text:
Publishing a review in a peer-reviewed Wiki vs a traditional journal?
The topic of Wikipedia contribution has come up before, but I am interested in the community's opinion on peer-reviewed wiki publishing (e.g., Scholarpedia). I would like to know if there is any advantage for a PhD student to publish in such an online venue versus the traditional journal publication for review content. The advantages I see to the wiki approach is free of charge publication, open access for all, not necessarily being limited by character limits. However, the disadvantages I see could be the citation being completely ignored by the intended audience and therefore missing out on the benefits of scientific communication and the possible loss of accompanying reputation for the publication. I would also worry these publications would be ignored or minimized by future supervisors and review committees.

Scholarpedia has adapted many of the processes of a peer-reviewed journal.  However, it is still a kind of encyclopedia and not a research journal at all.  Note that I'm not making any kind of judgment or evaluation in the previous sentence: the main page of the site reads

Welcome to Scholarpedia, the peer-reviewed open-access encyclopedia,
  where knowledge is curated by communities of experts.

So you seem to be asking: "Should I publish my paper in an encyclopedia rather than a research journal?"  I think that's a kind of strange question: have you really written something which lies ambiguously between a research paper and an encyclopedia article?
The above is not a rhetorical question: please let us know!
It is also possible that I have fixated too much on "scholarpedia" and it is not the type wiki publication that you really intended.  If so, please let us know.  It would be helpful to give at least one specific example of the kind of "peer-reviewed wiki" you have in mind as a plausible alternative to a research journal.
Added: @MHH has helpfully clarified that the OP is probably talking about a review paper, or what in my field would be called a "survey paper".  (The word "review" was also used at least twice in a different sense in the OP's question, and that was enough to confuse me.)  I must begin by admitting that review/survey papers are rare in my field (mathematics), and that they would be written by PhD students is almost unprecedented.  So I am almost at the point of wanting to delete my answer for lack of understanding and relevant expertise.
However, let me first try this:
it seems to me that a review paper should be published in a research journal if it contains original research: i.e., some kind of synthesis, analysis, new perspectives, helpful simplifications, and so forth are being added.  Of course "original research" is exactly what is not wanted in an encyclopedia article, although I don't see why this would necessarily be the case for all peer-reviewed wikis.  So going more from general academic common sense than specific insight (i.e., caveat emptor), I would say that this should be the deciding factor between publishing a survey paper in a research journal or in a wiki.  Let me further say that most or all of the advantages cited by publication in a wiki can be achieved by publishing in certain kinds of research journals: "free of charge publication, open access for all" certainly.  Many electronic journals do not advertise hard "character limits", but of course there must be some kind of upper bound must exist, right?  No one wants a 5000 page survey of the literature.

He did say a "review paper" though. Perhaps that actually is what scholarpedia is looking for? I assume that is what he means by review content

@MHH: Thanks very much for your comment.  I have tried to push things back on track, but maybe this question is simply not for me to answer.  We'll see...

While I am referring to a review paper (common in biology), there certainly is new content being communicated as you describe. The inherent value I see in publishing a scholarly Wiki would be somewhat transformed from the traditional review to fit the format of an encyclopedia entry. It seems the cynical view would be that such wikis are currently not worth it.

Also with respect to character/page limits, that's entirely dependent on the journal. Absolutely no one will read 5000 pages, but some reviews are "mini" (3-5 pages) and others are more comprehensive (more than 20 to 30 pages).

@leonardo: I agree entirely with your second comment and mostly with your first.  What you say is probably "the cynical view", yes, but one could also have this view without being cynical.  For instance I contributed a lot to wikipedia over a period of several years, and more recently much, much more to math.SE and mathoverflow.net, sites which -- though distinct in mechanics from a traditional wiki, evidently come from a similar spirit.  I just don't try to publish my research or formal exposition in such places.

It states in its FAQ that the article published in the site will also be published in its journal

I think there is no definite answer at the moment since one can not judge now how scholarpedia will develop. At the present stage I think that the impact will  be low and many colleagues may not know about scholarpedia. However, this may change in the future and the outcome will depend a lot on the quality of contributions. If you think that scholarpedia is a valuable resource, a good project and that you can contribute something, I'd say: Go ahead.
I also remember a quote by Gian-Carlo Rota: "You'll be better known for your expository work." I am not sure if this applies to everybody equally but it is a point.

"I also remember a quote by Gian-Carlo Rota: "You'll be better known for your expository work."" I remember that too and really believe it (I expect that it will apply to me more than most).  But is that really applicable here?  The choice is not between taking time out to do expository writing rather than pure hard-nosed research, but rather where to publish a given piece of writing (for which the exact combination of research vs. exposition unfortunately remains unclarified).

It seems most sensible to assume that some "original research" has been done (otherwise publication in a journal would not be possible).  Given that, is there a good argument for a very junior person to publish in a newfangled venue like a wiki where they will get little or no "academic credit" versus a (possibly open-access) journal in which they will get the "credit" they should for doing research?  I am having a hard time seeing such an argument.

Everybody is better known for their expository work, but, alas, everybody also only gets PhDs or tenure due to original research :)

As far as I know, having expository work besides original research greatly helps for getting jobs or tenure. So, if the work is a review work, it may be difficult to publish it in a journal as a newcomer.

What I find most interesting about wikis is that they are collaborative platforms with a public version history. This allows updates in addition to the "version of record" functionality of traditional publishing.
Scholarpedia has both, though if you are after Open Access in the sense of the Budapest definition (which allows reuse by anyone for any purpose), it is not there yet.
I am involved with a scheme in which the version of record (of review articles) is published classically in the journal, but in a way that allows the article to lead a second life as an updatable article on the English Wikipedia. Further details can be found here and here.

Both answers are excellent, I would like to add that today is too soon to answers because we don't know how the publication system will evolve.
Right now, we are following a traditional, centuries old system in with scientists gain reputation from their publications, which in very recent years were (and in some countries and some disciplines still are) just in paper.
Open access is "disruptive technology" for this system, but it may regard not only the licenses of research publications, but the very shape they can assume. There are experiments with peer review too. We can definitely imagine a future when sites like academia.se (or math.se, or others) will be taken into account for evaluation a scholar profile. For coders, is somehow customary to look at their GitHub or StackOverflow account...
And I remember at least one case (I don't have a reference, sorry) in which, among other things, a professor gained his tenure also for his concrete and excellent contributions to Wikipedia.
It is a matter of customs, habits, technology and culture of academia and his communities.

