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Disposing of old written notes
Many a times, I study some topic or research paper and make my own notes (it could be figuring out the math in paper, or something else). But after say 7-8 months, these notes just pile up on table and when I look at them I don't think I will be using them for any future work. But I also feel like I'm trashing my study, and the effort was pointless if I dispose of it. Is it okay to dispose of them? What strategy do you have about disposing of written notes?

Get a filing cabinet, or some bank boxes, and a couple of packages of manila folders.  (Unless you want to scan everything, as others have suggested.)  You will feel better if you hold on to your notes, and you may want to go back and consult them later.

Your notes are not your study: your study is your study.

you may want to go back and consult them later — Or you may not.  I've been writing notes into research journals for decades. The act of writing is immensely helpful for organizing my thoughts, but I honestly don't remember ever looking at anything in these journals more than a couple of weeks after I wrote it. Once I admitted this to myself (and got over the "sin" of actually discarding a book), I started recycling each journal almost as soon as I fill its last page.  (On the rare occasions that I think I have a good idea, I latex it up. Those notes I do look at later.)

Quick rule of thumb: Keep papers for a number of weeks equal to the amount of minutes it takes you to reproduce the document, or about a year of shelf-life per hour of work. Adjust as necessary.

I still have a couple of big carrier bags full with paper printouts from my PhD times... all those notes in the margins! I even had a special thin-tipped pen to fit more in the margins. They're collecting dust at home, I didn't even drag them to the office but I just can't... make myself... throw them out...

It may help you to understand that much of the value of those notes has been the very act of writing them.  As such, you may find that you have less compunction against throwing them out.
Personally, I maintain an "aging pile" for notes, in which I keep them until they stop feeling relevant.  For some things, that's a week; for others it was a box in my closet and a decade.  You can also remove the physical clutter aspect by scanning and archiving in something with cloud storage: you'll be trading physical clutter for electronic clutter, but I at least find that electronic clutter is much easier to ignore.

Electronic space is cheaper and generally easier to index/search than physical space.

And, I find that my notes rapidly become less useful over time. If the point was to work something out 'properly' and I can't quite remember how, generally the only way to figure it out is to do it again so it is all fresh in my mind. For class notes back in the day, well, the value truly was in the writing and I never would go back to review them - I just tossed them at the end of the semester. The clutter on my desk is more from laziness than anything else.

Regarding the article you mention, it is possible to take "handwritten" notes with an electronic tablet and stylus, which would thus retain the aspect of forcing students to synthesize and summarize concepts in their notes, while also retaining the advantage provided by electronic devices, namely, that storage and organization of files is much cleaner and more efficient. Thus one may not ever need to consider giving up on old notes, since the "clutter" they produce is minimal.

I have taken extensive notes with a tablet and stylus. It certainly saves on weight, clutter, organization, search ability, and cost of paper. At the same time, it has never been the same visceral writing experience, and can sometimes be quite frustrating. It seems in most situations, taking notes electronically would require accepting the bad along with enjoying the good.

Good point on the act of writing... When learning another language, its useful to write the word repeatedly to help in learning the translation, method of writing etc.  Yet there would be little need to save half a page of the same word, when you could just save the word once.

You could always scan them and store them electronically if you feel that some of these notes may be beneficial in the future.
I personally kept the notes that I felt would be beneficial. Classes related to my major and classes I had taken an interest in, I would keep. Notes I had that didn't seem useful long-term, I would recycle. I would use this same strategy for your notes for papers. If it could be useful for a future paper, keep it. Otherwise, dispose of it.

+1. Find a scanning machine with an automatic feeder, scan to a pdf, then save to Evernote or another service. Some will even use OCR to let you scan the pdf for keywords.

One of my friends would use one of those big paper cutters to cut out the pages of all his notebooks and scan them once he was done with each class. Nowadays I wish I had started doing that earlier.

Scan whatever you may need again at some point so you have an electronic copy. If possible, OCR it so you can search.
This point has been made by others before, but here's what I would do going forward: try to take as many notes as possible directly in a big txt file, so you don't need to scan and OCR it afterwards. You can always search for relevant keywords in your txt later.
And you may want to browse through Personal Productivity, specifically its note-taking tag.

If your handwriting is amenable to OCR I salute you.  Mine, like that of most people I've met in academia, can be a mystery even to me.

In my experience OCR that is accessible to the average consumer is next to useless on handwriting. There may may be some academic products or expensive products that can scan hadnwriting though.

text file? I strongly recommend using a wiki such as gitit, which not only allows for typesetting equations (I'm a Physicist) via LaTeX-math embedded in Markdown (let alone Markdown's simple txt-ish syntax which yet allows for good structuring including an automated TOC) but also automatically keeps track of previous versions

@TobiasKienzler: to be honest, my txt file actually is tex, into which I embed scans or pictures of whiteboards. I have experimented with various desktop wiki systems and don't like them. It's yet another tool to learn and keep current, and you never know when they won't be supported any more. I'd rather use very few tools. Anything I can do using Npp and LaTeX, I will do using Npp and LaTeX. YMMV.

Then maybe you'll love to learn that gitit uses pandoc to allow exporting to/from LaTeX as well ;) Actually, I just tried and noticed that thanks to that you can use TeX instead of markdown by adding format: latex into the YAML-Header (i.e. between to lines of ---)

OCR is useless on my handwriting now.  But part of my hope in scanning and archiving all my notes is that some day, OCR will be up to the job, and then I’ll have all my old notes suddenly searchable!

@PLL Sounds familiar XD Maybe if everyone added a few pages of their handwriting plus a manual transcription to train tesseract-ocr somehow... – maybe a collective effort project? Further reading: 1 2

@TobiasKienzler The gitit link looks essentially dead. I think https://github.com/jgm/gitit is what you were shooting for.

@MichaelKjörling Unfortunately so, thanks for the update - too bad one cannot edit old commands...

@TobiasKienzler I know exactly what you mean.

I left academia some years ago.  When I left university, my notes were all neatly stored in folders and then boxed up.
I never looked at any of those notes again.  Eventually, I just decided that they were pointless clutter and dumped them in the recycling.
These days, if you need to know something, it's easier to look it up (in a book or on-line) than it is to wade through a pile of scribblings you did several years earlier.

+1 for it being easier to look it up fresh these days. Unless your notes storage, archive and search system is better than Google (mine certainly isn't!), it's almost always quicker to use Google.

When I make notes on a paper that I've printed, I make them on the paper.  This means in the margins, on the backs of sheets (single sided printing has its uses).  I haven't had to but extra sheets can always be added to the back.  Then I can file the paper in some way (normally a disorganised folder on a particular topic).
The equivalent if I'm working electronically (not preferred, but useful on a train) is to maintain a text file (which would proably start as .txt, but if any complicated equations are required, would contain LaTeX and would only need a few lines to be compilable.  This would be stored in the same folder as the .pdf and the .bib for the paper.  Even though I might be reading the papwer on a tablet and making notes on my laptop, papers are stored on dropbox, so everything is kept together.
I'm naturally disorganised, a piles-of-paper sort of person and this works for me.  Sketched-out ideas have to be typed in or photographed for long-term storage or I'll lose them.

If you read a paper as a .pdf, you can also annotate that for example with xournal (http://xournal.sourceforge.net/) to keep your notes right on the paper.

@Sumyrda,I've tried xournal, and if I have to take text only notes in the pdf prefer acrobat (for Android). I don't like either very much. Xournal might be ok with a pen interface but I don't have one.

I haven't tried acrobat for android yet, thanks for the hint. I use Xournal on my laptop without a pen interface, but I use it mostly for proofreading. That said, I hate having to keep track of two files (a .txt or .tex and the corresponding pdf) and I prefer pencil on the printed document above all the electronic alternatives - because in the end you're right, the electronig ones are all kind of tedious.

Too bad that margin was too narrow...

This doesn't help for the past, but in the future write your notes in a journal. And put them on a shelf when they are full. For important notes, use colorful page markers so you can find them later. If you no longer feel that a topic is important, just remove the page marker.
I picked up this habit from my husband, who startet doing it during his PhD. I found it very helpful during my masters and I continue to use it at work outside of academia.
edit: When you run out of shelf space, throw out the oldest journal that doesn't have any page markers.

I think most people here have said what I would say too, scan them.
The rationale behind scanning the notes is that they then are not lost in case you do want to get back to them, however, as others may have indicated, you should consider keeping the notes that you deem important on paper as it makes them a lot easier and more comfortable to read.
The other point people did not mention - when scanning, get a document scanner. Even a small document scanner will be a lot faster than a flatbed which would drive you insane.
I have scanned many of my own notes - without my (Fujitsu) document scanner that would not have happened as not only is it faster than a flatbed, but it can do double sided scans too, effectively, put in a stack of papers, press a button and done. (Unless a problem occurs in which case the scan is interrupted and you are informed of the problem.)
I would advise you to read reviews and compare different models before making a decision.
Some people have mentioned OCR: This is only practical for already a priory typeset and printed material.
I have not seen nor found affordable OCR software that can understand handwriting. It may exist as a research code or maybe as a more expensive code but this is of little use to the more average consumer, plus you cannot be sure it will read notes correctly if they contain mathematical notation or similar (this would also apply for prints though).
Something I didn't do in my scans - but you should consider - is organising these in a coherent manner.
Obviously use multi-page PDFs where content belongs together and possibly use folders/directories in the same way that you would use physical folders to help you find documents later on should you need to seek out any page.

