence in computer games) to a very weakly related field (Bioinformatics). The nice part is that I got a very interesting job offer at a Bioinformatics lab, starting next spring, and I will very likely take it. So my question is a bit different than those "How difficult/common it is to change fields". Since I have no publications in the new field, I will - for quite a while - have to fill my CV with publications from the old field. I would like to know how much do those older publications count in the new field, specifically:

How valuable are publications in a different field when asking for grants (especially EU H2020 and similar)?
Should I be forced to look for a different job after spending a while in the new field, how valuable are the older publications in my job application?

The thing is that I need to optimize the effort I give to my thesis and related publications in the forthcoming months versus preparing (reading literature...) for the new field.
I am speaking about 2-3 very good conference articles, 1-2 reasonably good journal articles and a book chapter (work in progress research included). So far very few citations, but all of the good stuff has been published in the last year or still in progress, so I hope to get some non-negligible citation counts.
I am in Europe (and do not expect to move).

Are the publications really weakly-related? For example if you published machine learning algorithms, it would be considered highly-related to bioinformatics. Many people doing bioinformatics belong to CS departments and also publish CS theoretical papers, especially in machine learning and graph theory.

@Bitwise Unfortunately, they are really only weakly related (I do reactive planning, state space search, interactive storytelling - all applied to video games)

I've had a somewhat similar experience, having done my Ph.D. in artificial intelligence / cognitive modeling and then later abandoning that area as I have moved into synthetic biology (my other line of research remained consistent, but that's a different story).
The good news is that you're at a perfect time in your career to make a field transition, and that a postdoc or two is the recommended way of doing so.  The bad news is that your prior publications count for pretty much nothing in the new field, and that this is further compounded by the fact that conference publications generally do not count in biomedical fields, only journals.
The reason that your prior publications don't count is simply that they are mostly not relevant evidence of what you can accomplish in the new field.  They are evidence of your fundamental technical skills, and since many of those are transferrable, that has no doubt helped with your current job applications.  A funding agency, however, will generally want a PI with a clear track record of accomplishment, particularly for highly competitive programs like Horizon 2020 (there's likely no problem including you as key personnel for your skills, though).  Likewise, after you've been in the field for a 2-3 years, people will expect you to start having some good journal publications in the new field, and it is these that you will be evaluated on in applying for future jobs, much more than your prior AI work.
Right now, then, the thing to do is buckle down and do good work, which can then fill up the future publication queue.  Making a transition is hard, but can be very rewarding, and all you likely need is a few solid mid-tier journal publications or one really high impact publication and you can bootstrap yourself nicely into your new chosen direction.

This effect of only very weakly related publications is very unstable and largely depends on the personality of the professor, covering the full scale of

This person can bring a new competence in
This person is competent but I do not see what he could do with us
These are strange people; I need a candidate with the straight CV.

All three points of view may be or may not be true and I have heard all three opinions in more or less random proportions. This just means you will need to write more applications, otherwise seems not a problem.


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Good first-time study pre-registration website/service
For my PhD thesis in artificial intelligence, I am designing a human study where subjects interact with multiple versions of an algorithm and rate their experience. I like the idea of pre-registering a study and want to try it out on this project.
Do you have any suggestions for a good pre-registration website/service? A collegue recommended https://aspredicted.org/, which I like for its simplicity - is it reputable? Are there any better? (I have struggled to find any that seem to be in use) First-hand experiences are very welcome and I hope they will benefit other readers of this site as well.

Looking around, it seems that there are a number of preregistration sites available, but they're not set up in the way you described.

A number of journals seem to have set up their own pre-registration processes, as described in the following two articles: [1] [2]
Some labs publish their own pre-registration papers (see these papers in the Harvard dataverse database).
Some fields are trying to set up pre-registration datasets specific to their field (e.g., political science), and they don't seem to be getting much traction
At least one other site seems to mirror AsPredicted.org in both scope and function: the Open Science Foundation Registered Reports site

All that said, though, it seems that pre-registration is still in its infancy. There are many articles discussing whether preregistration is a good idea at all ([3][4][5][6], as well as [1] and [2] from above), with some pointing out some very significant flaws with the concept. Additionally, while AsPredicted.org seems to be trying to do a good job, not all study paradigms can be encompassed within it's structure.
I fully recognize that your question is asking for a location where you can preregister, and that my answer is getting away from addressing that directly. That's intentional; given that (a) the concept is in its infancy, (b) the concept is nowhere near standard practice for any journal or field, and (c) it's unclear what role preregistration plays in peer-reviewed research anyways, my recommendation would be to simply follow your own lead and write down for yourself ahead of time the types of analysis you intend to perform, and use that as a guideline for yourself. Stated differently, even if you were able to put this sort of information in a centralized database (which doesn't currently exist), you would experience no more benefit than if you just wrote it down in a notebook and stored it in your office.


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When should one change advisors? When should one keep going?
I see the continuous growth of research potential as the most important measure of success of an advisor-advisee relationship.
I do not think there is the perfect advisor for a person. I see the relationship between advisor and advisee more like a romantic relationship where success is not so much dependent on the initial conditions but on the willingness to work on the relationship. But just like in real relationships it is sometimes better to break-off and try again with someone different.
When is it a wise choice to change advisors? What are the deal-breakers? When is it better to mend and keep going?
Personally, I am a first year master student and thinking about changing my advisor. My advisor is quite hands-off so that I have more independence in my research approach which I find quite valuable and fitting. However, the ideologies, ideals, and personalities of me and my advisor are quite the opposite. These opposites caused some conflict as my blog posts (my field explained to lay-people) and similar scientific communication clashed with my advisor's personally held views. I apologized, changed some blog content to be less offending towards his views, and promised to be more careful in the future which improved the relationship. But I feel that our relationship still remains affected by what had happened and feel that I cannot express my personal views freely anymore.
Additionally, I feel that my advisor on his own is not competent enough to help me grow my research potential for long. His PhD students and post-doc are more competent in some key-areas and provided valuable advice so far, but I feel that they lack expertise in my special sub-field and due to the lacking experience of a seasoned researcher they cannot provide the holistic advice that is required for long-term success in research.
One main long-term goal of graduate studies is also to become independent enough to publish research and acquire grants without supervision and I think in my current environment I learn a lot in this direction. However, looking one year from now to the point where I have to write PhD applications an approach which is more short-term oriented (to improve my PhD applications) might be more fitting for a successful path in academia.
I would like to know what you would consider signs that it is better to change advisors? What would you consider unfavourable in the advisor-advisee relationship but not detrimental to growth in research potential? What constitutes a good advisor-advisee relationship in your opinion? How does all this depend on where someone is in graduate school at the moment (e.g. 1st year masters vs 3rd year PhD)? What would the ideal advisor-advisee relationship look like?
You can orient your answer along my issue but more general answers should be more valuable to the community.