Open access is "disruptive technology" for this system — [citation needed]  Open access is an entirely orthogonal issue to OP's question.

among other things, a professor gained his tenure also for his concrete and excellent contributions to Wikipedia — David Eppstein is a computer scientist whose Wikipedia contributions were considered a serious part of his publication record for his full-professor promotion case.  That said, his Wikipedia efforts were likely considered as an additional bonus rather than as a replacement for his traditional publications.

I was referring to "open access" in a very broad sense: experiment on opening "peer review" are IMHO still part of the open access/open science wave, as criticism towards the "publishing articles only" system. I agree that these are experiments and the revolution is not happened yet.

I want to focus on one point touched on in a couple of the other answers: wiki is a class of software that tends to have a certain set of features (though the features vary from one wiki to another). The technical features might impact the value to the audience, but I don't think they have inherent advantages or disadvantages like those described, from the perspective of the author.
A wiki-based publication, a traditional journal, or other formats may have any number of approaches to charges for publication, open access to readers, character limits, and may have varying reputation.
I'd urge PhD candidates considering questions like these to focus more on the specific publication, as measured against criteria like this, rather than worrying about the technical underpinnings of the journal. A publication's policies, processes, and record will have more of an impact on its value to you, than will the technology it uses.


text:
Is my career over if thesis went bad?
I wrote a master thesis which went quite bad, due to communication problems with advisor, and my advisor said he is not willing to continue guiding me for PhD studies.
Specifically, I was asked to prove that the elementary theory of finite field is decidable, and I had no background on model theory. I had difficulty understanding, for example, the proofs of Riemann hypothesis for curves and Chebotarev's theorem. As such, I made mistakes when I wrote the thesis. It felt like the subject is too large for one thesis so I was unable to fill some details in some proofs. When I asked for guidance for some of the proofs, he did provide assistance, but only after six months time.
However, I have studied math on my own and I know that I am able to understand math by working on my own. Is there any hope for my math career if my thesis advisor said so? I have done couple of small new proofs for some old results, but they are so small that I guess I won't get a publication to any journal.

I just can't understand how a thesis can go bad without the thesis advisor being seriously responsible for that. I mean, it could be that both you and he didn't pay attention to this or that and the thesis stinks, but it is highly unlikely as most thesis advisors talk among themselves and with other people about the thesis development...The worse I ever met was to try to achieve something that, at the end, either proved to be imposible to achieve (and still then a thesis can be worth a lot), or else something that has already being worked out by someone else somewhere else...

+1 for the added clarity. Thanks! Hopefully the specifics are such that your advisor (or advisor's colleagues, your friends, etc.) won't recongize the situation if they stumble on this question, but I would bet otherwise. However, perhaps the size of the internet and people's finite amount of time will save you from this.

"Is there any hope my math career if my thesis advisor said so?" Said what?

Any chance of applying extension and switch supervisor? It is pretty common to be able to ask your school to change supervisor if you find them unhelpful. I am surprised you had difficulty in one particular research area but you didn't raise the question earlier and maybe change topic. The first year of my PhD I was investigating something that ended up nowhere, and I switched topic after discussing with my supervisor and now I have my PhD finished on time and had very good results.

This is a PhD thesis?  The advisor is there to be your advisor.  If it went wrong, then they are also responsible.  Followup with the advisor, and if that doesn't go well, then go to the Chair, then Dean.  Be professional, and get some help on how to approach it.

It's very hard to switch to a different advisor or even a comparable school when your thesis goes bad.  This is because the first question a potential advisor would ask is what happened with your old advisor ... if both you and the advisor don't have a reasonable answer to that, you will have a very hard time.
That said, there are alternatives:

You could try working for a year or two and then returning to PhD studies.
You could try switching to a different area.  There are lots of areas where a student with good mathematics abilities could find interesting problems (economics, computer science, physics, ...)
Switch to a less respectable school that might be willing to take a gamble on an unknown student with a good background.

In short, one of the most important decisions a student can make in his/her graduate career is an advisor.

source: Stack Exchange

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

sort: votes


text:
Must a PI who collected data but did not contribute to its final analysis be one of the authors in the paper?
A PI started a study and collected some data. The study was originally meant to evaluate the effectiveness of a treatment. After a year or so of collecting data, the PI decided to do some analyses. When I looked at the design of the study, I informed the PI that this design will not be able to provide any meaningful evaluation of effectiveness.
Some time later, I came across a novel method to analyse this data and tried it out. The results were quite interesting and with the PI's agreement, I decide to try and publish it.
My question is this:
Since the PI was not involved at all in the conceptualisation of this novel method and did not contribute in the interpretation of the results, should he be granted authorship? According to ICMJE guidelines, the answer should be no but I am unsure.
Addendum:
I would like to add, while thinking about this problem, I thought of big studies like the Framingham Heart Study, the Global Burden of Disease study. The PI of these studies are not automatically authors on every paper that came out of the data they collected. Would this be any different from my situation?

It is still PI's data. Without his data you would have no research.

@JackelR Have you written any other papers or is it your first?

If the situation was reverse, it was your data and someone wrote a paper after you gave him your hard earned data, would you be Ok without being an author?

@Alexandros If I did not contribute meaningfully in the paper, I see no merit for myself to be the author and indeed I have done such before though that does not automatically make me right in this situation.

Two questions: (i) What is your relationship to the PI?  Are you his student or postdoc?  Is your work on this paper clearly part of the scope of the funded project, or is it more ancillary? (ii) What was your understanding with the PI about the nature of the collaboration?  When he handed over the data (and other work) to you, what was the intended outcome?

@Pete L. Clark i) We are both in the industry in separate institutions so relationship wise is more of colleagues. ii) The understanding was to assist with analysis. Essentially, I did much of the data cleanup and a first cut analysis that by no means is robust to provide evidence for effectiveness. It was the best that can be done in the absence of the novel method.