In addition to other good answers... and as I intermittently sift through hand-written notes going back 35-40 years... :
Some things will have been truly, clearly superceded. Recycle.
Some things' disposition is less clear. One thing to do is to allocate some regular time to "reconsider/edit" such notes by typing them up (TeX, or whatever). And then you have an economical electronic (searchable!) copy. Then double-check that your typed version captures everything in the hand-written, and recycle.
Another point is that often organization by date, not by purported "topic", may work best. Or at least having things set-up so that it's easy to search by date... since often I realize that temporal proximity is more relevant than what I thought at the time about causality.

I am used to writing notes on different supports: post-its, text files... taken at very different moments (bedside, bus). Although I have a pretty good memory (with respect to most of my colleagues), I am amazed by how "a new thought" had appareared several times before in my notes, sometimes in a slightly different form.
Reading them again both refreshes and strenghtens those silent, unconscious cognitive processeses, described by many scientists, like J. Hadamard's The Psychology of Invention in the Mathematical Field, or H. Poincaré, that sometimes lead to those rare eureka or aha! moments.
I displine myself to always have something to take note (thoughts do not warn), to decorate my notes with a time and date, descriptions, mood, attitude and sights (was it rainy? what did it smell) to help me revive the moment when I read the note again, in a synesthetic manner. And I do my best to reopen old text files, to rebrowse old post-its once in a while, randomly.
I do not know if it is really effective, but I use it as a comforting ritual, for instance when I am not in mood to do real scientific work, and it does work as least like a placebo effect.
At least, I know it worked with dreams: taking notes of dream details in the morning helped me remember them more accurately, and dream them again with even richer details. It helped me getting rid of recurring nightmmares, by somehow completing them progressively, like one finishes a level of a computer game.

My strategy is to honestly assess the importance and use of the notes to myself and to others.
As an undergrad,
I kept my notes for some of my advanced physics, astronomy and math classes for grad school. Several of those notebooks were helpful, others were not. I kept my other notebooks for a year or two, but recycled them when I moved to grad school. After taking grad-level courses, I was able to condense and/or recycle my undergrad notes. Most of what I have left now are a couple essays or projects I'm really proud of, a few interesting "summary sheets", some thought-provoking handouts, and similar things -- maybe 5% of what I started with. (I lean slightly towards being a sentimental hoarder.)
As a grad student,
I kept the notebooks from several of my grad classes to review for my comprehensive exams and in case I'd ever need to teach a class on that topic someday. I also kept some things I was proud of from grad school and undergrad, as well as other things that were particularly interesting. I still occasionally refer to these, but it's becoming less and less often.
As a grad researcher,
I also kept a file with most of my dissertation research: key derivations (though most of these are in *TeX on a Git repository), meeting notes, a few key papers with my notes, a few super-useful diagrams, and some other things.
As an early-career scientist,
I have 3–4 bushel boxes in my basement with 15–25 notebooks or binders from undergrad through grad school, plus a few key reference textbooks. I may use them someday to help me teach a class or help a student I'm mentoring, but I generally don't use them. They're "archived", pending an office.
I really should have a place for research notes, but I don't. What I've done in the past is kept them in one of 2-3 modest piles and then gone through them all in a year or two. At those times, I have to be ruthless about what I'm really using.
As an instructor,
I sometimes make some notes to myself for a given lesson, but rarely keep these more than a day or two. I have to be super-organized with student papers, so I reserve certain drawers for different kinds of papers, and let those build up till the end of the semester. I also archive certain student papers (e.g. exams) for a certain university-mandated time (usually 1–5 years).
How might you apply this?

What is the nature of the notes?

Are the notes inherently valuable or important (e.g. contracts, stock certificates)?
I keep key derivations for my most important work
I keep some articles I've found to be meaningful to me.
I keep some helpful summary sheets (e.g. list of trig identities or vim commands)

What is the likelihood that you will use the notes?

Know yourself. Be honest with yourself. Be ruthless when you need to be ruthless.

Is there a chance that somebody else will benefit from your notes?

I keep tax documents, but not shopping lists....

I periodically go through some of my papers and try to reduce the number of things by something like 90%. That seems to work for me.
Personal Organization
I use index cards in my pocket, sticky notes on my desk and apps on my computer (e.g. Outlook, Apple Reminders, or Google Calendar) to remind me of meetings, to-do lists, shopping lists, and so on. I generally dispose of these within 0–3 days of not needing them, so these don't really build up.
Rule of Thumb
Keep papers for a number of weeks equal to the amount of minutes it takes you to reproduce the document, or about a year of shelf-life per hour of work.
Obviously, adjust this rule of thumb based on things like the value of the notes, how much space you have, your reluctance to part with notes, the relevance of the notes, and so on.

Recycle the lot, now, without grief. The effort of reading / indexing / typing would overwhelm you, and squash whatever creativity you might still have. The act of taking the notes might have helped, but that is long gone. If you need the facts again, consult google / wikipedia / mathworld / whatever.
There is a narrow exception to this: keep unique records of (say) the medical histories of very unusual patients, or tasting notes of very rare wines, or whatever is the equivalent in your field. But if you aren’t Oliver Sacks, this won’t apply. In which case, the recycling calls.

I am not too sure you are supposed to keep records of (say) the medical histories of very unusual patients as your personal notes.

There have been some general remarks about scanning things in and digitization, but here is a system that I used when I was taking paper notes.
I had a manilla envelope for each project that I was currently working on - I might have had 2-3 irons in the fire, so to speak. I kept the most recent material to the front of the folder. Eventually the project would wrap up (or I went and got a better job ;)
At the end of the project, I would go through all the screenshots and annotations that I had made. I would have a lot of duplicates and a lot of information that was no longer relevant. This got discarded. Most of the other information I had already digitized (e.g. if I took Sketchnotes at a meeting, or added cases to our issue tracker). If I found any information that still needed to be digitized, I'd add it to a Wiki, issue tracker, or email, and then I'd move the folder to a filing cabinet or drawer.
It seems like this (or a similar process) would work for you.

The old papers could be-

Scan and convert to PDF, which can then be managed with Zotero or any other reference management software.
The PDF could then be annotated with notes, and these could be exported to Markdown.
The markdown could be opened in a digital zettelkasten sytem like zettlr or obsidian to retain the notes and to make it resuable in future...

I'm surprised that none of these answers recommend the Zettelkasten method for knowledge management. This is an approach for creating a note repository, in which every note represents one piece of information. Notes can reference one another, and eventually a Zettelkasten (repository) will have enough content that one can use the Zettelkasten to discover new links between concepts. This can be a digital system (there are some apps designed for this specific approach to simple note-taking), or an analog system. The 'original' Zettelkasten was a system using index cards, developed by sociologist Niklas Luhmann.
Here is a blog post that discusses the situation in this specific question: starting with many old, unorganized hand-written notes, and distilling information into usable digital notes for your future self. I recently started reading about Zettelkasten methods a few months ago, and even with very imperfect implementation, I've been able to increase the usability of my older notes, and have been taking more effective notes in general.

I have notes going back about 20 years.  (Notes means daily logs, [like a daytimer] and all of course work as a college student.)
I save everything, first because it was easy, and I liked having access to my info, though, like others, thought I'd really never need it.
Then my second reason arose when I needed the info itself, or needed to show when certain concepts were originally documented by me.
Make it easy on yourself.
Take everything related to one project/study/class and put it in a pile.  Don't sort it, don't make it all face the same way, don't fuss with it!
Give this pile a name.
"Trigger Study - Small Mammals"
Take a ziplock bag and using a thick black permanent marker, write the name of the pile (BIG) just under the zipper.
Put the whole pile into the ziplock bag, zip it and stand it up in any long term storage container of your choice.
Walmart has clear Sterilite-brand tubs that work fine; clear helps you to see contents without manhandling it down off a shelf.
I use 2 gallon freezer bags... they hold about 400 pages.
You can either break down any monster sized pile into multiple bags, or order zippered bags any size you can imagine.  I use U-Line, but there are others.


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Is copying an image from a previous paper of mine and citing its source considered self-plagiarism or unprofessional?
Last year, I wrote a paper and it got accepted and was presented at a conference.
This year, I am writing a more in-depth paper about a similar subject; but since one of the figures in my first paper is adequate for my purpose, I want to reuse that one (of course citing it adequately).
Am I OK in doing that, or is that seen as self-plagiarism or unprofessional?

Jonah Lehrer was criticized for self-plagiarism and later resigned from The New Yorker for making up Bob Dylan quotes. It seems that it is not looked down upon in the UK. But in the USA, it is considered unethical.

