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Meeting professor for the first time to discuss ideas
So I have been talking to a professor in quantum game theory from a unversity in my city whom I have never met. We have been going back and forth on mails discussing ideas. I did alot of research and presented my ideas to him through mails. He has asked me to come meet him to further share the ideas face to face and introduce me to one of his colleagues. The main purpose of me contacting him was that I wanted to work on some research with him and probably find employment along side him as an RA or along those lines. I am really nervous to meet him. I feel that I may fumble while discussing with him. Could you please help as to what sort of discussions usually take place in meetings such as mine and what i should expect. Would the discussion be extremely technical that would test my knowledge to the core or will it be a casual and light exchange of theoretical ideas.

I know you are nervous, but it's only two people talking. We can't guess where the conversation will go, that's up to the two of you. And you are already talking to him via mail, this meeting is just the natural course for things, relax! That said, your question is way too broad for academia.se (country/field would help, not sure if it would be enough), as I said, we can't guess what the two of you will do, so expect some "vote to close"...

Usually, professors do not test students' knowledge at their first meeting because they also know that you are nervous and may be afraid to lose you as a student due to your fears. Likely, the professor will just talk about his or her own research project and will not expect that much input from you. It is what I usually do.

@phys_chem_prof Perhaps that's so for some professors: many, however, will test the students knowledge because they are highly selective about which students they wish to work with.

Since he wants to introduce you to others, I would say you already won. I would expect friendly conversation and discussion, and you should be prepared to answer the question how you would like to contribute to the topic in the future.
Let us know how the meeting ended ;).

Here's a starting point for your next letter to your potential advisor:

Dear Prof. So-and-So,
Our correspondence has been exciting and stimulating.  I am pleased
  about your invitation to visit your institute, but I'm also nervous.  My
  hope is to work on some research with you and possibly find employment
  alongside you, as an RA or something along those lines. Therefore I am
  really nervous about this meeting! I feel that I may fumble while
  discussing things with you in person. Could you please help as to what
  sort of discussion will take place in such a meeting, and what I
  should expect. Will the discussion be an opportunity for me to
  demonstrate my knowledge?  Is there a particular topic I should
  prepare in advance of our meeting?


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What does it meant " assignment of paper with decision in prosess " in the same time?
I have submitted the paper to JFA journal after the stage "submitted to the journal" (14 days ) ,I have received the message that paper is assigned with current stage " Decision in process " in the same time , Is this can say anything about acceptenece or reject of my paper ?

If I understand your question correctly, your paper had status 'submitted to journal' for 14 days and then jumped immediately to 'decision in process'. In principle this means the editorial board is making a decision - possibly the assigned editor has already made a recommendation, and now it just remains for the editor-in-chief to make the final decision.
However this would also indicate that the paper skipped the peer review stage entirely. This is not a good sign I'm afraid. Either your paper is so groundbreaking that its correctness is self-evident (leading to an immediate accept decision) or it's being editorially rejected.
EDIT: There's something else that looks pretty possible - a revise decision because the editors can't understand your English. They might also say reject and resubmit.

your answer convince me, it's stay to send to you my paper and give me then your opinion if it is possible just to share me your Email, probably my english is not good

@zeraouliarafik what do you want me to do though? If you want to improve your paper's English, you'd need to approach a professional editor, e.g. Enago, Cactus, etc - Google for "professional english editing".

Thanks ,just to check the paper and to say me if it will suitable for publication .

It means that the editorial board is in the process of making the final decision about your paper.

Thank you for your answer , but my question is to know anything about acceptenece or rejectness of my paper , but i feel it will be reject since rarely journal accept paper within this short time

@zeraouliarafik Being in final stages of making the decision means a decision has not been made yet. So, you cannot conclude anything from this status and you have to be patient and stay positive.

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Should I submit my paper to a different journal after not receiving any acknowledgment for five months?
I submitted a paper to a low to mid-tier online-only journal in my field last January. I did not receive any acknowledgment from the editors that they received my paper and the journal has already published papers that were submitted after I submitted mine. Having been busy since January I forgot to ask the editors for an update. I was only able to send an email a week ago, and I still did not receive a reply. Should I submit my paper to a different journal or should I wait a bit more for a reply?

Is there a web based submission system where the status of your paper is indicated?

Related, but probably no duplicate (given that this seems to be a technical problem or similar): Is my paper under review (or similar) for too long and if yes, how should I react?

Give them another week, then decide.
Sending two messages within one week may be considered as pushy, I would try to avoid this. However, if you have serious concerns about the status of the paper it may be justified nevertheless. Whether or not your concerns are serious depends on the history so far: if you have not received any notification at all (via any submission system or similar), then maybe the paper actually got lost.
Personally, I would have contacted the editor earlier since in my field the review duration is 2-3 months -- of course, this may be different in your discipline. Some journals state certain statistics on their web page, such as the time from submission to the first decision. This gives you a hint what time spans you can expect until your paper is reviewed.

At least there should be a receipt notification, automatic or not. I would even follow your recommendation to wait then search out for a retraction. Review duration is one thing. Not knowing the status at all is unacceptable.

Not receiving an email reply after a week isn't unusual, but not receiving any communication for five months is. A short (days) wait for that email might be worth it, but simply waiting generally is unlikely to be fruitful.
I would take steps to prepare to submit elsewhere while you wait for the reply. But if you do decide to submit to a different journal, make sure that you formally withdraw your paper from this one to avoid problems of multiple submissions.
But, it is possible, perhaps even likely, that something has gone wrong and your paper was either submitted incorrectly or somehow lost. You should have gotten at least an acknowledgement that it was submitted.

I would contact the journal first if I were you. Bear in mind, submit one manuscript to two journals at the same time is a big no-no in the academic field.
So contact that journal, ask what happened, or even request to cancel your submission. You haven't heard anything from 5 months, this is highly weird. I've never met this kind of problem.

I agree that 5 months is a long time without any information. Definitely inquire and in the meantime, prepare it for another journal. I would even consider calling someone (editor? administrative personnel?) if you can find a number, but honestly if it comes to that, I would consider submitting it elswhere.

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Citing someone directly with additional information in footnote
I would like to directly quote some sentences of another author who uses a word A which is a synonym for a word B I'm using in my text. Note: I would like to use my word B as the word A is very rare.
So I placed the text of the author into quotation marks and a footnote at the word A stating that in the following the word B will be used in my text. At the end of the quotation I put the source of the quote.
Is that correct or could it be misinterpreted as a footnote of the text I'm quoting? Should I add e.g. "Authors note:" before my footnote text?

Why not just put it in the main text? It seems important.

@BillBarth It isn't important just a word. The footnote is for the convenience of the reader so that he knows that the quoted text has sth. to do with my text, because the words are synonyms.

My preference would be to avoid the footnote altogether, as I find them distracting. Keep the quote verbatim, give the source, and then explain the terminology in the next sentence of your text:

Smith claims that "the best breakfast is a soft boiled ovum" [Smith87]. (Smith's "ovum" refers to what our paper calls an "egg.")

Another option, if you don't really care about  showing  Smith's exact words to the reader, is to make the change in the quote itself, indicating the change with brackets.

Smith claims that "the best breakfast is a soft boiled [egg]" [Smith87].

I have no idea what your field is ... so I'm going to give a slightly different piece of advice than Nate Eldredge's answer.
When writing in Chinese philosophy, it is acceptable practice to at the beginning of your paper indicate that you are going to use Pinyin throughout including in quotations and then to change all quotations to Pinyin rather than marking each and every instance of such a change with [].
I have seen a few other places where similar conventions are allowed for changes in the common name used for a text, e.g., Practice in Christianity instead of Training in Christianity the for the Kierkegaard [Anti-Climacus]' text.

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How to set bibliographic entry to display author only when applicable?
I'm writing my bachelor's thesis with OpenOffice Writer. Most of my sources are websites, and the author or publication year is often absent.
With Writer's bibliography system, you can specify whether to display author, publication year etc. for a certain type of entry, eg. WWW document, but the same settings will be used for every WWW document (whereas I would like to have the author displayed when and only when applicable).
I know there are "user-defined" entries, but this system seems a bit clumsy, as you can't rename them from "User-Defined1" and so on.
I think MS Office Word has a better system, but I've heard that the open-source alternatives are just as good, so why buy it? I've also tried Zotero and Mendeley, but it seems they can't display inline citations in the [1][2] style, which I would prefer.
Would rather avoid using LaTeX/BibTeX, since they seem like overkill.

Not saying that LaTeX/BibTeX are the only or best alternative, but if your current software cannot do what you want, while LaTeX/BibTeX can, you may want to reconsider what is or is not "overkill".

Mendeley uses the same styles as Zotero (CSL) - as do a large percentage of the reference managers available. You can edit the styles yourself to do exactly what you want, they are just XML files.

Okay, apparently you can get the [1] style in Zotero, but it's not installed by default.
Also, there's a "protect from manual changes" checkbox which can be unchecked in Writer. This way you can edit the entries in pretty much any way. It's far from ideal though, as manual changes are overwritten every time you update the bibliography.