@Pete L. Clark As for the nature of collaboration. We were not explicit in what the nature was. On hindsight, we should have discussed authorship right at the start before embarking on anything, planned or unplanned.

@JackeJR: "On hindsight, we should have discussed authorship right at the start before embarking on anything, planned or unplanned." That's definitely the moral of the story, I agree. If both of you are outside of academia, then you are way outside of my own experience....

I can tell you what I would do, but you have to decide whether it feels at all applicable in your situation: no one should get "locked out" of authorship for their joint work.  In the absence of a clear discussion of the nature and requirements of the collaboration, each party who was involved in any way should decide for herself whether to be an author.  Ideally each would give an explanation for their decision, and that can be used to decide whether the collaboration should continue.

There must be a more poignant way to say "don't start collaborating with someone on a paper if you don't want them to be a co-author on the paper"

I suggest changing the title of the question. As discussed in the (good) answers below, this isn't about whether the PI should automatically be a co-author, but whether data collection is an intellectual contribution.

This doesn't seem to be related much to the fact that the other person is a PI. According to the question, someone collected data, and you have analyzed it.
Unless the data was published elsewhere, you cannot cite it. So you will need to include the person who collected it as an author in order to have a source for the data. It's hard to expect otherwise, if you want to use unpublished data as the source for a paper.
The ICMJE guidelines agree; one of their criteria for authorship is:

Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND

The other person has met this point through acquisition of the data.
The most gracious thing to do would be to offer the other person a co-authorship, which will then allow them to meet the other three bullet points in the ICMJE guidelines.
The other person can then decide whether to accept the co-authorship, or whether to take a smaller form of acknowledgment for the data collection.

@JackeJR, but conditions 2 and 3 of the ICMJE guidelines are basically help with the drafting the manuscript and final approval. Many people consider the helping with the drafting aspect to be easily satisfied.

Just to point out that this answers you addendum questions: if a dataset has been published, anyone can use it (with appropriate citation).

Thanks @StrongBad for the link. That is the point I wanted to make: once someone has satisfied the first point of the ICMJE criteria, it is straightforward for them to satisfy the other two. The person just needs to have a genuine opportunity to revise the content of the paper before it is submitted, and they must approve of its publication. It would seem strange for someone to agree to have a paper published with their name on it, because they collected data, without reading a draft of the paper before it is published.

Let me get this straight:

Your PI (who is on a different institution than you) made a study and
collected some data
He gave his data to you
He proposed some ways to process the data which did not work out
You made a better method and you plan to publish without him.

From what I understand, this is not the way collaboration works. Even the fact that he proposed some methodology to process the data (even if it did not work out) it still proves that this work is a joint work and he did not simply handed the data, in the notion that you can do what you want with it.
After all, those simple facts remain:

If you were in his shoes, would you ever collaborate again with a guy who takes your data and does not give you co-authorship, even if you were part of the entire process? The answer is a big NO, because there is nothing to gain from such a collaboration.
What do you have to lose by sharing co-authorship? You will be first author, he takes credit and he will willingly share his data again if needed. Then he will be a reference for you which in the long run, means more papers for you.
What if your paper gets rejected and he finds out? You got nothing and you just burned a bridge with this man.
Imagine the other case. Even, if the other guy was an undergraduate student and he collected the data under your supervision, would not it be unethical not to include this student as a co-author?

Do not be short-sighted. Share co-authorship

+1 for the last bullet point. So many times I see on this site undergrads being slighted because they're just interns/undergrads/whatever and they "only" collected data. It's a big deal.

I remember seeing a paper or Letter to the Editor discussing the requirements to be an author on the paper.  They came up with the 5 types of contributions towards a paper, as I remember they were:

Initial Idea
Data Acquisition
Data Analysis
Write the paper
Revising the paper

As long as someone made a significant contribution toward two of these items they should be an author on the paper.
It completely depends on conventions in your particular area.  For example in my field the supervisor is always the last author.  I know some fields might have them as first author.
But, what it comes down to is what many others have said... don't burn your bridges. You need collaborations!

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


text:
Postdoc without letter of recommendation
What if my PhD advisor doesn't want to give me a letter of recommendation, because he doesn't want me to leave on postdoc? None of his young assistants have ever been on any postdoc or fellowship exchange.

not to be captain foresight, but that is a HUGE red flag to begin with.

In brief, you should find some other faculty in your department (perhaps the member of your thesis committee) or perhaps some prominent researcher in your field from the other place who knows you well enough and would be willing to write a (favorable) recommendation. You should be prepared to explain in a convincing fashion the absence of recommendation from your Ph.D. advisor at the interview and/or in the cover letter.

Thanks for the comment, I believe that recommendations from others won't be a problem, as well as my CV.

Are you sure you understand what a postdoc is? I don't mean to be insulting, but if none of his students have ever done a postdoc, where did they go after they graduated with their PhD? Did they all get jobs in your advisor's group at your university after they finished?

Yes, they got jobs with your advisor and didn't leave? That's a bit unusual. What country is this?

It's been a few years now, how did things turn out for you?

Based on your comment responses, I think that you are working for a young faculty member who is trying to build his group and encouraged his first two PhD students to stay on after they graduated. It's an admirable goal to start building a research group, but in the US it would be discouraged to do so by keeping all of your own students in my experience. US academic research has a bias towards sending one's students out into the world to cross-pollinate ideas and avoid stagnation and closed-mindedness.
That being said, refusing to provide a letter of recommendation to a good student for this purpose is borderline if not outright professional misconduct and wouldn't be tolerated at most US universities (though I'm constantly surprised what weak administrators let star faculty get away with sometimes).
I think you should sit down with your advisor and explain your life goals to him. Include the fact that you are eager to get out into the world and learn more in a different environment. Try to convince him to see it from your perspective without getting antagonistic. If that doesn't work, go see your department chair, but only as a last resort.
You are in a bit of a tenuous position since your advisor could refuse to sign off on your dissertation (or let you defend, or drag his feet on revisions, etc) if he becomes scared by feelings of abandonment in your desire to leave. Bringing in higher authorities could make this worse. It would be best to convince him with the power of good arguments than to make the situation adversarial.
The timing of this can be tricky. He's probably going to find out that you applied for postdocs with out his recommendation and blessing, and given the usual schedule for postdoc recruiting, I'm assuming you will have to apply before you defend. I think it's probably better to be open with him that you are definitely going to apply, find a postdoc, and leave than to do so behind his back. Maybe when he sees your resolve to do so, he will change his mind about writing you a good letter.