Your actual questions are rather broad.  Can you focus your question to be more specific?  (and make it shorter)

I would like to know what you would consider signs that it is better to change advisors?``

1) Not getting along
2) Difference in methodology and study design
3) not willing to discuss in depth your research plans
4) treat you as a lab technician (some people like this)
 5) harrassing ( mentally, physically, sexually)
 6)changing your thesis topic frequently/ not giving you title of your thesis for long time
7) not paying much attention to you or provide you with advice that cant benefit to your progress
8) dont provide grant for your research
9) delaying consultations and skipping lab progress hours(consultation hours)
10) Steals your work
11) No constructive criticism
`What would you consider unfavourable in the advisor-advisee relationship but not detrimental to growth in research potential?

wy advisor look, talk and personally behave, these things shouldnt influence research potential
 What constitutes a good advisor-advisee relationship in your opinion?

You can become independent researcher and valuable contributor to science after finishing PhD. Your advisor method and behavior can shape you in adequate PhD holder
How does all this depend on where someone is in graduate school at the moment (e.g. 1st year masters vs 3rd year PhD)?
it is much easier to change advisors and programs in 1st year of master then in 3rd year of PhD, procedure is really hard, especially when you are until the end of studies
 What would the ideal advisor-advisee relationship look like?

I dont know, there is no unique example, everyone is different, you need to get along that is for sure, ideal situation for me is not ideal for you,
I like advisors that can be there all the time, some people and student like different style, important thing is that you can benefit from your advisor in professional sense !

You can become independent researcher and valuable contributor to science after finishing PhD. — Strongly disagree. The entire point of a PhD is to become an independent researcher. The degree is the signal that you've done it.

your sentence is tautology, I don't understand @JeffE on what are you referring when you disagree?

If my interpretation of @JeffE 's comment is correct, his point is the word "after" you use.

Ohhh, I am so sorry "after" dont exclude before @scaaahu Many PhD positions are like stuff or research assistant hire! Prospective students should avoid those advisors, In europe it is common to have sandwich thesis now, to publish several papers and you will get PhD


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Mention two-body-problem in PhD applications? If so, where?
My significant other and I finish our master degrees at the same time and thus we are applying for PhD programmes at the same time. One major factor of accepting a potential offer would be if we could study at the same university, so I feel that mentioning a two-body problem would be advantageous for both, us and the admission committee. But where do I mention this? Is a line in the statement of purpose suitable here?

If you admit me, please also consider admitting my significant other Jane Roe.

Some additional information: We both do research in computer science. While I do research in natural language processing my partner does research in computer vision.

Related: https://academia.stackexchange.com/questions/14337/should-an-applicant-to-an-university-mention-that-her-spouse-is-currently-a-stud

My wife and I applied to a large number of universities, and went to one that accepted both of us.  We are in different fields though.

You should both apply to a school that you know will easily accept you both. Not only because it may serve a backup, but because you may use the fact that you have have an option for both of you as leverage at a school which has only accepted one of you.

I would not do this. For faculty applications there is an argument to be made that alerting the search committee about the two-body problem gives them time to come up with solutions. A faculty candidate is a large enough investment on the part of a department/university that spousal hires/accommodations are a reasonable thing. I have never seen a PhD student, however, who is so good that the admissions committee would give the idea of offering a place to the trailing spouse a second of consideration. They might, however, decide you are not worth the effort if they know a partner is involved.

"...they might, however, decide you are not worth the effort if they know a partner is involved." Sorry, I do not at all understand the implication behind this sentence. There is more effort on the part of the university if they admit a student who is not single? Can you be more specific about the supposed consequences?

If a partner is involved, the university may assume that you'd rather stay with your partner if they are not accepted (which should IMO be the case). So, they may think that you are less likely to accept their offer - so they may not want to invest into you.

Do you think that they would discount the candidate with a partner, even if the partner is going to be given a similar consideration/offer? Like, do you think it likely they would pass over the candidate simply for the existence of another partner as opposed to checking to see if the other partner is separately going to receive a consideration? Because if not then it seems that there is no loss to mentioning the two-body problem: If the candidate wouldn't accept an offer where the partner didn't get accepted, that is.

It may be so. In many cases, the interviewers do not have a possibility to check if the partner is also accepted (or they may have to do their decision first) and/or if there are many good candidate, they do a "random" decision and discount people on very small factors (such as the partner's existence). Of course, this may be unfair. Anyway, while there may be no disadvantage, I don't think mentioning the two-body-problem could do any good (in a phD-interview).

"I have never seen a PhD student, however, who is so good that the admissions committee would give the idea of offering a place to the trailing spouse a second of consideration."  I disagree.  Lots of places are desperate for more PhD students and would be quite pleased to get a trailing spouse.  Remember a bad PhD student is much cheaper than a postdoc.

I had the exact same experience two years ago, also both being in Computer Science in slightly different fields.
In our case our chances were pretty similar as well. However, your sentence ('If you admit me, please also consider admitting my significant other Jane Roe') makes it seem your chances are much higher than your partner's.
If your chances are similar I would mention it in convenient places. For instance when mentioning a project together, talking in person with professors or when a university has a special place to put it (I remember U.Washington had a special field), always remarking that your partner has a similar/better academic level.
If they are not, you can always apply to different tier universities nearby (for example Boston has lots of colleges). Moreover, you should think about how strong the requirement of being in the same university/city is for you. In our case we ended up together in our top choice so there was nothing to reflect upon. However, looking backwards there's two things that I didn't expect that may be useful to think about:

Having your partner with you makes it much easier to handle day-to-day research's ups-and-downs.
PhD life has a lot more flexibility than expected: choosing a flexible advisor you could travel and spend multiple days a month together. Specially because in CS you can work from home/abroad.

"choosing a flexible advisor": I would, however, avoid asking the advisor in an interview whether I could be flexible - this could easily come across as being lazy.

@yupsi you're right; I've added a clarification. In CS you can easily work from home, so you could frame it this way.