Citing your own work gives a (teny) tiny bit of credit to your previous paper (Better if some one else cites it though) and improve search rankings (etc) (slightly, if you don't over do it).

Tricky legal aspects aside, I'd just like to comment on the unprofessional notion. I may be seeing this (too much?) from a software development point of view, but IMO, extracting reusable bits and pieces and creating components of your work to be abstract enough so as to be reusable without adaptation is a very basic skill for creating anything noteworthy. Any somewhat experienced developer has probably accumulated a plethora of reusable code snippets and components, and I'm tempted to call not having such a toolbox "unprofessional". I see no reason to use a different development ...

... methodology there for natural language documents.

There is such a thing as self-plagiarism, but I would say that your case (reusing a figure that you created and providing a citation to it) is not an instance of it.  I also don't think it is unethical or unprofessional.  As Ran G. says in his answer, just make sure you ask permission from the copyright holder (if it isn't you).

This ridiculous notion of self-plagiarism currently promulgating within academia needs to be curbed. There is no such thing. Plagiarism is stealing from another, you cannot do it against yourself.  Now, journals may not like like text or figure re-use or self copying, and there do exist copyright issues with self copying, but it still doesn't make it plagiarism.  Duplicate submission(s) != plagiarism.  Copyright violations != plagiarism.

@daaxix I have sympathy and I think most of it is just journal nonsense but repeatedly submitting the exact same idea in a different order of words I think would be a form of plagiarism more than a copyright issue.

Self-plagiarism is a misleading term. The misconduct that this term addresses is to attempt to gain credit more than once - i.e. undeserved credit -  for the same piece of work (the analogy to plagiarism is that the latter is to gain undeserved credit from work by others; clearly, the "undeserved credit" issue is the point here, while plagiarism also involves withholding credit from others). If you very clearly state where the picture comes from, there is no academic problem, only potentially a copyright one. We have once paid money for the permission to use an important picture.

(EDT: "in this case.." ) There's no such thing as self-plagiarism. It's your figure. you drew it, you have the right to use it anywhere you want any time you wish and as much as possible. I don't even see a need to cite previous appearances of the same figure (unless this figure is the main theorem/claim/result rather than an explanatory tool.)
The only thing to check is that the conf that published your paper doesn't  hold some rights on it, due to editing it, improving it or that you gave up your rights when you signed a copyright-transfer form (as the Anonymous Mathematician mentioned in his comment)

That settles it; I had forgotten about the rights issue. Thanks!

There is such a thing as self-plagiarism. http://en.wikipedia.org/wiki/Self-plagiarism#Self-plagiarism

@joel, I would call such a thing, simply, `a fraud'. Indeed, if you present old result as new this can be considered as "self" plagiarism. If you copy the same section (usually, Notations and definition, motivations, examples) to your new paper - this is not plagiarism

I would point out that reusing data figures make for a much more ethically interesting problem.

See also http://academia.stackexchange.com/questions/2893/attitudes-towards-self-plagiarism

The rights issue is a little more subtle than this.  It is not simply a matter of whether they edited/improved the figure.  If you signed over copyright to the paper, then they now own the figure and you have no more rights to it than anyone else.  On the other hand, if you retain copyright then you can do whatever you want with it, legally.  (Morally you still have an obligation to cite where it originally appeared, to give credit there and to avoid giving the impression that it is new work, but it sounds like you are doing that anyway.)

This is a bit old but...as a teacher, I fail students all the time for submitting their previously submitted work without citation. Self-plagiarism is serious in some schools and when you are presenting work as 'original' work, then it must not be just original to you but original to the time (not created before and reused). Citing is the proper solution, which the op already mentioned.

source: Stack Exchange

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

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Are relationships allowed between students and faculty?
What sorts of restrictions do universities place on romantic or sexual relationships between faculty and graduate students, and what are the underlying issues that motivate these restrictions?
For example, suppose the student has previously taken a class from the professor but has no plans for further academic contact.  What other factors could help determine whether a relationship would be allowed or considered appropriate?

Wouldn't that depend on the expectations of the particular institution?

I second Charles, I see nothing wrong with this question. And surely nothing "not constructive". The implicit question is 1) is this legal, 2) if yes, is there rules in some universities about that, 3) if no, can this be a problem. This sounds like a legit question.

I'd argue that it is not constructive.  The "is it allowed" question has no useful answer without knowing which university it is (why should someone in this situation care whether it is allowed at someone else's university?).  And it comes across somewhat like an attempt to stir things up via a provocative question, but I'll try answering it anyway.

@AnonymousMathematician: I disagree.  Since the question raises relevant issues in academia such as the "mentor-apprenticeship model", politics, and ethics, the question can be interpreted not as being specific to an institution, but as "is it allowable, in general and why?"  I feel it is well within the scope of an acceptable question.

I'll try editing the question to reflect these more general issues.

Related (to some extent): Romantic relationships between faculty and students

To give one data point on how this issue is actually framed and enforced by universities (or at least public universities in the US), let me quote from my university's Campus Administrative Manual:

An individual may not initiate or participate in institutional
  decisions involving a direct benefit or penalty to someone with whom
  that individual has had a sexual relationship.
Relationships such as those between supervisors and their subordinate
  employees are inherently asymmetric. Current or past sexual
  relationships can adversely affect decisions, distort judgments, and
  undermine morale. Any university employee who participates in academic
  supervisory or administrative decisions concerning another employee
  with whom he or she has or has had a sexual relationship has a
  conflict of interest in these situations.
Accordingly, no individual shall initiate or participate in
  institutional decisions involving a direct benefit or penalty
  (employment, retention, promotion, tenure, salary, leave of absence,
  etc.) to a person with whom that individual has or has had a sexual
  relationship. He or she must take specific actions to remove himself
  or herself from all decisions and actions that may influence the
  career or status of the other employee.

[...]

In cases where a conflict [of interest] is identified, the UEO [Unit Executive Officer] must develop a
  Supervisory Relationship Management Plan that redirects
  decision-making and bypasses involved parties. Such procedures must be
  agreed to in writing and approved through all administrative levels.
  For changes in existing positions that might create a supervisory
  relationship in the same unit, review and approval is also required.

[...]

The appropriate human resources office will conduct periodic
  compliance reviews. Failure to abide by this policy constitutes
  misconduct, subject to discipline under applicable University
  procedures.

tl;dr: Sexual relationships between students and faculty are not per se forbidden, but the conflicts of interest they create — either real or perceived — must be carefully and explicitly managed by multiple layers of campus administration.
It is worth emphasizing that these policies are invoked not only for sexual relationships that are generally considered inappropriate, such as undergraduates and their instructors, or graduate students and their advisors, but also with married (and formerly married) couples.

I think the tl;dr text should be clarified to "between students and their relevant faculty" or something along those lines. The text you cited explicitly talks about supervisors and their subordinates. Relationships between a student who, say, attends courses by department X with a university employee at department Y is not really mentioned by the cited text (and is probably pretty common in academia - think couples who get together while they are students, then one of the two graduates and takes on a job at the university while the other one is still a student).

I personally know of a Professor now at Princeton who was initially at Cornell, who not only had a sexual relationship with his graduate student, but eventually married her.  To my knowledge, no ethical investigation occurred, and there were no repercussions for the professor. I'm unsure how well enforced these policies are when incidents actually occur...

Is it allowed to have a sexual relationship between a Professor and a graduate student?

This depends on the university's rules.  Pretty much every plausible set of rules you can think of is used somewhere: everything is allowed (well, generally not explicitly, but by not having rules for this at all), nothing is allowed, it's allowed only if they are in different departments, it's allowed only if the professor is not teaching or supervising the student, etc.  If this issue is relevant to your life, then you need to figure out which rules apply.
On the other hand, I'd say it's always a bad idea if the student and professor are in the same department or even related fields, regardless of whether the university's rules allow it.  You could have a secret relationship, but it's wise to avoid awkward or troublesome secrets in your professional life (and all the problems of a known relationship will be magnified if you are discovered in a secret relationship).  On the other hand, if other people in your department are aware of your romantic involvement, then it is almost certain to lead to complications.  For example, the student will eventually need letters of recommendation, some of which will be written by colleagues of the professor.  If they write honest letters, can they feel confident that what they wrote won't make it back to the professor?  Probably not, so they will feel constrained in what they write.  People reading the letters will realize this, so nothing positive will be taken quite as seriously.  And letters of recommendation are just one issue - the relationship will keep coming up in different areas.
When you take into account all the important points made in other answers (power differentials, what happens if the relationship ends, improper appearances and effects on reputation, etc.), it's not hard to see why there are often rules against this.

The key issue of whether it is ethical or not reduces the question:  Is there a potential for a perceived imbalance of power that can be abused?
If the professor and graduate student are in separate departments, I think it is not an issue because a professor of one department has no power to influence any matters pertaining to the graduate student's academic life.
If they two are of the same field, things can get a bit delicate.  Speculation of an improper relationship alone can be devastating to one's reputation even if unfounded.  We all know that politics play a role in one's success in a department.
If one is maintaining a mentor-apprentice relationship (teacher-student, or advisor-mentee) and romantic relationship with the same person, it is difficult to determine whether certain actions (benefiting or detrimental to the apprentice or mentor) are biased due to emotion.  Furthermore, if the romantic relationship terminates, it is difficult to continue the mentor-apprenticeship relation.
While technically not "illegal", you have to ask yourself the question "is there a potential for a perceived imbalance in power in the relationship?".  If so, I strongly advise against it.