I edited out "duh": I think downvoters thought you were insulting the asker, not realizing that you are the asker. But maybe you could elaborate on how the "protect" checkbox helped?

Alternatively you can use the WWW-document type in every case instead of a second or third user-defined one. Build the bibliography entry for WWW-documents in a way that it always reflect an Author.
If no Author is given, you can fill the author-field with:

Unknown or Anonymous
a user name in case of publications under pseudonyms
a company name e.g. for white papers from tech companies. (W3C, Oracle...)

WWW documents are difficult to deal in citation at all. You may also miss a creation or publishing date and can sometimes only rely on the date you requested it from a web server.
Anyway you should ask your supervisor if he/she accepts WWW documents as cited sources at all. Some supervisors may reject sources without an author as not proof-able or not cite-able.

Tip: If you want to be sure, that a website did not change in the time between submitting it to the examination office and the reading by your supervisor, I suggest you to use a web preservation service like WebCite. With this you can provide an additional link to a preserved version, even if the original source is yet gone.

Early warning: I've made bad experiences with de-activating the "protect from manual changes"-option in LibreOffice/OpenOffice Writer. It kills the advantage of auto generating the bibliography cause everytime you update the bibliography after adding new sources your manual changes are gone with the wind.


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Coursea.org? Comparable to actual college level credit?
I have the option of undertaking a Coursera.org course in An Introduction to Interactive Programming in Python, which is stated to be eligable for a Fundamentals of Computing Specialization , which they state is a Verified Certificate. This certificate costs 50$ though, and even though I can and probably will take the course free, would this type of course be looked upon as something equivalent to a introductory comp. science course at the college level? Would it be resume worthy or am I just being "sold" something?
I am not trying to badmouth the people at Coursera, I am sure they have noble intentions, but I am a skeptic at heart. Here is a link to the course in question.


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How to prepare for undergraduate research of which I have no background in?
I recently applied and got accepted to a very large research lab in the U.S. Although the catch is that I did not get put into my major ( Biology ) and instead was placed into computer science ( simulations/super computing).
I reason this is because I had several computer science classes in the past, but I eventually changed majors to biology due to not flourishing with high level maths or coding.
I assume that to prepare for any research, one must read the supervisor's papers and self study. Although the issue is I feel I am totally outmatched for this position, due to my struggles in computer science before. Is there a good strategy for approaching this upcoming internship or should I resign instead?

I'm confused -- is the internship even a biology-oriented internship? Or did you explicitly apply for a computer science internship?

The internship was for all types of undergraduate STEM based science, as it is a very large lab that hosts it. I think the issue was I applied for biology research experience, but the closest host lab I could attend also had the smallest biology department.

@tonysdg if you turn that into an answer, I'll upvote it, because it makes the points "talk to them" and "biology is an important part of computational biology". I wouldn't say programming the simulation is "easy" but that it's fruitless if you haven't thought it through from the biology side. You could generalize that to: domain knowledge is an important part of most programming tasks because without it you're going to program the wrong thing. One of the  goals of the internship might be to practice working with/as the domain expert.

@tonysdg          Do you have any suggestions on how to word such a communication? I was thinking along the lines of:  "Hello Dr.  [Name], I was chosen to be a prospective undergraduate research assistant for the spring semester. However, I have to be honest with you in that I feel unprepared for the position as my computer science skills were always weaker than my Biology skills,as it is my current major. Do you have any advice for how I can be of most use to you for the spring semester, as in what I should be attempt to be more than proficient on before my arrival?   Regards Rosiv"

@Sumyrda: Done. Thanks for doing a much better job than I did at explaining why domain experts matter :)

@RoSiv: Can you move your comment to my answer below?

My advice is to discuss this matter directly with whoever your supervisor will be -- tell them about your past experience, your concerns, and ask for their advice. They may be able to have you shifted -- or they may tell you that they were explicitly looking for your biology background.
As to why they would be explicitly looking for your biology backgrounds -- computer scientists frequently collaborate with other scientists when working on large-scale simulations. The reason for this is that there's two sides to the simulation -- the actual code required to run it, and the domain knowledge required to design the code in the first place. As @Sumyrda pointed out, this may be one of the goals of the internship (to give you experience in working with/as the domain expert).


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Last minute master's application?
I've been gearing up to apply to grad school for some time now. Switching fields, working full time and other considerations mean that I keep pushing back my goal of applying. I have been strengthening my qualifications (small publication, open source work, git hub), but I still haven't applied.
I just ran across an interesting program that has the deadline date of March 15th. I'm tempted to just try and to get everything together in a month. I'm worried about being sloppy, or there not being any room in the program at this late date.
Is there any disadvantage to applying this late? Would it be more prudent to wait for fall, continue to work through the spring on improving and apply then?

Are you looking for scholarship considerations? I am applying to a school where the deadline is May 1, but the deadline to apply and be considered for financial aid is March 15. Depending on your situation, you may not need to rush then.

If you apply before the deadline, then I wouldn't consider it late.
Depending on the university and department, they might not review applications until after the deadline or they might review them as they come. So long as you make that deadline though, it should be fine! You may find this question helpful regarding the benefits of applying early.
I would certainly encourage you to apply now if you can. On a side note, I applied after my university's deadline and was still admitted but don't do that :)

I'm emailing them now. I haven't taken the GREs so if it would be possible for those to lag a bit, this might work.

The web-based application process will sometimes allow you to continue to attach supporting documentation even after application submission. For programs that select candidates over time instead of in batches, this may be beneficial: as long as you submitted and paid for the application by the deadline, you can still add the supporting documentation within reason before or after the deadline. Keep in mind they won't consider your application package until all the checkmarks can be made, and you should certainly contact program admissions ASAP and let them know your situation, and see what they have to say.
Note: Funding can depend heavily on your timely submissions.

If there are some documents/requisites you won't have on hand in a (reasonably) timely manner (ask them if they can give you some leeway!), better concentrate on putting all your ducks in row and apply next term/year.
Committees tend to get many more applications than places available, any excuse to weed out an application could be welcome to some... besides, an incomplete application just looks bad. So the applicant can't even get the complete application together, who says they won't run off after the next shiny program that comes to their attention?


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PhD admissions - Contacting multiple profs from the same university
Presently, I am writing to potential PhD guides in US universities. There are two professors from the same department who work on topics that cannot be considered closely related, but I would be happy to work under either of them.
I have already written to one of them, who has asked me to go ahead with the application process. I am now wondering whether I should mention in my mail that this (contact with first prof) has already been established, while still conveying that I am adequately interested.
Upon a positive reply from the second prof, what would be the best way to talk about both profs in my Statement of Purpose? I want to keep both options open, while not being rejected because the admissions office/the professors thought I wasn't specific enough with my application.

I am currently having the same question. Did you contact the second supervisor finally? Did you mention that you have talked with the first supervisor?

No, I did not contact.

May I know is it because you got the reply of the first one or you were afraid of those issues you mentioned above (these are exactly my concerns)?

After getting encouraging replies from other universities, I decided not to apply for the second professor. So, it's more the first case I guess.

I think there are no answers yet on this question because there is no problem here; being interested in two different research groups is acceptable.  In fact, interest in just one group increases your chances of rejection since that group may be full.


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My essay has been plagarized in a journal article - what to do?
I have an essay online on a dense philosophical text. One sentence of my paraphrasing or interpretation of this text has been copied verbatim in a now-published journal article. In that article, the sentence is attributed to the original author of the philosophical text, not to my essay. The article was published this year; my text was written over five years ago.
This upsets me because

I believe I have been plagiarized
The authors are asserting my paraphrasing and interpretation of the text as their own, and in the process skipping the work of interpreting the original text, along with misleading their readers. If the authors want to use the text to support their argument, they should paraphrase it themselves, or quote directly (and who knows, my interpretation could be wildly off!).

Regardless, can any one advise on the best way to report or address this, or what I should expect if I do so?

How many words in the sentence that you believe it was plagiarized?

@qsp: It could still be that the idea itself was plagiarized, regardless of the word count.  Harder to prove, perhaps, but still potentially plagiarism nonetheless.

@tonysdg: if my understanding is correct, the OP only paraphrased a text, so there is nothing new in the idea. If the sentence is too short, perhaps there is not many way to paraphrase that text, and hence it could just be an accident. Therefore, although lifting a sentence verbatim is plagiarism, this case may be too trivial and unprovable if the sentence is too short.

@qsp It's 26 words, but there is a key idea conveyed there, which is a lot of why I think it was lifted in the first place. I think if someone were to read the sentence they would agree it's been copied intentionally.

"In that article, the sentence is attributed to the original author of the philosophical text ... The authors are asserting my paraphrasing and interpretation of the text as their own". I'm confused.

In other words, the authors have lifted my sentence verbatim, which is partially an interpretation, and simply footnoted it to the original philosopher.