@yupsi I strongly disagree, as someone who has both asked and been asked this. As long as you frame it correctly, it's an important thing to know ahead of time. For example, I have known some people who are absolutely opposed to long periods of remote work, and some who don't care. You need to know that before you're making major decisions about working with them.

The literal meaning of "please also consider admitting my significant other Jane Roe" is already conveyed by Jane Roe submitting an application. So you must be making an implicit statement of "please give my significant other Jane Rose special consideration*". If they would admit your SO anyway, then this is not needed, so this only applies if they decide your SO is not the best applicant. Put yourself in their shoes. If you were charged with the task of finding the best candidates for a PhD program, and someone isn't your first choice, would you bump them up simply because they're dating someone who was admitted?


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"Cold-calling" for a post-doc position in a group that cites you
I know that "cold-calling" for positions is considered very poor etiquette in the academic community. But is this the case if one "cold-calls" a group which is familiar with your work? By familiar I mean the group cited (one or more of) your paper(s), but you don't know anyone in the group personally?
If this practice is somewhat acceptable in the academic community what would be the best option for inquiring about a post-doc position?

Depends on the field (and perhaps geographic area), so what field/area are you asking about?

More specifically, I was asking about physics (theoretical, if it makes a difference). Thanks!

Maybe you can talk to a senior (your advisor) that knows these people?

@Bubble well, you might have to be even more specific. In (some parts of) biophysics cold-calling is the norm, in particle physics it's unusual but not the worst thing, and there might be other subfields of physics in which it's considered quite rude.

@DavidZ It's a somewhat different field. Condensed matter, though I am interested in the research they're doing there.

@Prastt Advisor doesn't know them, either. We're in a somewhat different field.

If the group is already positively citing your first-author works, then I would say that it's not really a cold call.  You may not have met, but when you get in contact, they will have some reason to distinguish you from the constant barrage of random people who email them asking for postdocs.
I would thus recommend getting in touch by noting your shared interests directly, including the fact that you've noticed their citations of your work, and being very straight-forward about your interest: you're going on the postdoc market, you've noticed the shared interests, and want to get in touch to see if there are good opportunities---either for postdoc or otherwise.  This way, it's primarily about the professional relationship, not the job application, which is what's best for you as well.  If they really do like your work and have funding available, they may jump to hire you.  If not, it is likely to still help build future collaborations and other opportunities.
If they are negatively citing you or if you're Nth author on the works they cite, however, then it's effectively just a cold call, and you should follow the conventions of your field there.

Yes, these are first author publications. I will most likely follow your advice. Thanks!


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Self-plagiarism: Copy part of thesis for blog posts?
I am currently writing my master thesis and I am also running a popular blog about my research area. Some people asked me about certain topics and if I could write about them on my blog to make them more understandable to newcomers in our field.
Now it is tempting for me to just copy parts of my yet uncompleted thesis and mash together into blog posts. This will help me to save time writing them (I usually do not have the time) and it will benefit others. However, I worry that people see that as self-plagiarism. In particular people on the thesis committee might say I copied parts of the thesis from the internet.
What would be the right way to save me from trouble here. Shall I cite my unpublished thesis, or should my thesis cite my blog posts? Should the blog posts have clear indications that I copied verbatim from my unpublished thesis? Will I get into trouble if people see that in my thesis I copied verbatim from my blog posts (if I cite my blog posts  rather than the other way around).

You should do two things:
1) Discuss this with your advisor. He/she will know the regulations better than we do.
2) Make it clear on the blog that you the blog-writer and you the thesis-writer are the same person, e.g. by using your real name.
Another issue, that you didn't yet consider but that surely needs consideration is the copyright for your thesis. At some universities, the department/university library wants at least some rights on your thesis. If they then find parts of said thesis copied verbatim to an online platform, you might get into trouble. It might well be that this is not the case at your university or that they don't care as long as you cite your thesis, but this is something you need to clarify before posting stuff.

Once you've established 2, there's no need to cite your unpublished thesis nor your blog. Nor is there a need to indicate that you copied verbatim from my unpublished thesis. (That said, you may like to mention that your results have been disseminated via your blog, because dissemination is a contribution.)

sometime citing thesis in blog post is not allowed especially if your work is patent by the university.

@Kumar I think you mean: sometimes universities must be offered the opportunity to patent results, prior to any publication (including publication in a blog post). Merely citing an unpublished result needn't interfere with the patenting process.

Self-plagiarism in your thesis from previously published work during the course of degree program is totally acceptable. Even you don't need to cite your published work in thesis. However, this applies to work published in established journals and conferences, for blog posts you must check rules and regulations of your university. I my school it is not allowed to write a blog post before registering a patent or publishing work in Journal, conference or thesis.


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Entering academia as a high school dropout
I have a strong desire and determination to contribute to society by expanding the knowledge in my field of interest, but I feel that I am failing to get into a position to fulfill this dream. This is mainly due to being a high school dropout who now gets his bachelors through distance studies. How can I improve my chances to go along the path to become an academic?
My background: I failed high school mainly due to my learning disability, dyslexia, but depression and social anxiety also played a role.  Two years after dropping out I secured a placement for a mathematical and technical software development apprenticeship which included a vocational school with mathematics at an undergraduate level. I finished the apprenticeship as the best regional apprentice. My teachers also recognized my ability, but in the end I was unable to attend a normal university because I did not have the required high school degree.
I decided to start a part time distance BSc (Honours) degree with The Open University which does not have formal requirements. When I had enough money to fund my degree I quit my job as software engineer, to study full time and do some independent research in a mix of deep learning, high performance computing and mathematical optimization applied to natural language processing.
I could graduate July/August next year and probably score an upper second-class degree (first-class and lower second-class are possible). My research so far did not yield any significant results. I was able to improve on algorithms that are in the literature, but the improvement was only very marginal. I gained a lot of experience through my failures though, and I might be able to publish a paper about the some new but mediocre result and also give an overview over the small niche I worked on to help researchers to not tap into the same mistakes as I did.
My Problems:

My degree does not have a bachelor thesis where I could show off my ability of doing research
I do not have contacts with other academics that work in my area (The Open University does not do any research in my area of interest, and it is difficult to get people interested to work with someone who has a background like I do)
I will have good to great letters of recommendation in industry, but not in academia (a letter of recommendation from a professor/tutor at the distance university will be rather weak)
My field of interest is rather narrow; Master placements or PhD programs at the universities that do work in this area are very competitive, and it is unlikely that I will succeed with my current work/background/connections to secure any such placement. I do not know if I can work on other topics in mathematics or computer science with the same motivation and determination as I do now in my current area of interest.