I think what you said is true as far as it goes.  However, even if a romantic relationship between a student and a professor is ethical, it may still be against the rules of the particular institution.  Further, even if the rules permit it, it may still be inadvisable: Anonymous Mathematician's answer give some (but not all) of the reasons for this.

It depends on what allowed means. Many things are legal but not advisable.
Traditionally the teacher-student relationship is Platonic. It also often continues beyond the class that brings the two together. If that relationship morphs into something else, it can appear improper even if nothing is technically awry. We all know how important appearance is in university relations.
There is a further wrinkle. Do you mean an exclusively sexual relationship? That can create the appearance of a quid pro quo.
To second @Charles, this is an interesting question precisely because it is a delicate topic. For example, it appears that the OP is male and discussing a female professor. How would our reactions change if the genders were reversed? Or, if both were the same gender?

Official Answer: It depends on the tenets of your institution.
Real Answer: No.  Never with an active student at your institution.
Relationships may sometimes be allowed between former students and faculty by the letter, but I cannot think of when it would be advisable for a faculty member to have a relationship with a student.  Why not?

If there is ever a chance of you having power over their academic progress, it is at best a conflict of interest and at worst a setup for sexual harassment case.  If you're looking for a great reason to have your tenure file silently quashed by a dean, this is a great way to do it.
Even if you have no direct power over a student, there is the possibility that other students could complain if there is indirect influence (e.g., if you have connections to other faculty who do have power over that student or over rival students).  Even an indirect connection to the student has the potential for allegations of bias or preference.
You do not know the future and may run into a conflict later (e.g., student takes a course in your department, invited to work on a funded grant with member of their department). At that point, you're hosed.  Even if ended the relationship as soon as the conflict became evident, the prior history of the relationship still exists.  Alternatively, you could hurt your own (or the student's) academic trajectory by declining these opportunities.  At the point where you are hurting a students' academic trajectory, it's unethical.
It looks bad on the institution.  How many administrators would want it known that any of their professors are dating any of their students?  If you were a parent looking at a school for your kid, all else being equal, would you want the one where faculty are dating students?  Imagine if the relationship goes sour and you end up in shouting matches with a student in your office/lab (or theirs!).  In that light, dating a student is an anti-service to the institution.

If the student is really going to be the love of your life, you can wait until they're graduated to start a relationship.  If not, then it's certainly not worth the risk (even if your name is Professor Carlos Danger).
This sort of thing used to be allowed decades ago, where it wasn't uncommon for the (almost entirely male) faculty to end up marrying female grad students.  As we've become more aware of the power structures and negative externalities involved, it's become much less permissible.  Rightly so, in my opinion.  No school is bigger than 100,000 students and most students you meet will be done in 3-4 years maximum.  Given the risks (bias, bad press, potential lawsuits by the student or their peers), I don't think it's an undue restriction to not date a few thousand people rotating over a few years.

The only exception to this would be "preexisting" relationships, but otherwise "never" seems the right answer in most cases.

I personally don't think that pre-existing relationships are much better, since they still have the same potential for problems (unfair favor toward student, penalties due to bad breakup, etc).  The only difference is that the damage is already done (no way to "undo" a prior relationship) and it is the university's responsibility to take on new students/faculty (so, correspondingly, the risk was assumed by admitting them).

"Love of your life," eh?  Well, a {ahem} friend did wait.  He didn't know he was waiting until she showed up in his office ten months after graduation to say, "I've come to take you to dinner."  All was well for a couple of years, and then she decided to come back to school.  That generated a "Disclosure Statement" on the part of the faculty member.  More time passed, and then she dumped me... I mean him.  Oh, man...  Just don't do it.

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Research norms, looping in other researchers for ideas
Let's say that I and a couple of a researchers have made good progress on some work but got stuck on something, say, a biological system that we derived but it's not quite working the way it should.  Would I be breaking any research norms by looping in one of my former professors (in the same department) who specializes in computational biology and can likely help us?  Or should I really let the advisor of our group decide on who to loop in for ideas and help?

This may be field dependent, but in my field (math), where groups of people that work on a paper together are rather small, you should ask all involved people before you enlarge the team.
Note that there is a gray area, though. If you run into somebody and discuss your recent research and it seems like this discussion may be fruitful for the point where your team got stuck, it may or may not be a good idea to discuss your particular problem (depending on whether you know that guy before, there is a trusted relationship,…). When you are in this situation and are in doubt, you could resort to something like "It sounds like you could be the right person to discuss a particular problem we are having in our group. May I contact you later about this?" and then ask your group. In your situation, I would definitely ask the other group members before involving further people.

Yes, moreover it takes so little effort to ask the other group members that I can hardly imagine a reason for not to do so.

Same for biology and computational biology (relevant for OP).


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Does "scut work" contribution to a paper as a math undergrad carry weight in grad school application?
I got an opportunity to collaborate writing a mathematics paper with some professor at my university, but I'm suspecting my role won't be much more significant except doing menial work in the form of writing dozens of lines of code using Mathematica and helping my professor computing things. I can probably get in my name as a possible collaborator, but I am wondering is it really worth putting in the effort into it to do so?
While I'm aware that research experience is taken into account while considering grad school applications, I am also aware that putting into papers in which I had menial contribution into my CV might even carry negative weight, in the sense they might suspect I'm trying to game the system without really doing anything substantial.
Is it worth pursuing this project instead of, say, learning some new math by myself (not under the supervision of someone)? Even if I do, what are some ``red-flags" to notice for, which can indicate this might not be a great idea?
[PS: I don't want to go into details regarding the subject matter of the paper, but it's a relatively advanced topic that requires a fairly good mastery of the core undergrad curriculum to understand. I believe I have such an understanding, but I'm not sure if my role in writing the paper would reflect that/I would have the opportunity to use my understanding, especially if I'm not considering the professor as my main recommenders for grad schools].

Why do you want to go to grad school if you are not interested in solving/working on research math problems?

@lalala "Solving/working on research math problems" is very different, from what I understand, from "helping a professor who is working on a research problem by doing some computations for them"

Whats the (big) difference? The computations are still part of the research problem. I do not think you can be a master while skipping the apprentice step.

See https://academia.stackexchange.com/a/67732/19607

It wouldn't have negative weight, as long as you can explain the body of work in detail, then no interviewer would think you are trying to game the system.

You should not be thinking exclusively about applications. Do you want to do research? Do you think you will learn from working with more senior people? I expect you to get a lot of experience from that, but you may have a better idea of what you will be doing and how helpful it will be to you.

Evidence of having contributed to a published article will definitely count in your favour when applying to grad school (besides it being a ''learning experience'' or however you want to phrase it).  In general, it's good to see what research in an area is actually like, as this can be extremely different to just learning some existing results in that area from a textbook.

writing dozens of lines of code using Mathematica and helping my professor computing things

That sounds like normal undergraduate research to me.  It's probably not a menial contribution.  Very few people can write a dozen lines of Mathematica code.
If you do a good job, this could be a big help to your graduate school applications and even later career.

Yeah, doesn't really sound like "scut work". Just not "glamorous". :)

Very few people can write a dozen lines of Mathematica code.

Isn't this a gross understatement?

Apparently it is not used by enough people for TIOBE to monitor who uses it.  https://www.tiobe.com/tiobe-index/

@noobie If you work in a group where everyone uses Mathematica, it might appear that everyone everywhere uses it. In reality, while there are plenty of people who could use it, as AP points out its use is not widespread at all.

@noobie From my experience in industry, sponsoring university research (at PhD and post doc level), the number of academics who can write good quality and reliable code is zero, to a first order approximation.

@alephzero That said, if that's true (and I don't think it is, personally), it also seems unlikely that noobie would qualify as being able to write code, according to your definition.

@noobie some otherwise smart people, have a hard time grasping the concepts of programming. Mathematica in particular is weird in a number of aspects. If you can prove you can write a few lines of code you show (i) you can translate math into code, (ii) you are not afraid to do that (iii) you understand the math well enough to put it into Mathematica-sized bits, and (iv) you have some experience, so you will require less training.

If you have holes in your knowledge then a course might be (marginally) better, but any involvement in a research program is a plus. You want to arrange it so that you get an acknowledgement in the paper for your work (assuming co-authorship is impossible). Then it is a line you can put in your CV. I doubt that it would be seen in a negative light, but a formal ack is important. And, if the PI later turns out to be one of your letter writers, perhaps they can mention it also for reinforcement.
Beyond how it looks it is a good thing do do in itself, as it gives you an idea about research "as it is played". Even programming "at the edges" should give you a deeper insight in to the problem at hand. And insight is the real goal.