@wxs: Are you certain your own essay did not make it seem like you are quoting the original text? Maybe this was just a mistake made by the article's author? (I'm not saying this is okay, quoting a text without checking if what they are quoting is in the actual text is sloppy, at the very least, but, as they say, never attribute to malice that which can be explained by mere incompetence and/or laziness. Not the first time around, anyway. ;))

@tomasz That's a good point. Of course I can't know if it was an honest mistake or misunderstanding by the article author, but I can say that there are direct quotes (with the page number cited) in my essay. I would argue the authors should know when I'm using my own words or the philosopher's.

@wxs: Perhaps you could simply contact the authors and clear up the whole mess without going to the editor over their heads? I don't have any directly relevant experience, but I believe that it's generally better to solve problems cordially, without involving higher authority, whenever it's possible.

Contact the editor of the journal, present your suspicions, and be prepared to submit evidence supporting your claim.

I'm not so sure that a journal editor would, or even should, proceed with plagiarism charges on the basis of a single sentence.

With one sentence, there is a high probability that this is just how the author wrote it himself, without copying the poster. For example, it would be quite possible that someone typed an answer identical to tonysdg's one sentence. No copying, no plagiarism. And then there is the question whether anyone would care if one sentence is copied without attribution.


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Learning Biology, methods?
I am not sure if this is the right fourm for this question or if it counts as opinion based/subjective (if its not moderators feel free to remove or delete it, I should know better by now), but are their any "objectively  better" ways for studying for biology tests/material than simply reading?
I usually try to read some of my texts before I sleep, but nothing seems to stick. And before a test I always try and rewrite my notes and the professors lecture notes with rewritten diagrams as well. And I have been getting average marks, I would like to improve on that though. I know this is "story-based" evidence, but pedagogy is not my strong suit.

I always found the best way to study was to rewrite all my notes. This makes you go over all of your material again. By writing it, you are also going over the material much more slowly.  In addition to rewriting my notes from class, I would supplement that material with the textbook to make even more comprehensive notes. Once that is done you have a nice set of notes to read over and over again leading up to the exam. I did this because my biology professor was old-school and all tests were fill the blank, short answer, and essays. Thus, I needed to practice writing the material. I would often make myself practice exams and test myself beforehand to make sure I was absorbing information. Flashcards are also helpful. I usually try to spend the night before exams just reading. At that point you should be just reviewing. Hope this helps! It got me through my biology degree and I used these techniques through all my PhD coursework as well. Everyone is not the same though when it comes to learning material so you just have to find what works best for you.

Thanks for the reply, would you think those skills would be suited to studying for the Biology GRE? Or any advice on studying for it in general, since you are/have been a graduate student?

I would suggest using a Kaplan GRE prep book.

The only one I can find is the 5th edition(2010), do you think that would suffice?

Don't go to your textbooks if it's not working. I struggle with science classes myself and all the textbooks ever did was confuse me and class lectures didn't help either.
What I did was my own research in relations to the class. For example, in my BIO we started with cells through the entire human body. I couldn't get my head around how it all worked with different bonds and fluids and such so I just did some basic googling and I found a site for middle schoolers which explained it simpler than my textbook but still had all of the information I needed. Throughout the entire course I looked up everything I needed online through other sources that simplified it by mostly using analogies.
This helped me, try things until it works.


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Asked to perform task I lack skills in
I am a undergrad student of biology, I was a computer science major but flunked out. One of my professors teaches/is learning genomics and wanted me to help him with a project since he assumed I had coding experience/skills. I told him that I lacked such skills and would not be a great fit to help him. Even as he described the project and his goals, I found myself stressed due to all the things he expected that I could assist with / do, so I am not really self-deprecating.
I am interested in genomics, but I was going to build my coding skill set slowly through following books and the like. My professor expects him and I  to tie up all of his research during the next spring, and I doubt I could learn how to work with big data and all the possible languages required in such a short amount of time(for me).
Should I try and "bite the bullet" and learn the task(s) he has at hand to finish the project or should I decline his offer on the basis of not being skillful enough to be of use?

Should I try and "bite the bullet" and learn the task(s) he has at hand to finish the project or should I decline his offer on the basis of not being skillful enough to be of use? — Neither, I suggest a third option: come clean about your skills/abilities, and ask your prof if they are willing to rescope the project.

You won't learn much coding by "following books and the like". You need to do real stuff. Of course, you learn by making many mistakes, that your professor may or may not be happy to have in the way, so you should discuss it with him.

Think for yourself. If you're very much interested in Genomics, then working with this Professor would be beneficial for you in the long run. But you're not at all interested in learning those programming languages, then it would be better if you decline his offer. Please keep in mind that you won't always get such an opportunity. So, think we'll and decide. All the best!


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When can a thesis get rejected or asked for a major revision?
I am planning to submit my thesis next month. I have 4 published SCI-indexed journals (Elsevier, Springer, IEEE transaction, World Scientific) and 2 more journals communicated (all first authors). My thesis is on Bioinformatics and Computational Biology. The thesis will be sent to two external examiners about whom I will not know (Institute policy). I am fearing what will happen if my thesis somehow gets rejected (I do not know why I am so scared right now).

Should I be worried that my thesis may get rejected?

Also, what happens when the thesis gets major revision?

Do I have to do the corrections and send the thesis again?

When a reviewer is checking a thesis, usually what does he want in
it?

Does he read the entire thesis line by line?

Kindly share any incident of thesis rejections if you know of any, why it was rejected and how the person finally got his degree.

Surely you have been a PhD student long enough to have asked other students what they went through? Have you asked your supervisor? Supervisors don’t usually allow submission until the work is ready and you should have agreed the work with your supervisor.

supervisor has agreed. However, I am the first student of my supervisor to submit thesis in my institute. Different student of my institute had different experiences. However, I wanted to get a more diverse view regarding this. Therefore posted the question...

Most examiners do not fail a student unless they absolutely have to.  For example, when the thesis has no contribution or there is academic misconduct.   Let's say an examiner fails you for reasons other than academic misconduct, the thesis will usually go to a third examiner.    Your supervisors should know whether you will pass based on his/her own PhD thesis standard.  I would also suggest you look at the examination criteria of your university

With several journal publications in solid or better journals, it's very unlikely to be rejected. If the supervisor gave you green light, they assume you are fine. It is good to be anxious to some extent, but at this stage, according to what you report, it does not look like an existential matter. Of course, we do not know the details of the case, but I do not see red flags here.

where are you? Thesis submission and marking processes vary wildly between different academic cultures.

This is a question you should be asking to your advisor and committee.  It is not a question for strangers on the internet.

@Roland You might find this Q&A interesting: https://academia.stackexchange.com/q/12187/72855

@DavidKetcheson I agree that in an ideal world, the student would have been told these things by their supervisor. However, in many non-US systems (e.g. the UK), students often don't have committees. And if you are the supersivsor's first student, they might not have much more idea than the student, especially if they got their PhD in  a different system.

This very much depends on which system you are in. I can answer from the point of view of the UK system.

It is very unlikely your thesis will be outright rejected.

It is very likely you will be asked to make some corrections.

Yes, you will have to make the corrections and send the thesis again.

Requirements for a thesis are generally set out by the university. They normally specify you must have made a "novel contribution to the field" and the work is, in principle, of publication quality.  Or something similar.

Yes, a good examiner will read the thesis line by line.

There are five possible outcomes from the examination of a thesis.

Accepted without corrections
Minor corrections - generally textual changes only - 3 month time limit
Major corrections - might involve some reanalysis, but no new experiments - 6 month time limit.
Resubmit - this thesis does not pass, but contains sufficient material to convince the examiners you are capable of passing. You are giving leave to rewrite and resubmit the thesis. May involve new experiments - often 1 year time limit.
Fail (either with or without a Master of Philosophy degree).

Almost all students are given minor or major corrections - I'd say 90% fall into these categories. Slightly more in minor corrections probably. Maybe 8% get no corrections, and perhaps 1.5% are asked to resubmit. Very, very few fail outright.

I'm in the UK system as well. I've been supervisor and examiner and I've seen what happened to other students. From my experience 1.5% is far too low a percentage for resubmission. I'd say 10% or even more. I have made this decision as examiner, and had it made by other examiners for one of my students (although that was apparently not based on the thesis in the first place, more on viva performance); I have examined less than 10 and supervised 5-10. I've also seen this happening in other cases. I agree with the rest, by and large.

Disciplinary differences I guess - I've never done it, nor had it done to one of my students. Of my colleagues, I only know of one or two occasions where they have given out a re-submission.

This would match my US experience in biology. I would say the number for anything worse than "major corrections" is effectively zero when the advisor supports the thesis, and 4 or 5 become much more likely if not. Most who would otherwise fall into 4 or especially 5 would likely not even submit a thesis.

Should I be worried that my thesis may get rejected?

Four published journal articles and two under review, that sounds impressive to me! It's natural to fear your thesis will get rejected, it's natural to be scared: Search this forum for impostor syndrome

Also, what happens when the thesis gets major revision? Do I have to do the corrections and send the thesis again?

That'll likely depend on your institute and country. I suspect you'll need to make corrections in a timely fashion, perhaps your examiners will need to check they are satisfied.