One advantage of doing distance studies is that I can work and do internships at the same time as studying. I could spend an additional year on my bachelors and do some research in the meantime to graduate with some papers. But I am 27 already and I feel that I cannot spend much more time on my bachelor’s degree.
There is already some good general information on academia.stackexchange concerning how to improve an unfavorable background. But I feel that my situation is rather different as a distance student. I mainly feel that I failed to create a social network within academia because there is so little opportunity for me, and more specific information how to overcome this isolation from other academics would be appreciated. For example should I try to publish a paper first and then reach out for interships in research, or should I should try now without anything research related results in my hands?
To put the question in more general terms, what can a socially isolated student with weak background do to extend his or her chances to enter academia?
If I continue to finish my degree next year, rather than doing an additional year, I will need to apply for a masters quite soon. What kind of masters should somebody with potential but weak background chose? How can I polish up my application for such masters? One simple thing which comes to my mind is to blog about my attempts of doing research – does this make sense to invest time into?

Conferences are one place for people in industry can easily and casually meet academics. Look for conferences in your field of interest over the next year in your country, or where you manage to travel. For CS the main two associations that would sponsor such conference are IEEE (IEEE Computer Society and IEEE itself) and ACM. For Math/CS there is also SIAM, and likely several I am not familiar with.

First of all, before you even think of anything, you need to change your attitude towards yourself. I have a feeling that you underestimate yourself and use yourself as an excuse for not doing something.
It doesn't matters if you have a substantial research background to apply to grad school. Usually Masters programs do not even put too much weightage on that. Plus, you have great recommendations from industry professionals. May be that was what you always liked, and that is what the admission would be based on. The department would see your interests and how you have put them to good use. They pay much attention to your personal statement and letters of recommendations, along with your undergraduate transcripts.
To successfully get admitted, do not day dream! Research on the institutes. Decide on them based on your profile and the kind of profile those universities look for. Keep practical expectations. Show them the interest in grad school. Show them that you would be able to get something out of your grad studies and that they are not wasting their resources.
Do not get disheartened if you don't get your dream university, there are always future chances.
Oh and did I mention, have atleast 4-5 universities in mind, when you plan to start applying to grad school.
Without a research experience, PhD might be tough to get in to, but not impossible. But masters is the safest bet.
Good luck!! :)


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Career Paths for Mathematics and Physics
I'm just looking at the Mathematics & Physics program at University of Toronto (I think it's like Mathematical Physics, correct me if I'm wrong), I'm wondering what career paths I can choose if I take this program.
Would this allow my to work in either field or just in the physics field? And would this allow me to go to grad school for either one I want, or is it restricted to one of the two fields?
If it makes any difference, here's a link to the university's program calendar:
http://www.artsandscience.utoronto.ca/ofr/calendar/crs_mat.htm
Thanks.

Go to which ever school that allows for the most flexibility in making your choice (i. e. The ability to take classes in both to decide which you like better). It is hard at this stage to say which is best until you decide on either mathematic or physics (mathematical physics as a subfield itself tends to be more in mathatics depts in my experience, but it depends on subfield).

It depends on what you mean by "career paths".  Outside academia, the possibilities are very broad and largely off-topic here.  Within academia, the main question is preparation for graduate school.  To get into a good graduate school, you'll typically have to go beyond the minimal requirements in even a very strong undergraduate program.  It's not likely that this problem by itself would prepare you well to apply to both math and physics grad schools.  However, you could presumably apply to whichever you prefer if you do some additional work (courses, summer research experience, etc.).

I'm an alumnus of the Mathematics and Physics specialist programme, if that's what you're looking at, and my (typically small) graduating year had people going into pure mathematics, applied mathematics, and physics graduate school; I myself am a pure mathematician with research interests related to mathematical physics. You'd definitely be able to apply for summer research in either department, but to some extent it would be best to figure out whether you want to do mathematics or physics by the end of second year, some time in third year at the latest...

...so that you can get at much research experience and advanced (viz, graduate) level coursework as possible in the field you really want to graduate school in. If it's physics that you want, you should make sure that get enough lab courses in for the graduate schools you're applying to, since the math and physics specialist requires substantially fewer lab courses than the straight-up physics specialist. In any event, the traditional target audience for the programme is people preparing for grad school in mathematics (with a possible eye to mathematical physics) or in theoretical physics.

For grad school applications, after making it through GRE cuts, the biggest decider will be the research that you've done. You'll want to develop programming skills in multiple languages, even if they don't cover them in class. For math and physics, MATLAB, Mathematica, and R are the most commonly used languages. If you don't find any research opportunities at Toronto, look for REU programs in the summer elsewhere. A math/physics degree can get you into grad school for math, physics, all manner of engineering (I went from astrophysics to aerospace engineering), chemistry. There are probably others as well.
Outside of grad school, the options are pretty varied. Again, if you can program that will open many more doors. My friends from undergrad in physics went on into banking/economics, General Electric, CERN, Seagate, Boeing, Lockheed Martin, the air force, and NASA. The majority, however, went to grad school. That keeps all those former options open, but also opens up the academic track (becoming a professor or a research scientist at all kinds of places like NIST or NOAA, but there are hundreds).


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Should I mention this health issue I had on my graduate school application?
Towards the end of one particular semester, I had some health issues which forced me to travel in order to get treated. This resulted in me missing the last two weeks of courses and all my final exams. I arranged so that I got grades of "incomplete" in all my courses, until I took the exams and finished my coursework after my recovery. I ended up doing okay, but I did get a B+ in a very important course. It's hard to say whether this was the reason for that, though. Should I mention this on my graduate school application, or will it look like I'm just making excuses?

There isn't even a need to make excuses for ONE B+ in your undergraduate work -- even in your major.  It would be different if you had earned several B+'s in a master's program.  Please don't mention it or give it another thought.  Just concentrate on celebrating your recovery, and enjoying your studies.  And congratulations!

In my view, an outlier in the marks is always possible and, unless you apply for a very competitive position, supervisors will account for some slack; often, the most creative people may have blips, and good supervisors know that.
Since you clearly state that you cannot even be sure that the B+ is due to your illness, it may indeed radiate an element of "excuse". However, as dan1111 says, depending on the illness, it may signal your ability to overcome adversity.
Perhaps the cleanest solution is to just mention just factually that you missed your 2 weeks because of the illness, postponed the examinations and retook them after recovery, with the results shown and leave the conclusions to the readers.