Even if you do not make it as a coauthor to the paper this still can be in the CV as research experience. More so if you do a good job you will have a professor who can write a recommendation letter for your application about real work you did and not only about your lectures or GPA.

"And, if the PI later turns out to be one of your letter writers, perhaps they can mention it also for reinforcement." This should be a when not an if! Working with a professor on an individual basis like this is a perfect and rare opportunity to get a letter of recommendation that speaks directly to your ability to do graduate-level research.

The level of involvement you describe is what admission people will expect when they see that an undergraduate student coauthored a mathematics research paper with a professor. In the rare cases where an undergraduate contributed more significantly, it would be up to the professor to explain this in their letter of recommendation. Thus, there is no reason to feel that you'd be claiming more recognition than you deserve.
Of course, having a publication on your CV makes it a natural topic for questions during admissions interviews. The idea here would be that a curious and smart person will pick up enough about a project they are contributing to to have an engaged conversation about it.
Having contributed to a mathematics research project is a strong plus for a PhD application, because it means that you have at least a faint idea of what mathematics research is, and your decision to engage in more of it is thus better informed. Mathematics research is quite different from learning pre-existing math, and not everyone who enjoys and excells at the latter will also do so for the former.

I just want to clarify something: writing the code that will solve the problem your professor wants solved should NOT be considered "scut work". This needs to happen anyway regardless of who does it, and is actually a meaningful contribution. This code will most likely be part of the final research document that gets reviewed, and as such can probably be considered a critical part of the paper. It's important that this code does exactly what the algorithm in the paper describes, and being able to correctly transcribe these formulas into Mathematica code shows domain knowledge in both the research domain and Mathematica. This is valuable knowledge for the time when you're doing your own research projects and don't have someone under your tutelage to do this work for you. And who knows, you might be able to suggest improvements to your professor and provide an even more meaningful contribution beyond just converting their work to a computer-readable format.
REAL scut work would be manual data entry: thoughtlessly transcribing thousands of lines of data that were unable to be read in manually for whatever reason, with no domain knowledge required and no option to even consult with the professor for potential ways to optimize things that may or may not be possible and change your contribution to something that rises above menial labor.

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Ethics: Is it ethical for a professor to conduct research using a student's ideas without giving them credit?
I pointed a professor (my major advisor) to a resource (a data set), in an email exchange during the beginning of the semester, he published a paper based on this data set several months later, however I had no idea he was working on the project. He did not notify or mention to me about using the data set.
The email that I sent to him earlier when I pointed out the resource had no reply back, however it did indicate in his response that he did not know about the existence of this data set.
When I had a brief (15 minute) meeting with him, he denied that the data set was my idea and said that it was his research colleagues who he got the data set from. I must mention that this data set is freely available and open to the public (online).
My questions are: Is this professor's behavior ethical? and Would I be able to bring this  as a complaint to a higher person in the department (since I have email evidence that he did not have knowledge of this data set prior to my informing him).
My final question to you all is whether I should stay with this person as a major advisor because I am having trust issues with sharing my ideas. The only problem is that anyone else I might choose as my advisor would result in me completely changing my area of research. Thank you.
Edit: Responding to the commenters, when I met with him in person, I he mentioned a paper which he authored, and when I asked for the citation he refused to give it to me saying, "I'll think about it". While my gut feeling is that I should change advisors, the other people in the department are not involved in my area of interest, and the other person who is conducting research in this field refused to be my advisor. What would you do in this situation?
Edit: Thank you for everyone's responses. Perhaps this was just a misunderstanding on my part.

It would help to know your area. Pointing someone to a data set is not necessarily a significant contribution to the research, depending on the field. I'm guessing something to do with machine learning?

@Johanna, agreed. It seems a bit thin as stated. Especially to conclude that it is time to change advisors.

Your edit doesn't make any sense to me... he mentioned a paper about what? Also, if there was no reply to your email, how does the response indicate he did not know about it?

On more than one occasion, a student has pointed out a resource to me that I am already familiar with. In those situations, I always thank the student but don't always mention that I was familiar with it. I don't lie and say that I hadn't seen it before, but see no reason to bring it up (since doing so might make them feel slightly disappointed). If it is open data which has relevance for their field of study it is quite possible that they were already familiar with it. Perhaps in their e-mail they meant that they were unfamiliar with a certain source that contained the data, even though they were familiar with the data itself from another source (such as, from research colleagues who presumably were aware of the source).
The fact that he published a paper several months later is strong evidence that this is indeed the case. The time frame seems too small for him to have begun the research after your email exchange, found something which was publishable, written the paper, and gotten it through peer review. Obviously I don't know the specifics of the case, but I find it implausible that he was unethical in the way that you claim.
I don't see any reason for you to switch advisors. If you unjustly accused him of dishonesty, the real question is if this advisor would still want to work with you as a student. Unless you have evidence which goes beyond what you have communicated here, an apology might be in order.

I didn't accuse him of being dishonest. Nothing of the sort happened. Actually, I do think it is possible for someone to get a paper through peer review in a matter of months, depending on the journal, so I do not see how this is implausible as you say.

@Emily Glad to here that, but the way that you said the professor "denied" being indebted to you on that point suggests that you informed him that you thought that he was. It seems that at least something of that sort happened.

I mean, when I met with him, I asked him where the data set came from and he said that it came from his colleagues on the paper. When I asked him about about the paper, he would not answer any of my questions about how the data was analyzed and the methods of how he conducted the research study. I didn't accuse him of anything.

@Emily If so -- why did you say "he denied that the data set was my idea"? It sounds like he denied nothing but simply affirmatively answered your question, albeit not in the way that you had hoped.

@MorganRodgers I think you turned 'several months' into 'a couple months'. Without the OP providing dates, we don't know how long the time period was and these two phrases connote periods of different length.

@T_M True that we don't really know, but OP talks about "the beginning of the semester" for the original e-mail and "several months later" for the paper, which suggests it is all within a single semester. Furthermore, it isn't just peer-review, OP seemed to think that in an astonishingly short period of time, the professor looked at a data set for the first time, did research on it, wrote a paper, submitted it, and had it published. Possible perhaps, but more likely than not the paper was already in the publishing pipeline prior to OP's original e-mail.

"I don't lie and say that I hadn't seen it before, but see no reason to bring it up (since doing so might make them feel slightly disappointed)"... I'm sure offering them a cup of coffee and telling them "Actually, I'm already working on that. But - excellent find! I'll have to remember your name. You've got an eye for important details!" wouldn't disappoint them either. And might spare you future problems like this one.

@jvb unless this concerns research on coffee and assuming OP isn't the only person in email communication with the professor, there could be a time constraint.

You pointed out a dataset and had a 15 minute conversation with your advisor, and now you are expecting credit for it. This certainly does not warrant authorship (even under the most lenient definitions of contribution I can think of), and perhaps not even an acknowledgement. Bringing this up to the department head will not do anything to help since it sounds like you have no cause. If I were your advisor and you came to me asking for authorship over this I would have found it rather off-putting (and probably would have had a serious conversation with you about authorship and credit).
Generally speaking, chasing credit for every little thing that you contribute paints you as petty and makes people not want to share ideas with you. If you let that happen, you can seriously damage your research career. Sometimes you contribute ideas, sometimes others help you; if it's minor stuff that requires minimal time commitment from you, I wouldn't think of authorship.
That said, you don't want to be a pushover: if you sit in brainstorming sessions, contribute significantly to the analysis, help with developing and writing the paper - by all means you should be an author, and fight for your right to be one!
Should you stay with this advisor? I would say that if this is the only issue, then they did nothing wrong and you should. If you do not trust them and feel like this cannot be repaired by a simple conversation, then perhaps you should reconsider. I would think though that if you have this kind of attitude towards research you will have a hard time finding a good fit for an advisor - you should probably reconsider your position.

Well I didn't ask for authorship. I know it doesn't warrant being given credit in that way. But I do feel slighted. Thank you for your perspective. I do understand that research is about give and take.

@Emily if you don’t want authorship or acknowledgement (the options I cover), what do you want?

Upvoted, especially for the second paragraph

I once had dinner with a friend and she said "why don't you use  in your thesis?". It was a passing remark which took maybe 2 minutes, and which significantly changed the way I approached the problem and made ~50% of my thesis and two papers. I certainly made sure to profusely thank and credit her in the thesis and the papers for the idea. The length of the conversation is not always relevant. EDIT: I am referring to the first part of your first your sentence - not the overall hunt for credit discussion, here I completely agree with you.

I think @Emily wanted an informal "thank you" from her supervisor. If the supervisor was unaware of the data set prior to the project, that is warranted. However, it seems very possible that the supervisor was previously aware of the data set through collaborators, and simply either forgot about it or didn't let Emily know they were aware of it in reply to the initial email.

Let's flip sides here. Your professors have pointed you to many ideas and useful resources (e.g. textbooks) in the subjects you study. Some years later, you will probably be writing a paper based on the techniques you learnt. Will you credit all your professors in it?

@Heutl The answer is not talking about credititing the textbooks, which are parallel to the data set in the original question, but crediting the professors who pointed out the textbooks. This is exactly parallel to the original question, where the OP pointed out a data set and seems to want credit for that. The OP has no papers about that data set to reference.