When a reviewer is checking a thesis, usually what does he want in it?

A novel (valid) contribution to your field (just like a journal article), mastery of the material, and a broad understand of your domain.

Does he read the entire thesis line by line?

That depends on the examiner.

The other answers have generally good advice, to address a specific question you had:

Kindly share any incident of thesis rejections if you know of any, why it was rejected and how the person finally got his degree.

I only know of one thesis that was completely rejected. In this case:

The student had a very weak publication record.
The student decided it was time for them to graduate (not the advisor).
The procedure for a defense didn't require the advisors signature, so they submitted the form and schedule the exam without their consent. (And initially without their knowledge.)
The advisor told them they weren't ready to graduate.
At the defense I'm told they couldn't answer even basic questions on the field properly.
After a year they were able to try one more time, and nothing changed, so they failed out of the program.

From what you've posted, this is far from your situation. So, while occasion anxiety is understandable, it is probably unwarranted in your case.
I also know of one case where someone's PhD was found to highly overlap with another PhD in another area with completely different terminology. (Math vs CS) That was awful for everyone involved - in that case they were given more time by the committee to come back and address it, and eventually they graduated.

It is possible but unlikely that your thesis is rejected.
Although probably technically illegal, it is also probable that any sensible examiner would quietly contact your supervisor before submitting a report if there was a major problem with the thesis, if only to make sure there was no major misunderstanding and avoid embarrassment for the student but also for those like the thesis director who allowed the thesis to go forward.  My experience is that examiners will prefer to hold their noses and accept a marginal or bad thesis rather than cause trouble and reject the submission.
The most likely outcome is that you will be asked to make minor revisions, and then your school will have some procedure to handle this time-wise.  Usually the examiners do not need to see the thesis again when resubmitted after minor corrections.
Depending on how closely the thesis is examined, it may be accepted as is, but this  very rare in my experience, and not necessarily desirable and one wonders how closely the examiner did his/her job.  You want the examiner to engage with and improve the outcome to raise the visibility of the results.
In 35 or so years of experience, I know for certain of only three cases where a thesis was rejected: in two instances a document was submitted over the objection of the thesis director; in the third instance a real error was found in the thesis. Since this is exceptionally rare, you tend to hear about such instances when they happen.
Thankfully, I was not involved directly in any of the situations.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Help me choose section title
I finished writing a paper and I'm currently putting finishing touches, but I'm finding it difficult to choose a good title for the first section.
Basically this section is written for a lay audience and talks about how the research was conducted and how I ended up discovering the main result. It includes lots of motivation, any pitfalls I encountered, etc.

I'm voting to close this question as off-topic because it does not concern academia as defined by the help center.

I think its a very lazy question, but not off topic.

Typically, such a section is called "Introduction" or "Motivation."


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Get citation relations from a given collection of papers
I have a pretty big collection of papers (as bibtex records) for which I'd like to add citation relations, i.e. a collection of cites(a,b) where a and b are two keys identifying the citing and cited paper respectively.
I want to avoid doing this annotation manually.
Is there some web service to extract this information automatically?


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Is it possible for a conference not to be published?
I was quoting a paper from the ICLR 13 and noticed that I could not find any information about the publishing of the conference. So far I have only seen proceedings which published the papers of the conference in a book entitled 'proceedings of the xth international conference ...'
Q: Is it possible for a conference not to be published, i.e. the papers can only be found online (or via a database, e.g. arXiv). Is this a common thing? Why?

Yann Lecun (one of the chairs of ICLR13) has well defined views on the future of publishing papers, http://yann.lecun.com/ex/pamphlets/publishing-models.html,
Which it seems is the basis for what ICRL is doing

This is probably field dependent. In mathematics, there are only very few conferences that have published proceedings at all. For the most part math conferences are just talks, and if you have a paper you publish it wherever you want.

ok that explains a lot, so I assume it is not a common thing (so far) but will be more and more common in the future in order to speed up exchange?!

In my field, electronic conference proceedings are very uncommon, and printed versions almost inexistent. Generally they attract little attention in contrast with journal articles.

Printed proceedings are becoming much less popular even in computer science; many proceeding are "only" online.

Things that are online are published.

The important distinction that you want to pay attention to here is whether the proceedings are archival or not.  Fewer and fewer publications (conference or journal) are actually put onto dead trees: it's expensive and heavy and takes up lots of space in your office.
An archival publication is one whose proceedings are in the custody of an institution that guarantees their long-term preservation and availability.  This can be anything from a traditional journal to a large society like IEEE or ACS to a database like arXiv or even a memo collection like the IETF RFCs.  If it's archival, it's a "real" publication because it will be there if somebody goes looking for it in 20 years.  Prestige of the venue is a completely orthogonal question...
Anything that is not archival is transient, and might vanish at any moment.  This happens often with communities that don't have peer reviewed conferences (e.g., many biology communities).  This is fine if the point of what you wrote was to have a ticket to give a presentation or to have a discussion.  If it's not archived somewhere, though, it's not really a publication, because there is no persistent reference that can be followed.


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Are there tools to implement an institutional open access policy?
Many universities have adopted open access policies, giving their employees an incentive to make their scholarly articles freely available online.
To enforce this policy, universities should ideally keep track of the research output of their employees, and remind them to upload their papers if they are not freely available yet.
This is a rather time-consuming task: I wonder whether there are tools to facilitate or automate this process.
Such tools could perform some of the following tasks:

Track the published papers and match their authors with the employees list (probably using some bibliometric platform like crossref.org)
Locate freely available versions of these papers
Run a repository where the papers can be uploaded (there are plenty of tools available for this task)
Manage waiver requests from researchers who want to opt out of the policy
Provide statistics about the publication practices within the institution

One year after this question, we have launched the http://dissem.in project! This does most of what I was looking for. Comments are welcome!

I hope you checked with the library of your institution, since these are the people who are typically involved in that sort of things.
There are softwares to create institution repository of articles (often pre-prints) to allow free access and comply with most government funding regulation. There are probably many options, but one of these softwares is called infoscience and is used by institutions like the CERN in Geneva.
This system allows researchers to have an up-to-date, automatically populated  publication list with links to the downloadable documents, enables keyword search, run stats, etc. It is useful as well if you are writing an annual report of your group/department, etc.

Thank you for your reply! I haven't checked what my librarians do yet, but of course I plan to do so. Infoscience is very interesting. The OAI-PMH protocol seems to be close to what I am looking for, if it is widespread enough.

Building on Cape Code answer, what you seek for is an institutional repository. There are many, but it depends by the single institution. You should ask yours.
Software used are often DSpace and Eprints (but there are others): these systems let users upload pre-prints and other documents; release them with Creative Commons licenses, use DOIs (sometime provided by the very same institutional repository); provide digital preservation, provide statistics, etc.
The open access movement has a strong component in librarians, who in the last decades built protocols and best practices.
Every institution is different and offers different services.

I'd go for a simpler approach. Just ask the researchers to fill in a simple online form whenever they publish an article. Make it extremely simple: just the DOI (or alternative citation if not available) and a checkbox if it is open access with a link to it. Don't make it take more than a minute to submit.
As a compensation, you can, for example, provide Natbib files free to download and a nice list of OA articles, so other researchers can find easy to cite and find your articles.
It is not much work if everybody does their part, and you just need to make it easy enough and worth to do it.

The software I mentioned in my answer has an online user interface, much in the form of an 'online form'. How are pre-prints stored with your approach?

@Jigg I would just store links. Automatisms are good, as long as the involved parties adhere to standards.

Links to what? Each researcher's personal webpage (many of whom don't have any, let alone an up-to-date one)?

@Jigg when you register it into the DB, you would provide a link to the article (or just the DOI if it is in a OA journal). As I said, it is quite low-tech, but so much easier to manntain.

I don't get it. Where would the pre-prints be hosted? (you need to host things before you can provide a link).

If the open access policy does not designate a preferred institutional repository, the authors are free to choose the repository they prefer (mathematicians will go to the arXiv, biologists to PubMed, and so on). In this case it is interesting to do what Davidmh proposes.


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Are there boycotts against publishers other than Elsevier?
Academics have called for a boycott against Elsevier, with some success for instance because it has led to resignations (recently in the Lingua journal).
As I understand it, Elsevier is not the only publisher with absurd subscription prices, but it is being targeted because it is the largest one. Are there any similar initiatives against other publishers? (Springer, Wiley, Taylor and Francis, ...) If not, why?

On similar lines, 'Elife' was formulated.

Elife is interesting but not analogous to the Elsevier boycott, it is an open access publisher. Not sure I got your point.

What I think @Dexter meant was that the creation of Elife was a move away from the commerical publishers.  Its existence is a a form of boycott, taken to the next level of ".. and we'll do it better".

Yes, in addition, one of big reasons why Elife was formulated is to break monopoly of Nature - Science journals.