A small portion of postdoc positions do not require a letter of recommendation.  People who have not got access to a letter have received those jobs.
It is not always possible to identify if a job requires a letter until after you have applied.
Normally, a PhD supervisor would only refuse a PhD student a letter if the student committed major misconduct.  Not writing a great letter reflects poorly on the supervisor.

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


text:
3 - 4 years since I graduated, how should I time asking for recommendations?
Since I graduated as an undergrad three years ago, I've been planning to go back into graduate school, so I saved all my assignments and heavily kept up on studying and research. My transcript looks good and I've had a lot of time to focus on GREs.
The most uncertain and anxious part is getting letter of recommendations from my former professors. Due to my nature, I haven't maintained contact with the three professors I have in mind, especially given the job I have. I'm confident that they'll remember me if I send them a quick e-mail, but I'm hesitant about the timing. It seems a bit awkward to re-establish contact out of nowhere without letting them know my intention, but at the same time, I feel it's a bit too early to let them know I would like to start looking into graduate school.
I was thinking of sending them e-mails stating my intention to apply to graduate schools, be able to provide documents/statements so they have something to remember and write about me, and ask if they were interested on writing the recommendation. If so, I would follow up and provide them the application details several months ahead.
Is this better than asking them out of the blue when graduate application crunch time starts?
Also, for professors and those who wrote letter of recommendations, what are your experiences of writing recommendations for former students reaching back 3 - 4 years later?
Edit: Update on this below

After about four years in industry, I decided to apply to graduate school.  I forget the exact timing, but I talked face-to-face to my undergraduate professors about five months before application deadlines, when I had narrowed my choices down to four programs.  When I had things set up properly, they were happy to assist.  I think giving them a heads up (and perhaps a face-to-face) with proper follow up is the thing to do.  Even if you later change your mind and don't use their recommendation, they often appreciate knowing how their former students did.  Just respect their time.

Anything that gives them a reasonable amount of time to write the letters should be fine. Unless you're looking for advice, I'm not sure there's much point sending them a vague email along the lines of "Hey, I'm thinking of applying for grad school, would you be able to write me a reference for some as-yet-undecided school(s) at some point in the near-ish future?" but, once your plans have firmed up a bit, giving them some notice can't hurt.

My recommendation is similar to those posted in comments. I worked for several years before applying to graduate school and did not stay in touch with my professors during that time. Approximately 4 months before I applied to graduate school, I sent each professor a brief (1 paragraph) email explaining my graduate education plans and career interests, and asking if they would be willing to write letters of recommendation, which would be due in November. I also indicated that if they were willing, I would send them my CV and a summary sheet of my college activities for their reference. I contacted them via email, as I lived in a different state than the college, and face-to-face meetings were impractical.
When they agreed to write the letters I sent them:

A summary sheet listing each program I was applying to. For each program I listed the address and contact person (so the letter could be properly addressed), 1 line about why the program interested me, the names of faculty I was interested in, the application deadline, and specific application letter forms or links to online applications, if relevant.
My CV
A summary sheet highlighting specific grades in major-related courses; research projects and activities I engaged in during college; a 1 paragraph narrative explaining what I had done since graduating and why I was interested in pursuing another degree; and a list of courses I took with that particular professor/letter writer, along with the grade for the course and any special projects completed in those courses. Try to keep this to 1 page.

Although this sounds like a lot of information, work to keep it as brief as possible, while ensuring the professor has the information they need to write a strong letter.
You may choose to time this differently, but the four month window ensured that I had committed to applying and gave me time to identify alternative writers if they had declined. I'm not sure it would be useful to ask your professors a year in advance, as 1) your plans may change, and 2) they may not recall a commitment they make that far in advance. That said, I would make initial contact in the summer before you apply; if you wait until the school year kicks into full gear, your email might get lost in the shuffle. When I was applying I was advised by multiple people to provide all materials to my letter-writers a minimum of 2 months prior to the deadline. Many schools require letters to be written on specific forms, have surveys your letter writers are asked to complete, or even ask the letters be submitted online; it's unlikely the most recent application will be available more than a few months prior to the application deadline.
A few final notes:

Be sure to ask if they feel they can write you a strong letter, not just a letter of recommendation. Most faculty will be honest about this.
Send your letter writers an email two weeks prior to the application deadline to thank them and remind them of the approaching deadline. Many online applications will indicate when your letters of recommendation have been uploaded.
Be sure to thank them, both when they agree to write the letter and when the letter is submitted. Consider writing and mailing a formal thank you note, once the application is submitted. Also, contact them once you're accepted and have decided on a school; they like to know how it's worked out!

So it's been 4+ years since I graduated from undergrad and more than a year since I asked this. I should write an update since this one got a lot of visibility. To keep it short, I got accepted into graduate schools that required recommendations.
My earliest application deadline was at the end of December, so I sent out e-mails to my past professors in August and September. One declined but two responded enthusiastically. Most applications requiring 3 recommendations, I had my boss's boss in my workplace write one for me as well. He could at least speak for my character, performance, and professionalism.
I sent these writers my CV, unofficial transcripts, statement of purpose, and list of graduate schools that needed these recommendations. In that list, I included each school's application deadline, which specific program I was shooting for, and a short note why I chose each of them.
The tone of the e-mail was akin to coming with "hat in hand", being honest with the fact they probably do not remember me, and offering to send the mentioned documents for them to decide if they would write a positive letter. I didn't outright ask them if they could write a recommendation, but if they would simply consider it given more information.
I've read so much horror stories about writers not responding or sending their recommendations on time, but I experienced none of it. These writers were awesome and I'm extremely grateful for them. Every time I got an acknowledgement that a recommendation was received, I would send an e-mail out thanking them and attached an updated list of schools still needing recommendations.
Thanks for all the help and comments in this thread as well.