Voted this up, like the « reverse side » - it’s clear enough ...

This seems like a bit of an irrelevant comparison to me. Not only is the advisor-student relationship asymmetric in nature, but textbooks do not compare with the data set that a study is based off as point out in other comments.

@Heutl Perhaps if you posted an answer then it could attract the votes it deserves...

@Heutl and you got that after 15 days... some of us feel we have more to offer.

I was acknowledged in a colleague’s phd thesis as I showed him how to use the statistcal functions in excel.
I did not expect any acknowledgment at all...
If you had produced said data set then you may have some case but as it was publically available and others seem to have found it as well then I don’t think you deserve acknowledgment.

Being acknowledged in a book (with your name in a list with dozens of other and often including a section for this) is different from being acknowledged in a paper (which is limited in space and where normally you either are an author a cited author or nothing).

@QuoraFeans the issue is about the level or amount of work...

Your colleague was probably trying to establish blame ;-)  http://biostat.mc.vanderbilt.edu/wiki/pub/Main/TheresaScott/StatsInExcel.TAScott.slides.pdf

@ScottSeidman no, he passed and was one of the best that year...

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text:
Personal cover letter for visa application for TV-L 13 PhD Position
I have been offered a Ph.D. position with a TV-L13 (50%) salary. I am in the process of applying for an employment visa (as I am a non-EU citizen). The work contract provided by the university is for a part-time scientific associate. I am unsure of what exactly to write in the personal cover letter (explaining the exact purpose and duration of the stay) for the visa application. Should I write about both the part-time scientific associate position and Ph.D. or only about the part-time scientific associate position?

Also, possible duplicate of https://academia.stackexchange.com/questions/84913. (The cover letter is not really relevant; what matters are the forms.)

I can only take an educated guess here, but the extra information that you are a PhD student can only be in your favour as it explains what you are doing with the other 50 % of your time and gives you additional good reason to reside in Germany. As this is a common situation (the vast majority of German PhD employments are like this), I doubt that anybody is going to bite your head off for telling the truth here.
That being said, the institution where you will do your PhD is likely to have some experts or other resources to assist you with this.


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When is a not updated software considered deprecated in the academic world?
Currently I'm writing a thesis in Computer Science for which I need to introduce and compare several open source tools that are available for performing a certain type of testing (mutation testing) on some piece of code.
To reduce the number of tools (initially  more than 25), I set two limits :

The tool must have been updated in the last 5 years to be present in the list, otherwise it is considered obsolete.
Only tools that work for one of the 3 most used languages are considered. I defined them with the TIOBE index (Java, C/C++ are equivalent for the tools and Python).

I arbitrarily set the first condition to five years, but I would not be able to justify this number if needed. I didn't find a study or article with a point of view on the subject.
So my question is: After how many years without updates would such a software (or any software) be considered deprecated?

In my field lots of people still use Windows XP and Matlab 2007. I don't think anyone is still using Windows 98, so maybe 20 years is enough, but don't tell that to the TeX crowd.

@StrongBad these aren't academia, but: https://windowsreport.com/windows-95-98-pentagon/ https://www.pcworld.com/article/3075284/hardware/us-government-agencies-are-still-using-windows-31-floppy-disks-and-1970s-computers.html

@GeoffreyBrent They also kept using floppies and IBM Series/1 computers longer than most.

You already have justified that number, though. "Keeping the project scope manageable" is a perfectly valid reason for this kind of decision.

I don't think there is such a standard, certainly not one applicable to all of academia. For your thesis, I would suggest that it might be more useful to talk about "recently updated" / "currently developed" software, rather than labeling the rest as obsolete.
"Deprecated" signals that the creator no longer recommends using the software. I can't think of any real examples for a full software package (i.e. going beyond deprecating part of an API), but I guess it might happen if the software is known to produce bad results.
Software might be "obsolete" if it has been de facto replaced by a better option, but certainly not just because it's old. Even then, the old option might be good enough. Visit a couple of (established) experimental labs in the sciences, and you'll likely see lots of old equipment still running old software. Changing it all out would just be needless overhead, and not be guaranteed to help. There's almost always a better place to spend the money you might have... From another angle, if you consider numerical algorithm implementations and libraries as tools, there's a number of them that have gone decades without updates, yet are still routinely imported and used in new software development.

The most common usage of "deprecated" is quite different and has nothing to do with the date of the last update. It means that the developer (or group) responsible for the overall system (Java libraries, say) has decided that in the future the feature may be dropped or modified so as to not be backward compatible. It is a promise about the possible future, not a statement about the past.
Somewhat related, an organization, usually a large one, can deprecate the use of a piece of software, meaning that they permit employees to continue using it for company projects, but will no longer provide IT support. But that is an individual company decision and could occur at any time.
Even your "obsolete" idea is flawed. It isn't about when it was last changed, but when it last was used for important work. Software can be regularly updated, but if no one cares, it is effectively obsolete.
Of course, you may reduce the number of tools you consider to suit yourself. But you should most likely focus on the most commonly used tools, rather than ones that haven't been updated for a while. After all, a stable release is valued if it is fit for purpose. If the problem space doesn't change, older tools may have a benefit. Likewise a tool built in a domain-specific language might be quite valuable to users, so excluding it arbitrarily might be a mistake.

So, just two points:
1) you "set" 5 years, that is justifiable as "what can be argued is a reasonable limit", it is as valid as any other assumption as you mention there is not other study with a comparable point of view.
2) you could make a case for only admitting software that is currently being fully supported and is being updated. While older software can still be used, you have a "limit" that the software is still capable of being developed to change as developments happen.
If, as I understand, you are just "drawing a line in the sand" then making the parameters clear should be sufficient. Many can, and possibly correctly, argue that X & Y software could or should have been included, but to keep the thesis within sensible parameters of time & length then some arbitrary decisions have to be made.
Best of luck anyway.


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I am in systems Phd program, but I want to do theoretical research
I am 3rd year Phd student. So far I have been doing systems research in top US university. I realized that I want to do theory (in particular machine learning (ML) theory), but unfortunately I do not have any publications in that area. I do not have good math background, I never majored in math, and I did only basic math classes back in undergrad more than 6 years ago. So you realize that my math skills are very-very weak.
But I truly enjoy learning maths, read ML papers, read theory papers, even though I struggle. It makes me feel happy, intellectually inspired and motivated.
Meantime I completely do not care about systems research.
That said I am def much much much less qualified than most Phd students in theory who majored in math, have tons of experience and publications.
Do I even have a chance to switch to theory? Should I even talked to professors? I am completely fine to stretch my Phd for the next 5-6 years (since if I switch I will need to start from the beginning and have a long period of learning).
Do you think I should give it a shot? Is it even feasible?

Of course you should give it a shot!  People switch fields all the time.  One of my most successful PhD students (in algorithms) started in my department as a systems PhD student.
Your first step should be to talk to faculty who do ML theory in your department, and ask them how to get involved, given your current background.  They might suggest classes to take for remediation; they might suggest specific papers to read/problems to work on that exploit your systems background; they might suggest first getting a master's degree (if you don't have one already) and then reapplying broadly to PhD programs.  If you are very very lucky, they may be willing to take you on as a student and offer you funding while you transition.
But one word of warning.  As I'm sure you already  know, competition for PhD admission in machine learning is incredibly fierce.  AI has always been the default subfield for smart CS students who want to go to grad school but really know what they want to do, but the popularity of machine learning has exploded over the last five years.  Last year, half of the almost 1000 applications for my CS department's PhD program listed AI/ML as their primary research area, and two-thirds listed AI/ML as a possible research area, even though only a small minority of our faculty work in that area.  (Of those roughly 500 applicants, we offered admission to about 50, and about 20 accepted our offer.)  This competition may make it harder for you to pursue a PhD in ML at your current institution.  That doesn't mean that moving to ML is impossible, but it may be difficult, and you may need to pursue multiple avenues to make it happen.
Best of luck!

So do you mean I will need to re-apply for Phd programs? I thought it is not required if I am already a student and just switching areas within my university.

@JayLo - You would not have to re-apply if you are staying in your department.  However, it's entirely possible that none of the faculty doing ML theory in your department are willing to accept you as a student, in which case you would have to go to a different university to do ML theory.

@AlexanderWoo  I cannot imagine someone accepting me in another university if I say I cannot find anyone to advise me in mine (top uni). Like how can I even motivate myself "So nobody want to work with me in my amazing university, but yet I am so well qualified..." )

@JayLo You motivate yourself by doing what you actually want to do.  Your current university thought you were qualified to be a PhD student in systems; they've expressed no opinion about your qualifications to be a PhD student in ML.  You can't change fields if your self-image is bound up in others' people's opinions about your abilities in your old field.

@JayLo - it's quite possible that you would have to go to a less prestigious university (where it will be easier to find a supervisor willing to take you) and or take a chance on a supervisor who is also moving into the ML field from another.  Whether that would be a good move is a separate question.