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Graduate school applicant visiting a department he has applied to - advantageous?
I've applied to several graduate schools in the US for a physics PhD. As I currently have some free time, I'm willing to travel around and visit graduate schools that I've applied to. My current research advisor (who is also one of my letter writers) can possibly establish contact between me and some of the people I have expressed interest in at different schools. My question is that whether in your opinion this is something that can actually boost my chances of getting admitted (provided a meeting with a person of interest goes well). Could pursuing this plan be advantageous?

Many departments explicitly tell applicants not to contact anyone at the department between the time of application and the time of the decision, so whatever you do make sure it is not perceived as trying to influence the people responsible for the decision.

It may not give you an advantage at being admitted, but it could help in other ways.  I visited my first-choice program (also in physics) around Thanksgiving of my senior year, and scheduled meetings with two PIs I wanted to work with.  The first stood me up, but the second took several hours to meet with me and show me the lab, and at the end of the visit he told me "If you get in and want to start early, let me know and I could probably give you an RA for the summer".  This ended up being a big help -- the visit made clear who would be better to work with, and also helped me get started with research shortly after graduating.

Definitely true.  Even if it doesn't help you get in, it can help you figure out whether you actually want to go there if you do get in.

It depends when you are visiting. At my department, we welcome visits in the Fall semester -- before the applications are due. I'm not sure if these visits are that useful -- a few times, I've been much more intrigued; but many more times I've been convinced that the applicant is not suitable after an in-person visit. If you do come, come well prepared (i.e., knowing which faculty you want to talk to, what questions you want to ask, and what impression you are seeking to make). (see FN1)
In the spring semester (after applications have been handed in) we tend to disincline visits initiated by candidates.  (See FN2 and FN3)

FN1. I do think that campus visits are very useful for candidates. You get to meet faculty and see what they're like and more importantly - talk to other graduate students. In many cases, you can glean insight about the department that can help improve your application.
FN2. We interview all candidates by skype or telephone in the third round. We tend to fo2llow the same protocol for all such interviews so as to keep the playing field equal.
FN3. After we have made offers to finalists, we then again welcome visits so that we can convince them to come to our program.

During my last semester of undergrad, I happened to be driving by a department I was applying to on the way back from an out of state trip, and decided I'd stop by to check out the digs. The administration evidently saw this as me gaming for admission, and were not very welcoming. They promised me a tour and then left me in a waiting room for a couple hours, before finally telling me that the advisor did not have time and I should go home.
I ended up going off on my own and meeting some of the professors there who I would have wanted to work with. That part was fun. I got to have some cordial conversation with legends in my field. One of them had heard through the grapevine that I'd just published a paper with his coauthor, and requested a preprint, which I emailed to him later. I think this may have improved my chances for admission; however, the experience of networking with these professors was surely of greater value (and non-conditional).
After hanging around for a few hours, I ran into a couple of grad students, and took them out for a beer. They told me that the cold and dismissive treatment I'd gotten from the staff was actually just how they acted all the time. I learned that, internally, the department refers to itself as an engine in a factory school, and that many of the TAs felt undervalued and exploited, rather than just "roughing it" on a low stipend.
The whole experience painted a picture of a department that has abandoned common courtesy and respect, which I personally place a lot of value in, so by the end of the day, I decided I would turn this school down, if admitted. And as it turns out, I never had to, because they never sent me a decision letter one way or another! (I did call to ask check my application status once, just out of curiosity, and was put on hold until the system hung up on me. Go figure.) I might have been very upset by this if I'd never stopped by, but since I had, I felt free to accept an offer from another school without concern for this loose end. So, sometimes it can be very worth it to visit a department, whether it improves your chances or not.

Yes! Most definitely seeing your potential supervisor will effect their decision. Also, it might effect your decision in later stages, when more than one will accept your application. Remember, to also look at their environment they conduct the research in; as well as having a talk with one/two of his/her current Ph.D. students.

One of my students (I think my top undergraduate student ever) did, indeed, visit his top choices of graduate departments (all of which had already accepted him and offered financial support).  I think that the three departments even paid airfare for him to come.
So, I guess, this was not about improving chances of being admitted.  This was those departments trying to improve their chances of getting the student.

The answer depends a lot on the department. A POI at one department explicitly said that, at his particular department, visits had little to no effects. Then again it's an Ivy League physics dept, top-20 in the US; I wonder whether there is a correlation between program prestige and the impact of a visit.


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Asking to see a manuscript in preparation
Is it considered bad etiquette to ask to read a manuscript in preparation that appears in the citations of a paper? (It was cited in a paper from 2001 - I am not sure it has been published; I cannot find it - although the title may have changed...?)

Did you check the author's CV? If it's not there, the polite way to ask is if it were published under a different title. Be prepared for utter silence and a non response if not.

I have just realized what lack of a publication implies and I am feeling pretty embarrassed.
I mean that even if it were not published at all, I would like to read what exists of it --- is it impolite to ask for that? (guessing that it is, but I'm not sure if that changes things)

No worries. See http://academia.stackexchange.com/questions/26024/is-there-a-difference-between-forthcoming-and-in-press/26032

I can imagine that it might not be well-received, for the reasons given in other comments... but at the same time, it has been cited by them, so in the interests of reproducibility it seems perfectly reasonable to enquire after it! Especially if the paper that you are reading relies upon it in some way...

@pen What does lack of publication imply to you? As I see it, there could be many reasons. For example, it could be mostly a student's work, but that student left academia. Or perhaps the authors discovered errors in the manuscript and didn't know how to fix them. Regardless of the reason, it's perfectly alright to inquire politely.

@Mangara I was thinking of rejection --- thanks for pointing out these other possibilities.

No, it's not bad etiquette.  Most people will be happy to know that someone wants to read their work.  Of course, you should take the time to try to find it yourself first.  It may have been published under another title or in a hard-to-find place (like some conference proceedings).
From the comments, it seems that you're worried about hurting the author's feelings by reminding them of a paper rejection.  I don't think you should feel that way.  Rejected papers are part of a normal academic career, and in any case you don't know whether that paper was rejected.
If you ask me for a copy of a paper that happens to have been rejected, I'll send it to you.


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What is the most common way to change fields in academia?
If you are a young scientist, how can you change fields? Is it better to make one big leap and apply directly to a new job or postdoc or trying to make small consecutive steps during your current job? What should be those small steps?
Just for explanation - in this case it is not like a change from literature to rocket science. The change would be in one broader field and some theoretical and statistical background would remain the same. What would be the best strategy, if you have some good papers in top journals in your field, but you do not have any papers from a field where you would like to move? And there is no such laboratory in your country, so there is no personal contact.