Thank you so much for returning and sharing your experiences!

The above advice helped me so much. I needed at least 2 recommendations from professors who could attest to my quantitative skills. I reached out to two professors by email, asking for their office hours. Even though both showed some reluctance (one was on sabbatical and said that he could only write about how I did in his class and the other had some doubts and advised that I take additional courses), they ultimately wrote the letters. I asked them about a month before the earliest deadline but you should ask as early as possible (preferably over two months early because professors are busy). Definitely try to ask them in person and come prepared with anything that could help them write the letter (resume, transcripts, statement of purpose, info about each graduate program and their deadlines, and a few sentences about why you want to apply to each program).
When I first emailed them, I didn't get a response back saying that they were going to write the letter...so I decided that I won't be able to apply and stopped studying for the GRE. A month went by and then I received notifications that they both submitted a letter to the program with the earliest deadline! I then had only a week to cram for the GRE and applied two weeks late to my first choice. But despite all of this, I was accepted to my first choice.
What I learned is that even though I was afraid of asking, I should have emailed them again to confirm whether they would write the letter or not. I just assumed that no response meant they weren't going to write it. Also, I almost did not apply to my first choice because I knew my application would not be completed by their deadline. One of my transcripts, one of the recommendations, and my GRE scores were submitted late. However, if you believe you are a strong candidate (high GPA/GRE scores, excellent statement of purpose that clearly shows that your goals and interests align with the program, etc.) and it's a program that you are really interested in, the admissions office might be understanding and still consider your application even if it was completed late. Most of my application was submitted by their deadline, so if you are missing a few things, just try to get them submitted as soon as you can but no later than a week or two.

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


text:
Are Masters degrees from German universities of applied sciences (Fachhochschulen) eligible for PhD?
Are Masters degrees from German universities of applied sciences (Fachhochschulen) eligible for PhD?
If I do a Masters in any of the German universities of applied sciences (Fachhochschulen), would I be able to apply for a PhD in any other Universities/research institutes in Germany?

The basic answer is "Yes, but. . . ."
A master's degree is usually the minimum prerequisite for admission to PhD programs in Germany. However, many faculties within various German universities have established "qualification" procedures for degrees they do not believe to be "equivalent" to their own. This usually includes some combination of coursework (with the associated exams), plus evaluation of the master's thesis to show equivalency to the expected degree.
These criteria are often applied not only to international students, but to students from German Fachhochschule as well. However, these policies vary widely between universities, and between different departments at the same universities, so you should contact the specific programs you're interested for more details.

Since you have asked this question, the situation has changed. It is now becomming more common that people with a master degree from a university of applied sciences (or Fachhochschule, FH) are doing PhDs. The barriers that @aeismail mentioned still exist, but the willingness of university professors to supervise FH-students has increased. Often FH PhDs are done collaboratively between a FH (were most of the reserach is done) and a "regular" university (were the main supervisor is located, although the FH profoessors co-supervise as well).
There is even the possibility to do the PhD not at a "regular" university, but at a FH itself - withouth a univerity based supervising professor. This is so far only possible in 6 of the 16 Bundesländer (federal states) of Germany, though.


text:
How to correct plagiarism in my own Master's thesis, years later?
My situation is somewhat similar to this question, but I'm the plagiarizer.
Six years ago I did my Master's degree by coursework at university X, and wrote the Master's thesis under supervision of well-known Prof. A. For many reasons that I don't want to list here, I plagiarized. The first part of my thesis was background, and the second part was the original contribution.
In the background part, I copied an entire chapter from textbook T about algorithm S. Algorithm S was invented more than 50 years ago, and is described in several books, including the very well-known T. I didn't paraphrase at all, I started by citing T, and then copied the whole chapter word by word.
The contribution part is actually contribution. One year after I left the school, Prof. A found another student to extend it and published the extension with me as the second author. (The paper included the algorithm and experiment in my thesis, but I didn't write a single word of the paper.)
I have moved to university Y to do a PhD. I have published several papers in top conferences and have very good relationship with several well-known researchers. I want to advance in academia.
Will the Master's thesis destroy any possibility of a future academic career? If someone read my Master's thesis, it is very easy to recognize, since the part from the textbook is in perfect English, and the rest is in extremely poor English.
Can I contact the university to submit a revised Master's thesis which re-describes the algorithm S? This is the last thing I want to do.

+1 for a honest question, we all make mistakes, now what.
Disarming the latent bomb seems to be the right thing to do, asking university X how to proceed (with caution). Now, how hard can redescribing a well-known algorithm be ? (especially if you want to teach in the future)

If you go to the university and tell them, nobody will be thrilled about it, but they will also be invested in keeping the matter silent. Accepting plagiarized text as a graduate thesis does not reflect well on an institution. So don't be afraid that they will start a public scandal. Personally, I also think that they should let you re-defend your title, because this is the long-term winning strategy when it comes to human mistakes, but I can't promise you that the staff will see it that way.

Congratulations for recognizing that you made a mistake, and your willingness to make amends. The "road to redemption" may be rough, very rough even - but RESTORING YOUR INTEGRITY IS SO IMPORTANT, that even if it means re-writing, submitting, defending your thesis to get a degree you deserve, you should go through with it. Do try to get some professional advice - is there an ombuds person at your old university that you could contact (or maybe "a friend" could contact) to get a sense for how they might react?

I think this is up to your previous master program school policy. Does it allow students to revise their thesis after graduation?

I just stumbled upon this question. Would you mind sharing what you did and how it worked out?

Wait a minute. Am I the only one who doesn't think this is as big of a deal as it is being made out to be? You essentially reproduced a section from  a prior publication, but it was in your background section, where the material is understood to be non-original. Furthermore, you say that you cited the source. It isn't as if you took someone else's work and claimed that it was your own. I guess this would fall somewhere along the lines of "unauthorized reproduction", then?