If anyone wonders what "absurd subscription prices" mean, see Reference for annual journal subscription costs paid per university

The Elsevier boycott seems to be the largest one of its kind.  I understand the argument to be:

A boycott is easier to maintain against a single publisher than against several publishers at once, since it limits the cost to the participants while, if anything, making the boycott more painful to the publisher.
There's a short list of likely candidates for a single boycott---probably just Springer and Elsevier, and perhaps Wiley, as the largest and most expensive academic publishers.  Elsevier had been particularly active in lobbying on some related issues (SOPA, PIPA, and the Research Works Act), and had recently been involved in several publishing related scandals (the ones involving Chaos, Solitons, and Fractals, and the Australasian Journal of Bone & Joint Medicine).

(I personally found these arguments strong, but plenty of people didn't, and some people have refused to participate in the boycott precisely because they think such a boycott should be more widely targeted.)

From the Cost of Knowledge statement on the choice of Elsevier over Springer: "One reason for focusing on Elsevier rather than, say, Springer is that Springer has had a rich and productive history with the mathematical community. As well as journals, it has published important series of textbooks, monographs, and lecture notes; one could perhaps regard the prices of its journals as a means of subsidizing these other, less profitable, types of publications."

Example of boycott against Springer leading to the creation of an freely accessible scientific journal: the Journal of Machine Learning Research:

The journal was founded as an open-access alternative to the journal Machine Learning. In 2001, forty editors of Machine Learning resigned in order to support JMLR, saying that in the era of the internet, it was detrimental for researchers to continue publishing their papers in expensive journals with pay-access archives. Instead, they wrote, they supported the model of JMLR, in which authors retained copyright over their papers and archives were freely available on the internet.

The journal Machine Learning was published by Springer.
A number of people have called for boycotts against JSTOR after Aaron Swartz's death.

Elsevier isn't indeed the only publisher to have high prices, some examples:

Great, thanks! It would be useful to have sites such as The Cost of Knowledge for Springer and others, to make these local initiatives more visible, I think.

@pintoch As long as people don't pay from their own pockets directly, the motivation is low... unfortunately. Too bad for the taxpayers.

Guys, this does not seem to be a scientific comparison of prices - rather just some numbers out of context. Price per click is what people normally use - may be you could find some trusted sources and add them as referenceS? Also, is SIGMOD record OA journal or do you really believe there is free lunch?

@al_b Feel free to edit the answer. Some other numbers: http://academia.stackexchange.com/q/31605/452


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Is independent research a good long term goal for a bachelor's degree holder with experience and interest?
Bear with me while I put some biographical information here.
I'm a bachelor of engineering graduate from India with approximately a decade of work experience in design, engineering and project management. I've got a real fascination for the following subjects:

Optimization methods
Chaotic and dynamical systems
Data analysis and statistics (a field in which I work - as a quality management professional)

I have presented a couple of papers in international conferences in the first subject - based on work I did by teaching myself optimization methods. Learnt the ropes on researching papers/work, contacting researchers, running my own studies, writing concise papers, over many attempts in unpublished papers. I have only read books and papers on the remaining two subjects (#2 and #3) for over seven years but haven't really contributed anything significant or original.
Since I never was in the right financial state to pursue a masters or a PhD, I never earned one. I turned down an MS admit at Duke in 2010 for financial reasons too (didn't manage to secure funding). I considered and visited Indian universities including the IITs but find the entry barrier high for any univs worth going to, because I have a 7.0/10.0 GPA on my Bachelor's degree. Moreover, I hate going back and asking for recommendations from professors that I share no common interest with or who had no bearing or influence on my technical interests whatsoever. My mentors have all been in the industry, and all MS/PhD applications seem to want only academic recommendations, which I thought was stupid.
Having read a number of reports and accounts from researchers on the troubles PhD scholars face and the standard of life, I'm inclined to think that I wouldn't be happy giving up my job and my lifestyle (and compromising my wife's lifestyle) for a decade of research which may or may not lead to a PhD. I love the subjects but I'm looking for a way to learn and discover things in them without subjecting myself to the financial commitment that comes with a huge loan.
Is a life of independent research (something that is exciting for me personally) a viable way to move forward, or should I consider getting a formal research postgraduate degree? I'm eager to hear thoughts, advice, comments. Thanks for taking time out to read this.

What do you mean by a life of independent research (or, for that matter, a viable way to move forward)?  For example, you could mean doing research for your own satisfaction in your spare time while holding an unrelated job, finding an industrial job that involves more sophisticated technology, or finding a pure research job (in a university or research lab) without having a terminal degree.

It seems you have two options to weigh against each other:

Do research independently, viewing it more as a hobby than as your profession, or
become a professional researcher, which would require getting the appropriate formal education.

If you want to make research the most important aspect of your life, then option 2 would be the way to go. However, from your current biography, it seems that this may require more effort and changes to your life than you may be willing to invest. Getting a PhD is a definite requirement along this path.
If you go for option 1, it will still be possible to make research an important aspect of your life. It will be more difficult though to maintain sufficient investment of time in view of work and family commitments to keep things running.
Personally, I think that being a hobby researcher can be viable and satisfying in research fields where you don't need expensive equipment. While the examples I know mostly do something like locally focussed historical research or botanical/zoological research in their environment, it seems that mathematical or theoretical engineering topics will also be feasible for this. If you want to go that way, the internet certainly provides much more advice on being a hobby researcher than I can hope to give here. A link to start with may be this question on cstheory.stackexchange.com.

Honestly, independently researching on your own time could be a lot tougher than working in a research group.
Here's a tip: if you are serious about researching, go to graduate school. A lot of people do independent readings as a hobby as well. Find which category you fit into.


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Where do academics obtain HTML website templates with no attribution?
I have noticed that most .edu domains have a very "academic" looking simple HTML websites (Do academics look down on well-designed academic websites?) for professors and departments. My graduate school follows a template for the main department website and the professors and graduate students upload their own HTML websites on their sub domains.
I was recently tasked with uploading a simple HTML website for our group's research page. I have created websites before but my advisor asked me to put in minimal effort as I am busy writing research papers right now and should not be spending a whole lot of time playing with HTML and CSS.
I have noticed that a lot of professors have the same minimalist design of HTML websites. I know professors are pressed for time and so will adopt a minimalist HTML template and tweak it.
My question is: are there known resources where free simple HTML templates are available that require no attribution? I found several HTML templates that require attribution (linking back) to original designer and I would like to avoid that as I need something very simple that I can tweak.
I understand that professors might be writing the HTML from scratch. But if someone knows of a template I could use, that would be great.

Some universities provide templates. But nevertheless you should be able to create a decently good looking web page in a few hours (I assume you'd have two or three hours to spare), right? Use publicly available templates and libraries (such as Bootstrap) and don't reinvent the wheel. Or even, just use Markdown and write a little bit of CSS. Well, computer science professors just write the HTML because it (programming) is (usually) part of their job, but you don't have to; you can even use Wordpress if you want. Again, don't reinvent the wheel!

Maybe I'm not looking deeply enough, but a cursory Google search for "attribution free html template" yields a lot of promising-looking results. Is there anything particular that you couldn't find?

"I have noticed that a lot of professors have the same minimalist design of HTML websites." - are you sure that "template" is not simply the default appearance of the documents without applying any further formatting after using a basic set (headlines, paragraphs, bullet lists, links) of (a) HTML elements or (b) commands from the professor's favourite WYSIWYG editor that can output HTML?

@O.R.Mapper or perhaps plain Bootstrap in case of younger professors

@henning I did a lot of Google searching and those results are mostly clickbait, although they do look promising. Usually, attribution free means they require you to pay OR when you open an actual template it shows a CC3.0 or MIT License.

Isn't this a shopping question? and “Shopping” questions, which seek recommendations or lists of individual universities, academic programs, publishers, journals, research topics, or similar as an answer or seek an assessment or comparison of such, are off-topic here.

When I was looking for a CSS style for my personal academic website, I got a recommendation to use Twitter Bootstrap. Then, I bascially ripped only the style out of it, but acknowledged them in the page footer.
As I just checked, you can directly link to their style without copying it locally and the code is licensed under an MIT license.

Why not use one of the templates with a CC or MIT license that you found? (Avoid Share-Alike unless it is only about the markup and not the content.) In academia, having proper attribution will be looked on favorably, and it's clear that the professor just wants it done. If you find a nice solution that you can attribute and tweak, your advisor will see that you worked efficiently, by not reinventing the wheel.
My guess is that academic pages not attributed to a template:

Are hand-coded from basic HTML or created as exports from editing programs (even Word does this), as OR Mapper suggested in a comment
Are part of a university-level template or CSS scheme after all
Borrow code in ways that one could argue should be attributed
Take someone a lot of time to put together (possibly university staff rather than the professor)

If there's an existing academic's page you really like, you can check the source code and see if that gives clues about how it was produced. (Human-readable with indentations probably means hand-written; lots of needless tags being opened and closed probably means a WYSIWYG editor. Sometimes a code generator will be mentioned in meta tags or comments.) Do not copy the source code, just see if it leads you to a workable answer.
If you truly want to be minimalist, you can also work from a resource like this HTML tutorial which in my mind would not require attribution.