Related questions: 1, 2, 3

The "most common way" involves personal contact, which you have ruled out.

If this is a move within the same broad area (or a closely related field) your best bet is to get or keep a job in your own field, and then begin finding research that transects both of your fields. For example, if you're in political science currently and want to shift to, say, geography, then begin by publishing research on geospatial politics until you have enough publications in geography journals to get a geography job. Often, schools will have interests in more than one field, and so a background in more than one can be a benefit when looking to advance.
What would be best is if you are in a school that has both fields of research - in which case collaborations would be the easiest way to go. I'm currently in the process of doing something similar, but I have the benefit of being in a very broad school that has both people in my own field, and people in the field I am shifting to (slowly, but surely!).


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What to do in recitation?
Forgive me if this is not the right place to ask pedagogical questions, but it seemed the most appropriate.
I am a TA for a programming/CS course. This is my first time teaching recitation and I'm not really sure what the best approach is. What I've been doing is covering what the professor asked me to, with a mix of lecturing (which I don't really like as I feel the students get enough of that) and me solving problems on the board with their help (which is OK but it's usually the same students answering the questions).
I can think of several different methods of recitation:

Lecturing (elucidating ideas or going over proofs)
Solving problems with the students
Having a class discussion, which sounds great, but coming up with discussion topics for this type of course is difficult, I feel
Having the students solve worksheets (which seems unnecessary considering they already have enough homework)
Or having them work together in groups to solve more difficult problems

Can anyone provide insight for which of these ideas are most effective?
Further information: It's a summer course, so the pace is pretty fast. Furthermore there are three recitations a week, each an hour and a half. It's the second CS course, so it's mostly programming (data structures and safe code) with a bit of theory thrown in.

Ask your instructor. It is their responsibility (and secondarily the department's responsibility) to train you, not just toss you into the classroom.

@JeffE I agree that's how it should be, but that is unfortunately not what's happened. I'm in the fourth week already, and I've gone in totally blind, just winging it. The instructor seems to just want us (the TAs) to lecture. He doesn't provide much guidance.

Have you asked?

I train graduate students to lead biology discussion sections, but the philosophy should transfer...
I think your instincts are excellent - students do not need more lectures. What they often need help with is figuring out what they do not understand, and learning how to overcome being "stuck." That, and practice with feedback. Some suggestions, particularly since summer courses are so fast. I'm going to assume they have homework, and that the homework can be worked on in a discussion environment (you will not be "doing their homework for them").

Instruct students to bring their homework problem set. Look over the problems yourself the night before, and determine the easy ones from the hard ones, and make notes to yourself where students are likely to get stuck.
When students arrive, tell them to start work on a difficult problem. Plan on giving them 5-10 minutes -- whatever they need until many of them slow down. Walk around as they work and just see how they choose to work.
After several are stuck (it may take you practice to figure out what question to use to get this level of difficulty), have them get into groups of three and compare their techniques and what they found difficult. Walk around again and ask questions like, "Tell me how far you are. Can you show me a part that is difficult? Can you get out your lecture notes and find the section relevant to this problem?"
Usually at this point you will see a sticky point that more than one student is wrestling with. Now is a great time to pull everyone's attention back to the front of the room and you can work through that problem (or one similar) and answer questions for 5-10 minutes.
Have students return to the problem and complete it. Have them go back and do a simpler problem on their own to reinforce.
Rinse and repeat.

Using discussion time like this makes students happy because they are getting their homework done. Smarter students help slower students, which keeps them engaged. You as an instructor learn a lot about what students don't understand, which is often a complete surprise. Plus, it's active and not boring and doesn't require a huge amount of prep.
If this gets really dull, you can have small-group competitions where students have a single sheet of scratch paper and have to respond to a prompt you flash on the screen. I like to split the room into the right half (five groups of 3 students) and left half (five groups of 3 students) and have competitions like this for "basics" material. The half of the room with the groups with the most right answers gets a point for each round of competition. Everyone participates, but the answer is the group's and so shame for wrong answers is reduced.

Thanks so much for the detailed response! I'll try to do implement in my next class... it will probably take a couple tries to go smoothly though. Have you found that the competition really doesn't cause students to lose self esteem? College is already very competitive, and in general I'm very fostering a competitive winner/loser atmosphere.

Use competition delicately and only occasionally. In biology I reserve it for things that everyone should know (vocabulary) or things nobody will know (applying basics to new systems). Answering ing groups makes it more like pub trivia and less like war. But if your students don't respond well, don't use it again. Part of the fun of teaching is experimenting.


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Master's Degree Admission with a different Bachelor's specialization
I currently hold a bachelor's degree at Biomedical Engineering and I want to do a Master's Degree in Computer Science at California.
Would that be a problem?
Since I don't have a high GPA and the proper specialization, should I pursue a certificate of Computer Science first, increase my GPA and then apply for the Master's?

I graduated with a BS in Bioinformatics and I have a Master's in Computer Science. As long as you meet or take the pre-requisites, the education side of the Master's is covered. The GPA can be supported through stuff like the GRE, work experience, or whatever else you can think of. I'm not sure what type of Certificate you're looking for in Computer Science. I don't know how schools find certifications to be.

First of all, thank you. I thought about a certificate of achievement from a City College, like this one > http://www.sbcc.edu/apply/files/cert/compsci.pdf .
What do you think?

Those look to be prerequisite courses, for sure, but depending on the type of Master's you are going for, they may not be sufficient. An industry Master's, that's probably enough.

Every school is different, but as the department chair told me when I asked if I had a chance of admission in the CS Master's program with a BS in math, "If we only accepted people with a BS in CS, we would have no program."
Talk to the graduate coordinator at the dept. They may have some prereqs you need to take first, but this is a situation they've encountered many, many times.

I have an Engineering BASc and went on to do an MA and then PhD in Philosophy winning major Canadian and provincial scholarships.
Universities varied widely in how they interpreted their requirements for how many additional courses or years of study I would need for admittance to their MA programs. Some variation was likely due to the discretion of graduate admissions officers. It helped significantly that I had excellent marks, since one of the common admittance criteria is evidence that you will succeed as a graduate student.
I had taken a number of philosophy courses part-time after graduating, and got excellent marks. Several universities wanted me to start in second or third year in a second bachelor's program and then complete it in order to meet their requirement of a BA majoring in the discipline. One was willing to provisionally admit me once my total accumulated credits in philosophy amounted to the equivalent of those required for a double-major in philosophy (and another subject), which was their normal minimum requirement for background in the discipline. This allowed me to start after just 8 months in a specially designed qualifying program.
I don't think a Certificate is useful for entrance into a Master's. The courses themselves, how you do in them, and the reputation of the institution where you take them is more important.