I cannot tell you what the university will do if you confess; I am not employed in a position which would be involved in such a decision, and besides, I think that this will depend on cultural and legal factors, plus the personality of the decision makers in your case.
But I still think that it is better if you confess. There are several reasons for it:

Your own inner peace. By contemplating confession and posting here you show that you have matured and have higher integrity and a better understanding of academic rules and the seriousness of plagiarism than back when you submitted your thesis. If you don't confess, you will have to live with both 1)the guilt of not only having made the mistake once, but still actively deceiving people,
and 2) the anxiety of being discovered someday. I have been on both sides of a "hidden guilt" situation (although when it was on academic matters, it concerned milder cases), and I can tell you from experience that it is a bad situation, especially for the person who feels guilty and dreads discovery. It burdens you with a stress which can permeate to many unrelated areas of your life and make you miserable.
Your risk of discovery rises with time. Nowadays, universities start to routinely employ plagiarism software. Who knows what funky electronic agent will snuffle in your old thesis ten years from now? Twenty? What if such software becomes so ubiquitous and cheap that employers start running it on your old theses when you apply for a job?
If you confess, you will suffer negative consequences - but not nearly as bad as if you are discovered by a third party. Confession, especially if you are repentant, shows that you are capable of feeling remorse, have high integrity, also courage, and are willing to take responsibility. Being caught makes people see you as a cold-blooded fraud not deterred by social emotions like guilt and remorse. This makes you dangerous to them and reduces their empathy for you. They are much more likely to be lenient if you confess than if you are caught by others.
The later it comes out, the worse for you. If you are either caught, or confess yourself much later (e.g. because you notice the negative effects of guilt and anxiety - and yes, this happens, I have witnessed such late confessions), it will have negative effects on your career. But right now, you are at its beginning.

You have relatively little to lose yet. If you wait until later, you will have much more to restore after such a reputation blow.
The younger you are when it happens, the more time you have to build a solid career without having to start anew. At times when you advance into more leading positions, it would be better that this story is a thing of the past, forgotten by most, than that it hits you out of nowhere.
The sooner you confess after the mistake, the less reputation you lose. The less time you carry the problem hidden around, the less callous you appear, and also people feel less deceived.
Once it comes out, everybody who has relied on your thesis being correct will be miffed. The more your life progresses, the more this number of people grows. If you confess early, you limit this number.

Your university is not interested in a public scandal. The dean doesn't want to open the morning paper and see a "university duped by brazen plagiarist" title. They will be unpleasantly surprised by a private confession too, but they will not feel that the situation is out of their control, or that the worst that can happen has already happened. They will have some incentive to cooperate with you, as long as you confess. If you are caught, their best strategy becomes to distance themselves from you and denounce you.
Time has shown that redemption is more beneficial to society than punishment-as-deterrent. This has been repeatedly shown in many situations: religious context (most of the New Testament is based on it, even though many Christian churches have historically been on the side of harsh punishment), law enforcement (prisons which are pleasant for the prisoners show better reformation rates) and parenting. So many people who have advanced to leadership positions have the wisdom not to mete out severe punishment for misconduct. Especially if you indicate that you are unlikely to repeat the mistake (and a confession is a very important part of it), they can be lenient. There is no guarantee that the leaders of your university will share this belief, but it is not exceptionally rare either.

They will still have to enforce some consequences. It would be both unfair to the students who played by the rules to get their degree, and damaging to the university's reputation to just let you have your degree when you did not follow all requirements for it. But they will not be vengeful, seeking to end your career. This is something which certainly happens when academic misconduct is caught much later by a third party after the fact, see the German examples Peter Jansson cites (and notice that in some cases for the German politicians, their plagiarism was limited to a few sentences), but also cases like this one in which a renowned professor's academic career came to an end after academic misconduct (although not plagiarism) was proven.
You may want to find support before you go straight to the people who have the most to lose from the news. The behavior of your current employer is also hard to predict (they might be legally required to terminate you if a Master's degree was required for your acceptance into the Ph.D. program), but if you think they will be on your side, you might want to talk to them first so, when you come to the university, you have somebody who can testify that your current level of work is as good as one of a person who obtained a Master's degree regularly. Especially if you have coauthored with somebody with a good standing in your community, they may be interested in helping you rather than having a publication in coauthorship with somebody whose reputation was destroyed (but gauge them as a person too, some people will prefer to just drop you and forget you).
I hope everything turns out to the best for you. As Nikana Reklawyks said, we are all human and make mistakes. If you are willing to repair the damage yours caused, this makes you a better, not a worse, human being.

"If you confess, you will suffer negative consequences - but not nearly as bad as if you are discovered by a third party." This is the most important part. You may be able to "weather the storm" if you confess your actions. If someone makes an accusation, it will be a lot harder to sweep it under the rug.

Plagiarism is plagiarism and your existing thesis is the one which got you your degree. Since you have received your degree, the possibility is to confess to the plagiarism resulting in, possibly retraction of the thesis and removal of the degree. There have been a few highly publicized cases of plagiarism of PhD theses by people who have come to hold high positions in society (Example one and two). The exposure of these cases have led to them losing both their position and their degree. Having plagiarized your way to the degree could easily backfire at any time if, as you say, someone finds out. Now, we all make mistakes in life so I would think the best way to act responsibly is to contact a lawyer or the legal department of the university to discuss the matter and a way forward.
Regarding your publication, it seems as if it would not be affected by the story since it is your original work that has been published and I doubt that the authors copied the plagiarized chapter into the paper.

I realize that I may be late in seeing this and answering this, but I believe confessing is the way to go. I am a university administrator who has handled cases of plagiarism. In some cases, the plagiarism was discovered years after the student had received the degree. On discovery of plagiarism, the matter generally goes to a disciplinary committee. For academic misconduct, disciplinary committees look for remorse on the part of the student in considering penalties. In instances where sufficient remorse is shown, students are given the chance to revise their thesis instead of depriving them of their degree. In your situation, the revision is not difficult because it is in the "review of literature" part rather than the "innovation" part. There is no issue of whether the revised work will be degree-worthy, which makes it easier on the examiners who will have to review and approve the revised thesis.

It's awesome to have a person in your position contribute in this level of detail.  Is it possible for you to comment on how common your policies are?  Do you know how  likely it might be to find similar policies at other institutions?