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Are (computer science) workshops less prestigious than conferences in general?
I am a PhD student in computer science and I have noticed that my advisor tries to avoid having me submit to workshops in my field when I bring workshops to his attention that we could submit to. He, instead, prefers to publish in a conference, journal, or IEEE/ACM magazine instead. I almost feel like he treats workshops as not prestigious enough.
The workshops I bring to his attention are all good workshops in my opinion. These workshops are IEEE and ACM workshops demanding original research papers that are about 6 pages long (conference papers in my field are usually 8 to 10 pages long). The program committees for these workshop are known people in my field and previous year's workshop papers have a 5 or 6 citations (for example), so they do get attention (but I don't know how this compares to the attention that this same paper could have gotten if it was published at a conference).
My questions are: are workshops viewed as less prestigious in general than conferences? Is there an unspoken understanding that only new, inexperienced students present their papers at workshops? Would having workshop papers in my resume somehow lower the credibility of my work?
(Apologies if the questions sound naive. I have always been unable to understand the 'prestige' of a 'co-located' workshop when juxtaposed against the conference.)

Also relevant: What is the point in publishing a paper in a workshop rather than in a conference?

Workshops are usually for new topics, and I do rank them lower than conferences. Moreover, workshops usually publish/accept papers rejected from their co-located main conference; often than not, they are used to prop up the number of registrations or to cover the cost of the main conference.  Also, because they are new, it is usually very easy to get a paper accepted as the standard is not there yet.  However, if the topics of interest grow and attract experienced researchers, then a workshop can be quite hard to get into, and hence, its prestige grows.


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Digital whiteboard: your experience
We do need a Whiteboard in our new Meeting room. The question popped up, whether it makes sense to buy a digital whiteboard. We present mostly our results, sometimes we discuss something and and do use Flip-charts to draw something. However, we are not sure if a digital whiteboard would be beneficial in such a setting.
What is your experience with such a device ? Do you use it mostly for teaching or also for classical presentations ? Does it enable more lively discussions ? How much time and training does it need to use it in an efficient way ?

Do you only have the whiteboard for presentations, or do you use a beamer and only want a board for side notes? In the latter case, I would go with the good old blackboard and chalk (might just be because I'm a mathematician and we love our blackboards though...).

We had "smartboards" installed throughout our college some years ago; I believe they're totally ignored by faculty, never seen them in use.

We have a beamer and Flipcharts. Our walls are empty and we would like to use them.

I have been working around it by using a drawing tablet and a simple drawing software Manga Studio. Project it, and write. It's also easy to flip between Internet browser, drawing board, and other online media. Each of my "white board drawing" is in its own tab, and after class I just export them into png files for sharing.

If it's able to scan and archive the stuff you write during discussions and presentations, then this is extremely useful.

That is a good point

Whether a digital whiteboard is of use depends very much on what you want to use it for. It combines the advantages of a projector (being able to display a range of digital content) with those of a whiteboard (writing in real time).
In certain circumstances, there is more benefit than simply the sum of the two. I've been in video-conferenced lectures that used them - the actual screen is transmitted, and so is easier to see than a whiteboard captured with a camera. Sometimes it's useful to combine different backgrounds with real time writing, such as writing music on a stave. However, similar effects can be achieved with devices such as an ipad, which would be cheaper.
The downsides are: cost, training needed (and resistance), the start-up time required to get to an operational state, and the inevitable event that someone writes on the board with the wrong pen.
Also, I've found that the software being used on a digital whiteboard can have a major impact on its effectiveness. We got some at school, and a minor software 'upgrade' significantly reduced efficiency and increased frustration.


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Lab-meetings: How to establish a good setting?
I will finish my PhD soon. Until now I worked mostly on my own but tried to talk with my colleagues on a regular basis about methods, approaches, troubles and success. Good settings are coffee breaks or after sport. It can help a lot because I am forced to order my thoughts, try to explain them in a meaningful manner and most of the time I get helpful answers, comments or tips. Additionally, I learn a lot about the topic of my colleagues.
In my area (Biotechnology) we distinguish between upstream (producing stuff using living organisms) and downstream processing (purifying stuff). Usually two different working groups (or more) are covering those areas. It is really important to talk with each other because the downstream part can heavily depend on the upstream conditions.
One aim of the next project will be to bring those areas closer together and to strengthen our knowledge about the implications of the upstream process on the downstream part.
The team will consist of two professors, two post docs, two PhD students one or two technicians and several diploma students. Recently I talked with one of my colleagues about possible setups for the meetings. We came up with following scenario:

One team meeting every month.
Everyone prepares a short presentation (10 minutes max).
Following questions should be answered during the presentation:

What is my current (mid term) goal ?
How do I approach it ?
What was the (short term) goal of the experiments performed ?
Did the experiments worked out like expected ?
What are the results ?
Planned work for the following month ?

I expect the meeting to last for one to two hours. At least one of the profs will attend the meeting. The two post docs organize the meetings (schedule, remainder etc.). The meeting will take place between 12:00 and 13:30. All team members prepare some bread, meat, cheese, fruits,vegetables, drinks and coffee together. That is a bit more work than just going to the canteen but I think this setting may help to establish a relaxed atmosphere.
What experiences do you have with team meetings ? How do you organize them ? Who moderates them ? What worked out well and what did not ?

I think you should have smaller and faster meetings also: think about using Agile and scrum techniques. One possible missing question--are there any impediments?

This is a fine strategy. See how it goes, and discuss afterwards whether it was helpful or not. You should not allow your meeting to run any longer than ninety minutes though on any account. Most people will not be able to concentrate for that long. Also consider inserting a break if it is going to exceed 60 minutes.
Some other thoughts: Instead of having every contribute every month, consider having only one or two presentations each week. You will probably find that some people assume that 45 slides can be presented in eight minutes and you have to cut them short or cancel the later presenters.
Keep the first session very positive and upbeat, don't be afraid to step in as the moderator if anything is going wrong. If the students make a hash of things, so be it. The first meeting will set the tone for the rest, so if someone spends thirty minutes dissecting the student's presentation, no one will want to come to your next meeting.
In that respect consider giving a short presentation on your own work/goals yourself, so that everyone has a good example presentation to emulate.
I would say it is not really fair to insist that everyone prepares some food for the group to consume. Your team are scientists, not caterers. ;) My advisor used to contract external caterers for our team meetings but I think he was a bit over the top there.

The point with the food would be, that we prepare it together (including the professors). I think, it would help to establish a relaxed atmosphere. Some are cutting the vegetables, some others are preparing the bread, or coffee etc. There is time to talk about the wheater, the best technique how to cut stuff etc. etc.


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How bad does it look if I asked the director of graduate studies if I can change my program of study from pure to applied math after admission?
Although I am primarily interested in studying pure math, for certain personal reasons, I had to ask such a question. What I fear now is the mismatch that'll be noticed between my Personal Statement, where I intend to write about my interests in pure math and this query which clearly exhibits the fact that I have as yet not made up my mind. Even if I re-do my personal statement to reflect an interest in applied math instead of pure math, the fact that I wasn't sure at this terminal stage of the application process might go against me. Is there any way to rectify my mistake?
For reference, this question is with regards to a university in the UK.

"Although I am primarily interested in studying pure math, for certain personal reasons, I had to ask such a question." Sorry, I don't get it: what do personal reasons have to do with this?  (My intent is not to pry into your personal life, but to try to answer your question in a meaningful way.)

My personal reasons have to do with my financial status. Since this is a one year Master's program, the university will not be funding me. So, while pure math is what I am interested in and an academic is what I aspire to become, I feel compelled to re-consider my choice based on my constraints. So, while I am sure that a degree in pure math can fetch one jobs, I feel that a focus on the applied side might position me better to repay my source of funding. In any case my inquiry was meant to buy me time to make this decision, once I had all my cards in front me after all the admissions results.

Assuming your personal reasons are sound, a polite conversation cannot hurt you. Explain your reasons, and keep an open attitude. It is very common for people to change sub-fields (and fields) after their PhD, or even postdocs, so it will not strike as an big oddity.
Now, if it is possible or not, depends mainly on where does your funding come from; and if the university regulations allow it. This will be brought up in the conversation.
If your reasons for studying applied maths are your desire to clone green dogs, well, it will look bad.

Thank you for your response. While I agree with you that a change of mind is not uncommon, I feel that the fact that I have explicitly conveyed my  doubts regarding my choice jeopardizes my credibility, because I plan to focus on my interest in pure math as the core of my personal statement. The people that make a switch generally tend to do so after they have experienced either of the side's and feel that it is not a fit for them. But me raising such concerns before even sending my application, might make them question the conviction behind my choice, which will not look good.

@AdamK I am confused, have you been accepted? Wanting to eat is, in my opinion, a perfectly reasonable reason; but then you are focusing on the wrong side. What you should say is that you want funding, and you are willing to change to applied math, if that helps.