I have the same situation. I applied for a CS program after finishing a bachelor in Biomedical Engineering. I just gave an interview just because my bachelor was not relevant and then they accepted me. Depends on your field of interest and your background in that field.
My field was Machine Learning and Pattern Recognition sand I used to apply them to medical data/signal/images and I just continued the same as a master student in CS. As you see the huge overlap between these two made it easier for me so first think of what you are going to do next and some tips:

You need to know programming! in BME we used to use MATLAB but this is not enough for a computer scientist.
If you are going to do Analysis (algorithm based fields, data analysis and etc) you need to have a good impression of algorithms and math. Of course not professionally but you need an algorithmic & mathematical mind to work in analytics-based fields of CS.
If you are going to do something more related to software stuff or computer networks or information technology, you need to be comfortable with different softwares (depending on the field) and operating systems.
And finally the most important point: All what you read above was only my experience and point of view!

Hope I could help and good luck!

That's cool @kasramsh . Actually, I'm an Android developer with 3 years of programming experience, that's why I'm willing to do so. :-)

So go for it @Machado! you'll find your position in the community soon or late. Good luck!

@Machado, your experience in the field will be heavily weighted at some schools.  I don't know if the school in California takes that attitude, but some schools do, such as UW Madison....  Look at the prerequisites for the courses you're interested in taking.  That will help you detect any gaps you might have; you might want to resolve those as an unmatriculated student before starting the master's.


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How to quote a previous paper with different authors?
I am writing a paper that builds on a previous one, where another author was present. How should I quote the previous one?
For example:
"In a previous paper [1] we proposed ..."
or
"In a previous paper [1] we and a collaborator proposed ..."
What is the correct one both scientifically and linguistically?


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where to find the year and conference of a scientific article?
When writing the references at the end of my internship report, I needed to cite all the information that needs to be said about the scientific articles that I used while writing the report. But these articles, most of the time, do not mention the conference or journals in which they were presented nor their publication date. Is there a website in which one can have access to this kind of information about any scientific aticle? BTW, I am talking about the field of computer science.

You mean like Google Scholar?

Thanks aeismail, Google Scholar helps. Is there a website in which one can find the latest articles of a certain field or a certain subject (computer science for example)?

I'm not in CS, so I don't know if there's any specific aggregators for the entire field. But pretty much every journal will allow you to receive journal contents by email. (There are far too many journals to be able to keep track of everything!)

If your university subscribes to it, MathSciNet is a very good tool for this as well. Both this and Google Scholar let you export BibTeX directly (and probably other formats, but I've never used them).

I'm a bit confused. Scientific articles generally include all required citation information on the first page.

Rereading this question, I note a second point of confusion. Many academic papers (depending on the discipline) were never presented at conferences... so part of your conundrum could be that you are looking for data that does not exist.

@JeromyAnglim Citation data in many CS conference papers, even from major publishers, is incomplete (only the conference abbreviation and date) or missing entirely. And unofficial preprints, either on arXiv or on authors' web pages, generally have no citation data at all.

Background: Many researchers put their articles for download on their personal web pages. As most publishers insist on not allowing the researcher to put the "official" version there, but rather only the self-made PDF, this leads to articles often not having the journal/conference information on the first page (as this would require changing the article a bit, which is a bit of work to be done). Also, self-archived versions often appear before the conference, so that page numbers can only be missing, and might not be updated later.
Actual Answer: For CS, a good strategy is to just type "DBLP " into your favorite search engine. Many papers nowadays are listed on the DBLP page, which also allows you to just download the bibliographic information.
If a paper is not listed on DBLP, just searching for the paper title often yields the publisher's page of the article, which should have the information available.
If searching for the title does not yield any results, then the paper could be a limited circulation pre-print, which is stricly speaking not citeble. However, in such (hopefully few) cases, it makes sense to ask the person who gave you the article for bibliographic information.

It's rather unusual that the final version of a published research paper does not display the publication venue prominently on the first page of the paper. If you can't find anything there, try to remember where you got the manuscript from.

Did you download it from a website? The website should have contained all publication information.
Did someone give it to you directly? Ask that person for details on the publication information.
Is it copied out of a book? Try to find that book again.
If you don't remember where it came from, you simply may want to try an internet search for the article's exact title and all authors - if there's anything to be found, that should come up among the top results.

In some cases, you may have obtained a manuscript which is not formally published yet. After following the above steps to ensure that no published version is available in the meantime, these manuscripts can be cited as "Unpublished", "Technical report", or "Preprint", together with the information how to find them (URL, University where they were prepared, or other) and the year they were written in.

Elsevier's Scopus has pretty decent coverage and can also be used to create custom alerts that will email you when new manuscripts(s) matching a set of keywords (or authors) are found. With regards to proceedings it gets trickier as some times they do not get published by a source that gets captured by an aggregator (be it Google Scholar or Scopus or something else).

SCOPUS's depth greatly depends on your field of study. It's nearly useless in mine. Are you answering specifically for CS?

I was under the impression that Scopus's coverage is universal? Out of curiosity, what is your field? p.s. yes, I have used Scopus for CS amongst other things.

Most of my publications are in philosophy. Many don't show up in SCOPUS. I first learned about SCOPUS when applying for a highly-skilled worker VISA in Japan -- they only check SCOPUS to count publications

@Spiros That's exactly what SCOPUS would like you to think, but it's just not true, even within CS.


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What research expenses to request for early career fellowship?
I'm applying for an early career fellowship in the UK. The fellowship has a budget of up to £6k per year for research expenses to further the fellow's research activities, which must be requested upfront. Other than travel to conferences, small equipment, and perhaps organising a workshop, does anyone have any good ideas about what this money might be spent on?

Software licenses and open access fees maybe? Also don't forget money to invite people to come to visit you.

Books? At least in some fields, we still read those old musty things. :)

If you plan to participate one or two international conferences than is is not that of a big money. Also, depending on regulations you may be able to get a computer/laptop + some software you need for your work.