Edited completely, given correct comments below stating that I seemed to be advocating non-confession.
I think the comment above both understates the case re punishment - you likely would lose your degree and your place on the PhD programme and admiration for your confession won't count for much - and overstates your likelihood of being caught. Universities archive dissertations for x years then pulp them.
What is strong is this: you lied, the weight of that won't make for a comfortable career and you deserve a consequence, at least on the facts as presented.
In short, should you confess, be prepared for another career.
Apologies for coming across like I don't take the ethical issues seriously. My intent, very badly put, was rather to prepare you for the worst if you come clean.

I think this and most answers miss an important detail: He DID cite the source of the text.  Doesn't that make it NOT plagiarism?

No. It is plagiarism. Citation is not enough: if you are using someone else's words you indicate appropriately by placing the quote in quotation marks and/or blocking the text margins. UK institutions use something like "using the work of others as if it's the writer's own' or some such formulation. So in this case if the student had started the chapter with: this chapter in its entirety is paper x then maybe it would simply be atrocious scholarship and not an academic offence.

OK, I grant that it certainly should have been different, but perhaps OP can clarify whether it was intentional or inadvertent formatting error.  He did say his English was terrible at the time.

@WGroleau Yeah: that is an issue. For what it's worth my stance is that it's a separate one though. That is, whether work is plagiarised is a technical question. My judgement on the student's reported state of mind at the time might come into the question of consequences. But I recognise that this isn't the only possible view on the matter.


text:
How to get rid of annoying graduate student "supervisor"
I am an undergraduate student who has developed a novel new model which according to my PI (principal investigator) will have a high impact.
My PI assigned a grad student to supervise me. Supervision consisted of meeting once a week to update him on my progress so far. Sometimes he would provide certain helpful suggestions(none that are actual innovations just slight fixes/alterations that would improve the model).
During the course of the year he (the grad student) has become more and more annoying. Unhelpful suggestions/requests, etc.
During our last meeting the grad student made some bold claims on the model developed by me claiming to be an equal author/developer. He made it clear he wanted to get a large amount of credit for the model (co-authorship).
I do not think that he has done enough meaningful work to deserve credit for the model (although he would be listed in acknowledgements). Knowing his intentions I wish to distance myself from him(including not having him review the paper), as to lower his chance of becoming a co-author.
I would like to achieve this in such a way that does not negatively impact my relationship with my PI, as grad schools require reference letters.
EDIT:
I don't think I have been very clear and for that I apologize. I acknowledge that he has contributed to the work. I also understand that having more authors doesn't reflect badly on me(I didn't even know about the score system). I just have problems with his claims of equal authorship. As we are nearing final results/submissions of paper and he has better relation with the professor he may try to take the first authorship position.
Additional: By my university guideline policies about co-authorship he has not done enough to deserve even a co-author position.

You are currently being advised by a grad student, not by your advisor. So, will you list your advisor (PI) as a co-author?

I still remained under the advice of the PI, just not as frequently. I will list my advisor as a co-author as he was helped me/was crucial in the creation/implementation of the model. He doesn't advise on trivial/slight fixes, but on major paths upon which I investigate further. (On an unrelated note: even if he did not do very much, my future grad school application would require me to put him as co-author if he expressed his interest. But that is not the current case.)

possible duplicate of How to get rid of unwanted and annoying co-author?

I read that question before posting this but I thought mine differed in a few ways. (i) I was assigned this "supervisor", did not choose him. (ii) I did not promise co-authorship (iii) I am put in the position of still having to please my PI. It is this last point how do I go about doing such an action without upsetting the PI that I need help on.

It is your observation that the "annoying" grad student does not deserve co-authorship (I know of many cases of others getting the nod for co-authorship who have done much less than the grad student in your example). In this case, it is best to meet with your advisor (and possibly the grad student) to discuss an authorship plan. Pro tip: it is best to do this well in advance so that the situation you are experiencing now can be avoided.

Question: Did you start working on a totally new project, or did you carry over the work done in the past by the grad student? If it is a new project, then you should be the lead author but if he has worked on it for a long time (without any good results), then he getting equal credit is not too bad. As the above comment suggests, even I would advise to talk with advisor to sort out this issue.

Cheap behaviour on part of the grad student. Intellectual robbery. Please try to sustain these intellectual injuries and move ahead.

Not really an answer because I think you've got some good ones below but how unethical!  I don't believe you are at some inherent disadvantage (as some suggest) because you're an undergrad.  I have worked on literally hundreds of grad student projects as a professor and do not claim a single one of them as my own and am only listed as "co-author" if the student so chooses.  Welcome to the politics of academia!

It also depends on where you are publishing your work. Some journals expect all authors to contribute or understand all aspects of the work. If you had a 2nd author that contributed a piece of work and it was fake work then you and any other coauthors would also be blamed for falsifying data to get a publication.

With regard to your comment about not wanting him to review the paper, it's very unlikely that a journal editor would assign a reviewer in the same department of the same university as one of the authors, as that would be a clear conflict of interest. Indeed, if your PI is an author of the paper, there is no way in the world that one of his graduate students would be assigned as a reviewer.

I am an undergraduate student who has developed a novel new model which according to my PI (principal investigator) will have a high impact.

Great!

My PI assigned a grad student to supervise me. Supervision consisted of meeting once a week to update him on my progress so far. Sometimes he would provide certain helpful suggestions(none that are actual innovations just slight fixes/alterations that would improve the model). (...) Knowing his intentions I wish to distance myself from him(including not having him review the paper), as to lower his chance of becoming a co-author.

Less great. Much less great. Let me make something clear here: this is not your project alone, this is the project of you, your advisor, and the PhD student. The guy has invested a serious amount of time into this project (not as much as you, clearly, but still a significant amount), and now you have unilaterally decided that he is to be cut out when the time comes to publish your results? Likely, this is not to be going over well either with him or the advisor, and for good reasons.
Deteriorating professional relationships are never fun, but it is simply not feasible to decide midway through a project that you now would rather not have another researcher on board. If he has already made contributions to the project, and it certainly sounds like he has, it would be unethical to publish without him now.
EDIT: to make it clear, I am not saying that he should get equal credit to you. But it certainly sounds like he should get some credit.
The very least you need to do is follow user11192's recommendation:

it is best to meet with your advisor (and possibly the grad student) to discuss an authorship plan.