You can do it, but as you already realize it will take a lot of time and effort. You have to get the necessary background as well as get yourself to the research frontier.
But it might make more sense to finish the degree program you are in, since you are well along in it. Once you finish you can obtain some  position that gives you the resources to switch fields. You wouldn't need another doctorate, but you would need to learn all of the necessary skills.
But if you have few commitments and plenty of funding and don't care about time, there is little to stand in your way.

I don't really have fellowship or anything. If I leave my current lab I plan to TA


text:
Why are small fonts the norm in research papers?
Is it just me or are the published articles a strain on the eyes in general? Has there been(/shouldn't there be) a study on optimal font sizes for reading?

I really love this one. Both the question and answers are great. Is there any way to let those publishers know this problem?

I have this problem reading them using my kindle

Could you give a specific example (e.g. a screenshot, or a font reference)? Without that it's hard to address the problem (perhaps different people have different journals in mind, with different fonts).

There's no quick solution, and not as long as we have print journals.

This is a historical anachronism. The fonts are chosen for the print version of the journal.  For a print version, if you use a smaller font, you can squeeze more text onto the same page and print the same paper on fewer pages -- which saves money.  So, for print publications, the small font size arguably makes sense.  However, today print is less important and the digital format is more important, but journal requirements haven't caught up to this fact.
For instance, in computer science, the ACM is a notorious offender: they require papers to use 9pt fonts, which are very small.

One might add that even PDF hasn't caught up to the digital age. There should be a better way to render documents for use on different media devices, and PDF ain't it.

What's wrong with the people in charge of keeping the font at 9pt at ACM? What is the reasoning behind this?

Not clear. Journals still produce print versions, for which all these restrictions come into play. The relevant question is whether online-only journals still have strange font requirements or not.

If research papers were written in clean LaTeX and the source was freely distributable, people could compile their own PDF files in the font size they wanted.

@kush: depending on the field, many are (well, minus the “clean”): the arXiv offers LaTeX source download for almost all papers there.

Additionally, it's quite easy to zoom in on a PDF with small text, so there's no real need for larger fonts on the digital side as well (unless you're reading on a phone, of course).

Journal prescribed fonts haven't really caught up with the digital era. They were optimized for a time of print, where each page had a price. Unfortunately, researchers are required to use fonts specified by the publisher at a conference. But many people usually upload a more readable version on a web page or the arxiv - 11pt tends to be reasonable.

I prefer the old-fashioned way of reading papers: print it and read with text-marker, and I find the usual font sizes OK (sometimes too large when printing on A4 paper). Margins of ca. 4 cm per column are (would be) nice, though.
Monitor space is much too valuable for more than taking a glance which paper exactly I want to get from my collection. Where should I edit notes, do calculations and see graphs/images/man pages if most of the monitor is taken up by the paper?
I did print much less when I had 2 monitors, but at my new place I have only one. And anyways, no monitors can hold as much easily accessible information as a bunch of papers laid out on a large table.
(But I LaTeX my papers, so whoever wants larger fonts is welcome to rerun them with other settings).


text:
How do I overcome fear of rejection when writing academic papers?
I don't know how to put it. I have never published before. Previously my one paper was rejected, that was because the experiments were not ready and my advisor asked me to still submit it just to have practice.
Now, 6 months later, I am writing another paper (on a similar topic). I have done some experiments, some are still going on. My advisor had advised me that "even if your experiments are not complete you should still start writing the paper".
But I'm doing a lot of procrastination and I think I am scared of writing and possible rejection. I have done a lot of writing in other forms before, like blogging etc. But the thought of writing an academic paper with all the stringent rules (everything has to be clearly written, cited, nice flow of thoughts) is scary.
Please let me know how should one's mindset be while in the process of writing a paper.

Thanks @EnergyNumbers. Yes, reading some top papers certainly makes me feel "How in the heaven am I going to do something like this"! Also, yes, there are some papers which seem to be badly written. But I don't want to be like them :(

Do not listen to the Impostor Syndrome.

Read through this question and its answers: http://academia.stackexchange.com/questions/2219/how-should-i-deal-with-discouragement-as-a-graduate-student

We've all had papers rejected.  I had my first paper rejected, and I was gun shy for a while after that.  Eventually I got over it, and now I still have lots of papers that got rejected, but almost all of them eventually get published.

Rejection is a healthy sign.  If you are not getting rejected, you are not aiming high enough in the hierarchy of journals.  Your work won't get accepted to a 1st tier journal by submitting first to a 3rd tier.

i really feel for you. I am in the same state when it comes to project proposals... for me, it helps having someone else at my level, so not a senior, to exchange ideas and co-write. If the thing gets rejected, it's easier to have a laugh afterwards..

Read through this question and links to see that you are not alone: https://academia.stackexchange.com/questions/17873/

One thing that might help with the fear of rejection is to view your paper as though it was a blog post. Obviously, you won't submit something in blog style to an academic journal, but it might help to think about why you blog. You have ideas and thoughts you think are important and you want to share them with a wide audience, who might be interested in your ideas or use them as a jumping-off point for something they want to do. The purpose of an academic paper is the same (well, in addition to the career benefits of publishing). You want to share what you're doing with people who will be interested in the results, and who might find inspiration for their own work in what you've done.
It might even help, as an exercise to get past writer's block, to write a blog post about your research. (You may not want or be able to actually publish it on your blog, but it might help your thought process either way.) What are you investigating, what are your methods, how is it going so far, etc.? You can then take some of that material, formalize the language, add the appropriate citations, and include it in the appropriate sections of your paper. But picturing your blog audience, rather than some journal committee, reading your first draft might take some of the pressure off.
Another thing I find helps me with fear of failure is to accept that the first draft of anything I write will be crappy and focus on getting ideas down and revising later. I also found, at least as an undergrad English major, that it's easier to just write late at night. Something about being tired takes the edge off my self-criticism and gets the ideas flowing. I describe it as my internal editor going to sleep by ten o'clock.

This is not really a complete answer, but it's too long for a comment, so here goes...
Remember that whatever you write now is not going be submitted. You don't need to overcome your fear quite yet because you're just putting words on the paper for your own sake. Just open your favorite text editor and write down everything you can think of. Forget about editing. You are just taking notes so that you can read it later and understand what you did and what you had on your mind. Don't filter yourself. You are just emptying your head to make room for new things. Write to forget.
Then, when you run out of things to write, go back and clean it up a little -- until you think of something else to write. Rinse and repeat.
As the content gradually becomes more complete, you will have more time and peace of mind to work on the quality of the writing and aligning it with all the best practices and advice and theory and rules of academic writing.
But for now, what's the first thing you think of that you've been working on in your project? Now open your text editor and write that thought down.

Here is a great book about scientific writing, that concentrate on the article structure and the writing process more than on the grammar per se:
"Scientific Writing = Thinking in Words" by David Lindsay
This book gives good advices on the writing per se, such as:

What are the different section of a scientific article and what they should contain (e.g. how to choose a good title)
Tips on how to improve the message you want to transmit in your article
How to make a good poster/presentation
...

It also provides great advices on how to build a good scientific question. It explains how a good question can facilitate not only the writing process but also the overall research. For me it is actually the kind of book any young researcher should read even before starting their research.

@EnergyNumbers sorry for the lack of details. I just added them.

Like anything else in life, perform the task with the goal to succeed, and the likely outcome of failure.
Understand that rejection is all a part of the game. Very few people succeed more than they fail. As a matter of fact, upwards of 90% of all academic papers are rejected for one thing or another.
The most important thing is to keep track of mistakes that you've made with past academic papers. Write them down as bullet-points on a separate sheet of paper. Keep that paper right in front of you as you work on other academic papers to remind you of what NOT to do.
Practice makes perfect. If you're just starting out, it's likely that you're going to have many failures before you have a successful one.

If you didn't have any scientific writing class before, I think you should start buying a book about it, and read it.
There are many titles avilable.
If you get one, it can give you some good advice on how to write (good) scientific papers.

No. We didn't have such a class. Is there any book you'd like to suggest?

@user13107 I'd suggest to you "La scrittura tecnico-scientifica" of Emilio Matricciani but unfortunately it is available only in Italian. You can find many books on Play.com or Amazon.com

Ok. Unfortunately I don't understand Italian. Thanks anyway. Edit OMG! That's a 400 page book.


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

Guessing the motivation behind your question: If you (legally) want to obtain a copy of a paper, you might want to ask for ways to do this here (at least in a quick search I have not found that it has been asked yet).

@Wrzlprmft sorry I don't have that motivation. I am simply trying to think for the far future :)

There's no difference between research papers and any other copyrighted work.

What kind of obligations are you asking about?  Legal obligations?  Moral obligations?  If legal, in what jurisdiction, and what does the contract with the authors say?  The answer to your question is almost certainly going to be "no, of course not, not unless it made some promises to that extent -- why would it have any obligation?".

No, why should it? Running out of copyright explicitly means a loss of a right. It does not mean the beginning of any additional obligation.
Running out of copyright, however, means that anybody who already owns a copy may duplicate it and make it available under any conditions he chooses (including making it available free of charge). Many university libraries do this.

anybody who already owns a copy, what if there is no one alive (outside the pub. house) who owns a copy (hypothetical scenario)? If someone then approaches the pub. house, are they obliged to provide it?