Although I am primarily speaking from my experience in the US, my experience is that nobody will hold you to what you have written in your personal statement during your application. It is not a contract. You'll be lucky if anybody even remembers!
The point of the personal statement is (a) to show that you can think and write clearly about your research and preparation and (b) to ensure that your interests overlap with available resources in the department including both funding and faculty.
If you want to switch to something that the department (or individually faculty member admitting/funding you) can advise and support you in doing, people will likely not have a problem. If you want to switch to something that the people admitting you cannot supervise you effectively on, the problem is much more serious that you "looking bad" because you will either be supervised poorly or working on something you do not love.
If you heart lies in an area other than one you suggested in your personal statement, you should raise the issue before you say "yes" to a program so that you don't end up in a program that is poorly suited to supporting you in following your interests.

It will not go against you.  I shows that you have an enquiring mind and are willing to change your mind as new opportunities open.  To continue in a subject that is not right for you will be a really bad experience for you and may end up in failure - that's not good for you, or the institution.  Go ahead and ask the question, but frame it as a positive decision, rather than a negative one.


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What are the NCS journals?
I have seen people mentioning special group of journal, namely NCS journals, but what does it stand for? When people say that "faculty has to publish in NCS to get a shot at tenure", what does it mean? Googling doesn't return anything useful.

The NCS stands for "Nature, Cell, Science", the top journals in STEM and biomedical fields. The impact factors of these journals are among highest, between 36 and 41.
Some have noticed that publication in NCS journal correlates with academic career success (getting tenure-track position at the top university), while others commented that degree of attention to these top journals is bad for science.


text:
Is it okay to directly address your reader when writing a scientific paper?
I'm currently writing a paper that has some kind of tutorial parts in it. I have written sentences similar to:
«... depending on your operating system, the procedure is different»
Is addressing the reader directly like that in a scientific paper ok? Or should I try to rewrite these sentences?

I feel like, at the very least, "our" would be better than "your". Try reading it out and see how it sounds. It gives a much more collaborative feel, no? I'm sure some others would prefer "the reader's" as well.

Any chance you could provide us with the complete sentence so far? If you want to censor it a little just replace some nouns with underscores.

Another example from the paper: «You can choose how you run your scripts; either interactively, line per line, or as batch jobs, depending on what the script does.» If I change «your» with the «the reader's» it will be a bit too «heavy», no?

And what about not addressing the reader?: "... depending on the operating system, the procedure is different"

@ddiez this works for this sentence, but for other portions it's going to be a bit more complicated. For example: «You can use whatever text editor you are comfortable with to write your code in.» I have the feeling that to avoid addressing the reader I should switch to passive voice, which is also not recomended.

@cbrunos addressing the reader may be avoided in other cases by reworking the sentence a bit. For example "Users can write the code in any text editor of their choice", or something similar. Not being native speaker I find myself many times in your dilemma. But I always try to avoid referring the reader (unless appropriate) as much as I do with passive voice.

These questions may help you: What to use instead of academic 'we' when describing an experiment? and Choice of personal pronoun in single-author papers

Check the style guide for whichever publication you're submitting it to. Many editors have an absolutely religious adherence to never using second person, and some don't even like first, insisting that you refer yourself to, eg, "this author" or "this researcher" or whatever. I'm not convinced that any document can satisfy all editors and remain readable.

Except when outlining a motivation for a particular section in a paper, I would recommend speaking in third person as much as possible. An example of the exception is:

Because our primary interest is in ____ we have chosen to follow the method developed by ___.

For your case I would reword your sentence as:

Depending on the operating system used, the implementation will differ.

Always shift the focus to the things being manipulated, whether it be an experiment, computer program, or anything else.
As for your sentence in the comment you could write it as:

How the scripts are run is at the user's discretion; it may be interactive, line by line, or in batches, depending on its function.

I have used the at the user's discretion a lot in my work; it's a professional way of saying you can do this part however you like. Also, whenever I have to identify somebody whose completing a task, I try and identify them based on the task they are completing (e.g. the analyst, the user, or the programmer). If you say you, you are assuming that the reader is the one who will be carrying out these tasks, which may not be the case.
If you have to address the reader, then you can say something like:

For the reader's convenience, the pertinent information has been summarized in Table 5.

or the famous, albeit witty, cop out:

_____ is left as an exercise for the reader.

Whether to speak in third person or directly in first person is a matter of taste and tradition. However, when you consider reading papers that are written in an active voice and in a direct way, compared to third person and passive voice there is probably no contest which will put you to sleep first.
Using "this author" about yourself or "the reader" distances both you and the reader from the work, it is as if you are reading account which only concerns others. There is no question that appropriately using "I" for yourself and maybe you for the reader is more direct and makes the communication clear. In an account where you also involve the reader you can also use "we" as in the reader and you, jointly. This is not the royal "We" as used by some.
In your example of "...depending on your operating system, the procedure is different" skipping the "your" would not detract from the message: "...depending on the operating system, the procedure is different". But since you really want to say that differences appear because of the type of operating system used, I would suggest rephrasing to something like "...depending on the choice of operating system, the procedure is different". I am, in this case, not sure if "your" makes the point any clearer to the reader.


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Masters programs that require publication (with extra requirements)
My university requires me to publish* in order to defend my master thesis and receive my diploma. It took me four years to complete this requirement, instead of the usual two in my country. Because all deadlines have already expired, I have to request exceptional approval to defend my thesis. I would like to know about the situation in other universities in order to build my argumentation.
Is the requirement to publish during a masters degree common? What about the list of requirements below? If uncommon, what other universities/regions have similar requirements?

*: The full list of requirements for the publication in my program is:

Has to have acceptance letter (submission is not sufficient, but waiting for actual publication is not required).
Limited to a government-issued list of "good" journals and events. The list is admittedly large, but still incomplete, infrequently updated, and contains mistakes. During my masters there was no event of my area in my country, for example, but some predatory journals were included. This list was not created to evaluate students, and is being "reused" by the program.
The student must be the first author (to avoid just adding names to a submission).
The advisor must be a co-author.
The thesis content must be related to the publication.

I was not aware of any master's program that requires original publication until now. What is your country?

Brazil, masters program in computer science. I'm not aware of any other university with this requirement either. Note that most other students are fine, as the government list is more complete for their area, but my lab is struggling with this requirement.

@BoppreH, what does "During my masters there was no event of my area in my country" mean? Is "event" a conference or other opportunity to publish/present, etc.? And "area" is your field of study?

@shoover by event I mean conferences and other opportunities to present, and the sentence refers to the lack of conferences fulfilling the program's requirement. About the area, I was trying to be intentionally vague to avoid pointing fingers; if you think it's important, the "area" is computer security, as opposed to the more specific field of study that is crypto. Sorry if the vocabulary sounds odd, these are translations of precisely defined terms.

In my part of Europe this list is the minimum suggested for a PhD. By suggested I mean that it is common, in the sense that is customary, but not strictly required, i.e. there are ways to graduate without it, your advisor just needs to work extra hard to get the committee to approve you thesis.
Master students are encouraged to publish, but that is in no way a requirement. Many of them publish as first authors a short paper on a local conference, or a poster at an lower tiered international one. Papers with more impact are not unheard of, but are usually limited to co-authorship.
The "list of good" venues is a problematic point for many computer science departments. For example, while it is widely held that for computer science, conferences are the primary publication venues, my institution still insists on at least one journal publication for PhD students as it is a recommendation that holds for all departments at the university.


text:
Secret-Santa-like informal peer reviewing in a small community
I've been thinking about a way that researchers in a small community could stay informed about each other's work and commit to give each other feedback on preprints independently from formal conferences. (I'm thinking of a group of 10-20 researchers, who work in a common area and mostly know each other already; could be a research team in a university, or a group of people collaborating on a project.) Maybe it's the season, but it looks a bit like a secret Santa. :) My question is whether similar mechanisms already exists and have established names that I could use to think about how to organize it.
I'm thinking of something like this, with a calendar fixed in advance:

Signup phase (day D): everyone interested signs up and submits a paper for the group. It would ideally be a recent preprint, or otherwise recently accepted work on which the submitter would like feedback. Typically you'd want the preprint to be publicly posted (e.g., on a preprint server like arXiv) to ensure there are no worries about stealing each other's ideas.
Bidding phase (day D+7): everyone who submitted sees the list of submitted papers and bids for the papers they would most like to review.
Assignment phase (day D+14): everyone gets one paper assigned. The assignment of who reviews whom can be public or not depending on what people prefer.
Review submission phase (day D+28): people submit a review of their work, like they would have done if asked to peer review it. Since there is no question of accepting/rejecting papers, reviewers can focus on comments, suggestions for improvement, points they found unclear in the paper, etc.
Sharing reviews: once a participant submits their review, they receive the review that was submitted about their own work.