The following list is very subject dependent, but some items you might want to include are:

High Performance Computing time (e.g. comp-sci, physics, maths, chemistry etc)
Lab or equipment hire costs
Research technician time (i.e someone who might help acquire data or do some other more routine tasks)
The all-encompassing "computer-consumables" (that covers quite a lot)


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Is there any way to automatically link in-text citation to individual references on the reference list?
I have an article with in-text citations and list of references. I have not used any of reference managers, just used word.
Is there any way to automatically link in-text citation to individual references on the reference list?

I'm not sure how to do this in word but PDF LaTex outputs can do this quite easily.

As above, I don't know of a way to do this with Word, but if you use LaTeX, this can be done by including the hyperref package.

This solution works in Word 2010. Other versions may have different mechanisms. Move the cursor to your literature reference. Go to the "Insert" tab, click "Bookmark" in the "Links" group - now you have a bookmark for this particular reference. Then mark your in-text citation, go again to "Insert" and click on "Cross-reference" in the "Links" group. You'll get a dialog where you can link to the bookmark you previously established. Unfortunately, you'd have to do all this manually, no automation there... I guess you would need to use a ref manager or LaTeX with hyperref.

@CTKlein and Mangara: no, there would be the exact same problem with LaTeX if I understand correctly, and it cannot be solved automatically. If I read well, the OP has written citations in text form "[Knuth, 85]", not "\cite{Knuth85}", and wants to convert them automatically to the latter (or an equivalent version with Word).

In any case, @user92953, please edit the question and be more explicit or add an example. It is difficult to understand your exact problem. What do you mean by "link" for instance?

After reading @FedericoPoloni's comment to my answer, I am wondering if I misread the question. Do you want to do this for future documents or you want a way to scan existing text and auto-generate references for them. Please clarify because I think one and it seems at least one person thinks something else.

Yes. It is quite easy to do, once you know how.
First, go to the References tab, then click on Insert Citation and Add New Source.

Next, fill out the information as appropriate.

When you want your References List produced, go to Bibliography.

This is extremely helpful when you need to change some detail (say publication date) and you have many citations to the same material. Change it in one place and Word will update all of the in-text citations as well as the references list.

I don't think this is what the OP asked for (see my comment to the question).

@FedericoPoloni They are asking how to automatically add a link to a reference. In order to do this, it might be necessary to extract the document's title using a citation parser.

Highlight the link, right click, click "Link", Make sure you select the tab on the right that says "Existing File or Web Page" then click OK.


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Journal publishing timetables
I am about to submit my first article to a peer-reviewed journal.  I have basically already decided which one, but I have a shortlist and am still in principle considering my options.  One of the questions I have is about the timetable for eventual publication.  What should I expect?  (In the long run, it probably won't make a large difference, but for me, right now, it would be nice to get something out the door this side of New Year if it is at all possible.)
I am puzzled by the lack of information about timetables and deadlines on the sites of these journals.  I have looked at journals from related fields in the past and they all seem to be very secretive (or undecided?) about these things.  Is this on purpose?
I guess I can infer something from previous publication dates -- a biannual which was last published in May might be slated for a next issue in November and probably have a deadline several weeks before that, which I probably won't make (it is now late August and the review process would apparently take several months).  But why don't they simply put a date up front so authors won't have to fret?
Would it be out of line to email the editor of the journal and ask about the planned deadlines for the next couple of issues?

Trivia: if you were in the Italian system, it would be wise to do the opposite and look for a journal that will not publish your first paper before the end of the year. Indeed, some performance metrics are rescaled based on "years since your first publication". (I know, it's stupid, but that's how it works).

@FedericoPoloni: Thanks for the tip, any pointers for more information?  I'm in Finland but I won't personally be eligible for anything relating to expedient completion of my degree (I have been working in industry for many years, and am returning to academia as a side project).

I guess it won't matter much to you then. As far as I know, this behavior of the Italian system is just an oddball. I can't find a reasonable link in English explaining the details of the system.

What field are you in?

For this publication, corpus linguistics.

In most fields and for most journals, there is no time-table because it takes as long as it takes.
This means that after they receive your paper, they will send it out to a few referees, which have to be found first. How long finding referees takes is not under the control of the journal editors - they have to ask people until three of them said "yes".
Then, the referees have to write the review. Typically, they have about 3 months of time for that, and a request for extension is almost always granted. So think of it more like 6 months. Exceptions apply here (e.g., for the journal "Science", who manage to enforce shorter reviewing times).
Then your paper maybe accepted only conditional to changes. You do the changes within a month or so, and then reviewing starts again. So there goes another 3-6  months in addition to the time that the editor needs for organizing the process.
This means that for most reputable journals, there is a long pipeline of papers in-progress and whenever they make a new issue that is not a special issue, they take some papers that already went through the process and publish them. There can be a substatial "out-queue" of these papers, which is why some publishers came up with the concept of already publishing "done" papers before the paper has a journal issue assigned (e.g., for Springer, this is called "Online First").
As an example, in computer science, an overall time span of 1-3 years is common.
As a bottom line, the time to publish can only be influenced by the journal editors up to a certain, small, degree, e.g., how swiftly the editor performs actions whenever there is something that she can do at the respective point in time. So publishing a time line would make little sense.

+1. Some journals/editors are faster than others. It would make sense for the OP to discuss this with his advisor, who likely has already published in journals the OP is considering.

This will depend significantly on what your field is. For me, there would be no way anything other than a very short (and preferably very significant) paper would appear this year. For others a paper will be bordering on out-of-date by then (I'm told).

I personally use the information given in published papers (i.e. Elsevier journals provide dates for submission/submission after revision/acceptance or publication ). This can be somehow indicative yet I've personally experienced both ends of the spectrum (later/earlier than the average turnaround).


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How to deal with mistakenly reporting old GRE percentile scores
While filling my applications for PhD in computer science I used the percentile scores that I have on the paper score report I received from ETS by mail 3 years ago. However I just logged in to my GRE account to order a copy of the scores to be sent to a university, and I was surprised to see that the percentages have changed:

Verbal increased by 1%
Quantitative decreased by 2%
Analytical writing increased by 4%

Will my application get flagged for reporting wrong percentiles? Should I contact all the universities that I have applied to and inform them about the change in percentiles?

Well, you can contact the schools to change it on your application. I do not think that is gonna be a big deal since the admission staff always have acess to your application, and mistakes like this could always happen. Also, they gonna see the official report from the ETS, and they may not look at what you wrote in your applications. Good luck