That does not change anything. They do not have an obligation to give you a copy. Actually, they do not even have to do so while they have the copyright.

@user19905 so that presents a dismal scenario hundred years down the line if a pub. house turns rogue/becomes defunct in future and no one has any copies!

@user13107: That’s one of the reasons, why national libraries exist. Though, if a publisher was any good, there will be numerous libraries holding copies.

Theoretically yes, but not practically. Each scientific journal is subscribed to and archived by hundreds of libraries. A publication has to be extremely insignificant for libraries to not archive it. In that case, the publication probably deserves to be unobtainable.

@RobertBuchholz What about digital archives of publications? I suppose libraries don't have access to offline digital copies of all the papers. Do they? At uni. we download papers via going to publisher site and not from local library repository.

That's a slightly different situation. I suppose, libraries will not archive those digital subscriptions. However, in those cases the subscription is not based on "delivery of X physical journals per years", but usually rather "guaranteed access to all publications of type Y since year Z". In this case, the publisher has a contractual obligation to give the subscribers access to the publication no matter what the copyright status.

@user13107 That is what systems like LOCKSS (Lots Of Copies Keep Stuff Safe) are for: distributed digital archives. A significant fraction of university libraries and publishers are already participating, so that access to articles is not interrupted if a publisher goes under.

the publisher has a contractual obligation to give the subscribers access to the publication no matter what the copyright status — ...until the library's subscription ends, or the publisher goes out of business.  (In contrast, libraries can keep copies of paper journals after their publishers die.)

@JeffE: I believe some subscription contracts provide for perpetual digital access to anything published during (or even before) the subscription term, even if the subscription is later cancelled. That addresses your first point. I understand that in some such deals, the library gets their own digital copy of the entire archive, addressing your second point.

I believe some subscription contracts provide for perpetual digital access — I'm not aware of any such contracts, at least with major publishers like Elsevier or Springer.  But maybe things have changed since the last time I looked into it.


text:
What should/can I do on finding an error in a published article?
Recently I found a paper that has a number of typographical errors, esp in equations. Should one notify the authors or the publishers on such issues? How do the approach change if the article is somewhat aged?
When should/can one write a 'Comments on ...' article? How different is an Errata and a 'Comments on ...' article?

If the original version is, e.g., a badly written proof that is difficult to follow but that can be fixed, one possibility is to write up some kind of informal exposition or review of the same result. You could explain the same result in a survey article, textbook, lecture notes, Wikipedia article, etc. Or your student could write it up as a part of their BSc or MSc thesis on a related topic. This way there would be a more easily accessible version of the old result easily available online. There is no need to draw attention to the errors of the original paper; just offer a new version of it.

See also http://academia.stackexchange.com/q/12195/64

Here's what I would suggest:

First, alert the authors to the issues. Wait to see how they respond, or do not respond. But in all cases, they should be the first you write to.
If the issues do not severely impact the correctness of the work or its utility, stop there. It's probably not worth making a fuss about something most readers will either not use, or can easily correct themselves.
If you publish something on the topic yourself, especially if you build on the authors' equations or otherwise use them, you should make a note of the issue in your article.
Finally, if you believe the issue is important and/or the equations are widely used, you should contact the journal's editor and ask for guidance.

Errata are “authored” by the original authors. Publisher's corrections also exist, when the responsibility for the issue (typo in equation, misprint in figures, etc.) is that of the publisher.

Can you add response to the age related aspect in the question, as well? Also, about errata and comment article.

To answer your last question, an errata is always (almost always?) written by the authors of the article, whereas a "Comments on..." article can be written by anyone.  However, to write a "Comments on..." article, which in my experience are rare, you must have a substantial new idea.  It's not enough to say "I found typos in the original paper".
If the original paper contains a proof that is incorrect, and you have a proof that is correct, that could be enough for a paper.  In this case you probably also need to provide counterexamples to the original proof.  Similarly, if you can explain why the original data analysis was seriously flawed, and you have correct data analysis, that might be a paper.

Thank you for the nice answer. Can "Comments on..." article be published after many years (say more than 10 years) of the original article? Also, please add to the answer, the approach towards typos or minor errors.

@NobleP.Abraham This is just my opinion, but (a) "Comments on..." articles can be published any time that you have something worth saying and (b) For typos and minor errors, I recommend that you do nothing.  If it's something the average reader can work out, then what "value added" would an article or note offer?


text:
At what stage of research career one can write a 'review article'?
At what stage of research career one can write a 'review article'?
Obviously a graduate student in the beginning stages cannot/may not write one. But how experienced does one need to be before attempting to write reviews? Does authoring a number of papers in the relevant field equips one for that?
Can a graduate student publish a review article? Do acceptance of review article (for publication) depends on the reputation of the author or co-authors?
EDIT:  As @JeffE has pointed out anyone can write a review article; the question is about getting this write-up published.

I think it depends on the scope of the paper and the field but I would think a grad student that just spent several years immersed in the literature around a subject would be very well positioned to write a review.  I actually published a review article shortly after completing my MS but before beginning my PhD.

Obviously, a graduate student in the beginning stages cannot/may not write one. — What the...?  Not only can graduate students write review articles, they should!  They may not be able to publish their review paper, but that's a totally different issue.

@JeffE Thank you. I meant "write for publication". Will edit the question.

There is precedent for published (by which I mean peer-reviewed) survey articles by beginning graduate students. See for example http://arxiv.org/abs/0911.0063

First, I'll remark that (at least in fields close to me: physics and chemistry), the process for submitting review articles is typically handled in a different way than other articles (which I'll call “research articles”). Review articles take a lot of effort to write, and that their publication may depend not only on intrinsic quality and scientific criteria, but also on editorial policy: if the journal has already hosted a review on a given topic, it is unlikely to publish another soon afterwards. So, the common practice is to come to an agreement with the editor before writing the full article. Either the editor contacts a scientist to offer him to write a review on a given topic, either an author sends an abstract to the editor asking if the journal would welcome such a review (with no guarantee as to the results of the peer-review process, of course).
This has an important consequence for your question: you can actually ask the editor of the journal of your dreams if a review by you and your co-authors would be welcome. Practices may differ between fields, journals and editors, but asking exactly the person who is going to make the decision is the right course.
Then, we come to what I would call the “customs”. It is indeed typical to gain some authority in your field before writing review articles. This usually means working for a few years in a given field, publishing some articles of your own, in short: getting noticed by your community. As such, it is not a typical thing to do for a graduate student. Maybe at the end of your PhD, jointly with your adviser. Most probably, later in your career: either as an experienced post-doc, or after having gained a faculty position.
With more than a few years of experience, my personal experience is that you perfectly write reviews (and the editors will accept if the work is good). However, it gets easier with seniority, as you will (i) more easily have your work accepted in more prestigious journals, and especially (ii) more easily get invitations to write reviews.

You mention this in passing, but I think it's worth emphasizing that for a young researcher a good approach is coauthoring a paper with a more experienced person who can contribute a wider perspective.

There are a number of different types of "review articles."
There are book and "show" reviews, but I don't think this is what you mean. These can be written by anyone, but are often written by junior people who are willing to stick their necks out a little.
There are also systematic reviews in which the literature is search systematically and the quality of each piece of literature is assessed against a predetermined set of criteria. Systemic reviews often only focus on a handful of studies. If there are more studies a meta-analysis may be conducted. These again are written by people at all stages.
"Tutorial" reviews which attempts to summarize a large swath of research. A literature review in a thesis is a good example of this type of review. These types of reviews often are published as book chapters. Many are solicited by an editor, but some are submitted. Again people of all stages can publish these.

Obviously a graduate student in the beginning stages cannot/may not
  write one.

This is news to me, given my second paper was a review that appeared in a top ranked journal in my field. At the time, I was an undergraduate student.

But how experienced does one need to be before attempting to write
  reviews? Does authoring a number of papers in the relevant field
  equips one for that?

Authoring a number of papers can help you develop a reputation, but reading a number of papers is how you understand the field as a whole. The process for the literature review chapter of a dissertation and the process for writing a review are very, very similar.
Similarly, there is no reason why a graduate student could not write a meta-analysis or systematic review. Indeed, in my graduate program, this was a common first or second paper.

Can a graduate student publish a review article? Do acceptance of
  review article (for publication) depends on the reputation of the
  author or co-authors?

Often, review papers have to be invited, and this can depend on the reputation of a co-author, or an advisor that makes sure it makes its way to an editor's desk.

Could you provide a link to your review paper?  I think that would be interesting.  I guess you probably know that there are some fields (e.g. mathematics) in which review articles by students are very rare.  There are probably more fields though where students would be interested in publishing review articles and who could learn something from your success in this.

@PeteL.Clark Don't know how I missed this comment, but better late than never: http://jvi.asm.org/content/81/11/5429.full . I should also note that one of my first projects as a new graduate student was working on a review paper.