My question: do similar arrangements already exist? have people successfully set up such mechanisms, or written about their experience with such mechanisms?
Here is how it differs from similar systems in academia:

This is essentially like a small-scale conference or workshop, but without an in-person meeting, and without any question of formal publication of the papers, so this can be independent from standard peer reviewing. Also, these reviews can be done without worrying about conflicts of interest (many of the participants would be in COI anyways), so participants can bid on the submissions they really want to read, even if they are written by people they are in COI with.
Of course many people already send preprints of their works to colleagues and other collaborators, but usually with no strong expectation of receiving detailed feedback. I don't know of people with explicit reciprocity agreements "you read my work, I'll read yours".
I know about reading groups, book discussion clubs, and journal clubs. But these are typically about discussing specific works in depth as a group. Also, typically these are about reading works from people outside of the group, not about giving/receiving feedback within the group.
The closest I can find is preprint discussion or reviewing systems like Peer Community In. But these aim to have a large scope like a disciplinary journal, not to be an informal small-scale affair.
There seem to be this kind of reviewing circle arrangements outside of academia, e.g., Critique Circle for writers.

To give some context: my field is theoretical computer science, but this proposal seems pretty generic and would seem to be applicable to any other field where people typically post their work as a preprint. My motivation for such a system is that I find it hard to read the papers of people from my area (even when it's close to my interests), and hard to get feedback about my own work. The exception is standard peer review, where I manage to commit to a deadline and read in depth a specific paper: but there I typically end up with papers I don't care so much about, and I miss all the relevant work from people that I'm in COI with.

It seems like a lot of effort for little benefit. And it would be difficult to guarantee anonymity in any case since people would already know one another. Why not just emphasize collaboration?

And, if people with a COI can bid on and review an article, how can you trust any review?

People used to do this as a one time thing via Twitter for job market candidates… but not sure if that has continued …

PREreview is the closest thing I can think of, and most specifically their PREreview Clubs. It might be worth reaching out to them.

Thanks, I didn't know about this and it seems indeed very relevant. It looks like one difference is that they seem to focus on the club formally publishing reviews, as opposed to sending them privately to authors. Still a very interesting pointer.

Expanding on my comments in a Frame Challenge. And no, I don't have experience with it, nor do I expect there to be many with such experience.
This seems to be an attempt to reproduce a journal's single blind review.
However:
Someone will probably need to know what the author-reviewer linkage is and it is possible, even likely, that pressure could be applied to them to reveal things that would not be revealed by an editor who has something to offer beyond the review itself: publication.
If someone with a COI could bid on a paper without revealing it, or be assigned a review in spite of it, then no review could be trusted. Both overly optimistic and overly pessimistic reviews could easily arise.
If the community is small then people know one another and and probably surmise who the reviewer is. This could lead to conflicts if one depends on anonymity that isn't in place.
I suspect that, people being busy, this will be a low priority for some, both in bidding and in completing reviews. It would then be difficult to maintain.

In place of this, and already pretty standard, is that people simply request feedback on their work from a trusted colleague. If the person has conflicts that is already likely known and can be accounted for. If a person is too busy, they can just say so. They can offer to swap papers for review. All in the open.
Within a large university there are often working groups within subfields. These include both professors and students. Sharing papers and work in progress is pretty common. You get the feedback you need from people you already trust. The suggested framework in the question seems like a poor substitute for this.
Moreover, in the wider world it is also pretty common for academics to have working relationships with others outside the university. Ideas and papers can be shared and feedback can be given. In larger, better funded, places, visiting for a few days or weeks... can provide an opportunity for sharing ideas and getting feedback. This already happens. Early career academics are encouraged to form such associations, perhaps by joining the circle of their advisor(s).

Thanks for the answer. About "this already exists": I know of working groups and informal sharing of work in progress. But I have never seen people in this context (including me) who would commit to reading each other's work with the same reliability as most people (including me) do for peer review towards strangers. About COIs etc., the point is to give/receive feedback from collaborators, I don't see grave implications if a review turns out to be bad (or maybe insincerely positive). I think of it like "sharing papers and work in progress" but with more structure and with commitments.

About "people are busy", which I agree is a big challenge on anything new in academia: my observation is that we spend copious time giving feedback to strangers via peer review, even though in my experience this is often less interesting to me as a reader, and leads to less interesting feedback, than if I were to spend the same attention on papers from colleagues and collaborators. So why are we currently so generous with our time for formal peer review, while we seem to think it is less important to read in details what the people close to us are doing?


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How to publish a corrected proof for a claimed mathematical result?
I work in the field of theoretical computer science, and I have published a paper with several results. A few years later, a reader reported to us an error in the paper. The paper claims a theorem X, but the proof given actually shows a somewhat weaker result X'.
Thinking about it, I have been able to come up with a proof of the originally claimed result X, using somewhat different techniques. The new proof is not interesting to merit publication as a new paper, but the fix is not trivial either so I'm not fine with leaving the mistake as-is. Besides, result X is not central in the paper, and it is indeed correct (only the proof was not), so this is not a situation where we should think about retracting the original paper altogether.
I'd be interested in the community's opinion about what's the best way to proceed to publish this fix to an erroneous proof. I can see at least two options:

Option 1: publish a revised version of the paper with the original claim of X and the new proof (and a comment that the original version of the paper had a mistake). I think this would be the most comfortable option for future readers. That said, it may create confusion as the original buggy version of the paper will still be around. Plus, I would imagine that ethically I cannot do this without approval from all authors of the original paper (at least one of which has now left academia).
Option 2: publish a separate note on arXiv containing just the new proof of X, and publish a revised version of the paper providing the proof of X' plus a pointer to the new note for the proof of X. This has the advantage of leaving the original material essentially intact, plus the note can be authored only by the people who are still involved. But it is less pleasant to the reader (who must jump to ta different document), and it is more work for us (since one would need to re-explain the whole context in the note, etc.), all for a not-so-interesting fix.

[With both options, I would publish the updated version of the paper simply on arXiv -- dealing with the publisher would only complicate things I think.]
What do you think would be the best option? Essentially the question can be summed up as: when is it better to fix errors in a paper simply by updating it, and when is it better to publish the fix as a separate note?

Why not contact the publisher? If people read the published paper online, it'd be good if they had a note attached to it, and a correction that is published properly as a correction. OK it makes some effort, but I'd think it's worthwhile. These things happen all the time.

Option 3: publish a correction in the same journal. This will then (usually) be linked to the original paper.

I had a similar problem with one of my conference papers. We posted a revised version on arxiv, specifying in a footnote what the mistake was and how it was corrected. The correct proof made it official appearance in a journal paper that was partially based on the the conference one.

Right, publishing a journal version to fix an error in a conference paper is a great way to go, but unfortunately here the error is in the journal version (and in the conference version too), so that doesn't work for us. Thanks nevertheless!


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Publishing journal articles based on dissertation
My dissertation is drafted in a paper format which consists of three papers that I am planning to publish in future. Can I submit the manuscript to journals in 'as is' condition or I will have to draft new manuscripts based on the old manuscripts.
Please advise.
Thank you.

please edit the question to say whether you are looking for an answer addressing copyright and pre-print permissions or about the content.

It is often possible to republish your dissertation as articles but it depends on the publishers and it sometimes requires permission.
Journal publishers will generally not publish work that is published elsewhere but dissertations are a common exception. This page run by the MIT libraries lists many science and engineering publishers and their rules about publishing articles that first appeared in dissertations. For other publishers, you'll need to check websites or ask journal staff or editor.

Are you hoping to publish in a peer-reviewed journal? If so, I expect your dissertation will need to go through substantial revisions. More specifically, I expect your dissertation will need to be condensed to some extent. Many journals for example want articles less than 5000 words, and I expect your dissertation, even in three papers, would be larger than this.
It is possible that your dissertation is brief and will require minimal changes, but this is not often the case. I would check what journals you want to submit to, and check their length requirements. Often manuscripts based off of manuscripts feel like they were originally a manuscript, and not in a good way. Journal articles often get to the point quite quicker. For example, in original research articles (not reviews and such), introductions vary from 500-3000 words depending on the field (more is possible, of course). In a dissertation, an introduction might be 30 pages!
Your dissertation likely also covers a fair bit of breadth. Make sure to include in a manuscript only the information that is relevant to that specific paper and line of thinking.
I'm assuming this question is about the content/format, and not copyright and such. If you are wondering about copyright, my impression is what in most cases you can submit your dissertation exactly as it is for publication, unless you have already signed your copyright away.

You can extract three manuscripts from your dissertation and publish, but...
Your dissertation presumably comprises of the following sections: (1) Introduction, (2) Tools (filed dependent background material), (3) Manuscript 1, (4) Manuscript 2, (5) Manuscript 3, and (6) Conclusion. You can't simply pull-out Sections 3-5 and publish, because they lack sufficient introduction and tools. Moreover, before your dissertation is accepted, those sections might change. So,
I suggest that you:

Wait until your dissertation is accepted (hence, all sections are in final version),
(Assuming you're using LaTeX) add macros to Section 2 so that it can present tools for each of Manuscripts 1-3 individually (this avoids having to maintain three overlapping sections), and
Merge each of Sections 3-5 with Section 1 and the aforementioned tools section to derive three manuscripts.

If you are still drafting your dissertation, then you might be able to reduce the above work load a little, but, I'd suggest not worrying too much about that.