Finding a "sneaky" way to get rid of the grad student before publication time is not particularly ethical, and has a pretty high possibility of backfiring on you.

This is truly true answer. One important thing is that how can the OP measure significance of small hints given by PG student? Can he/she measure that the PG did MINOR contribution or major? It might be the case that one small hint in early stage of research can save huge amount of time for implementation and evaluation which is simply dismissed by OP because the hint was small. In academia/research things are not based on weight/size, but significance. If small comment/hint is significantly valuable, what else do you expect from someone's comment?

Great answer, but the OP never said that the grad student is a PhD student. Your answer sounds as if you are adding a 4th person to the mix.

Perfect answer. The rules should never be changed when the match has started. There will be more papers in the future.

The grad student not only has invested time in the project by supervising, he might as well have brought the whole project to the point were it was at a state of giving away some of the work to an undergraduate. Don't underestimate this work. How much credit both of you should get greatly depends on the scope of the paper you are going to write. If it only includes exactly what you did, your work might have been more. But it could also base heavily on the grad students work in the end.

Undergrads can be very bad at estimating how much others have contributed. Both over- as well as underestimating. It requires quite some experience to gauge how much (especially on the basis of regular meetings) is being contributed by meetings. You may want to consider that your estimate of contributions are wrong. I am not saying they are, but take it into account.

It looks to me like the coauthorship decision is being clouded by the graduate student supervisor's annoying behavior, including his claims of being "an equal author/developer".  Whether this graduate student should be a coauthor is not a part of the question -- rather the question is how "to get rid of" him.  But based on what you've said I think this is wrong: you do need to consider the case for his coauthorship.  To my mind it rests on two things:
1) He was assigned at the beginning by your PI, whom you say absolutely did supervise you and was crucial in the creation/implementation of the model, and whom you will be including as a coauthor.  Well, part of your PI's supervision was to assign this graduate student to you, whom you met with much more frequently than the PI.  Thus the three of you entered into a collaboration.
2) There seems to be no doubt that the graduate student followed through with the process of supervising you.  You write:

Supervision consisted of meeting once a week to update him on my progress so far. Sometimes he would provide certain helpful suggestions (none that are actual innovations just slight fixes/alterations that would improve the model).

So he met with you regularly -- more regularly than your busy PI.  Regular weekly meetings are amazingly helpful in keeping people on track (especially at the junior level...but also at the senior level, honestly).  He didn't just listen to you but provided helpful suggestions.  And not just suggestions that sounded helpful but some which actually improved the model.  Thus he made an intellectual contribution to the work.
The confluence of 1) and 2) makes your desire to have the graduate student supervisor not be a coauthor look unreasonable to me.  Coauthorship is a convenant that people enter into: it is an agreement that they will do certain work and as a result be part of the final product.  There is a certain base level of involvement that various professions and journals require for coauthorship: that seems to be safely met here.  Collaborators are also free to impose higher standards, but these standards should be made clear in advance.  It is very uncollegial for you to turn around after work has been done of the form that was specified and try to shut someone out of coauthorship.
In general, I would say that if someone does what they were asked to do procedurally for coauthorship but comes up a bit short intellectually -- i.e., it turns out in retrospect that their contributions are not so valuable or essential to the final paper -- then the decision on whether to withdraw from authorship rests with them and not the other collaborators.  If you feel that someone else didn't pull their intellectual weight, then the time to bring this up is in a discussion of whether the collaboration should continue.  (I should say that most people I know have a very acute sense of "not pulling their intellectual weight", and it is rather rare to see a math paper with a coauthor who could not point to a theorem or proof in a paper and say "I did this part".  But other fields may differ.)  This is still a delicate conversation, of course.
I think what you are really trying to say is that you want to be first author.  Based on your description of the work, it sounds reasonable that you would be either first author or co-first author with the PI.  That is a discussion for the three of you to have.

I would like to achieve this in such a way that does not negatively impact my relationship with my PI, as grad schools require reference letters.

Yes, be careful about this.  I am going to guess that the PI will not be pleased at an attempt to cut out his own student from the paper: that is going against the plan for the work that he set up.  Finally: "...as grad schools require reference letters".  Hmm.  True gratitude is golden, but knowing which side of your bread is buttered has got to be worth something.

I'm confused on why you wouldn't want to have him as a coauthor ? Does it some how diminish the work you did? On the contrary, publishing work with coauthors is not only expected, but essential to survive in academia.
My suggestion? Relax. If you publish as an undergraduate you are already golden. You can get letters from both the PhD student and the PI, glowing letters as you published. It certainly seems like both the PI and the graduate student deserve credit, making them 3rd and 2nd authors respectively seems very reasonable.
Before you go on destroying professional relationships, at least build them up first.

You mean getting a recommendation letter from a Phd student?

There are different metrics that are applied in several different contexts (e.g. applying for tenured position). In some of those metrics, authors are awarded a number of points for each paper depending on the number of authors. For example the one I know is 4 points sole author, 3, 2 and 1 points up to 4 authors and then I don't remember but for sure the score is below 1 (maybe 0.5).

I think an undergraduate who is worried about their 'score' is totally missing the more important point.

In the world we live, I feel it's all about the "score"... How will his publications be judged if he applies to study a PhD in a different university? Sure, he is "golden", but he could be "more golden" and he could lose the position against someone that is (or looks like) "more golden".

During the course of the year he (the grad student) has become more and more annoying. Unhelpful suggestions/requests, etc.

Since I don't know you personally, I hope you won't mind a candid question.  Is it possible that the graduate student is pointing out correct suggestions based on greater experience that you are stubbornly ignoring?  I've seen this happen several times, especially with bright undergraduates.

I do not think that he has done enough meaningful work to deserve credit for the model (although he would be listed in acknowledgements). Knowing his intentions I wish to distance myself from him(including not having him review the paper), as to lower his chance of becoming a co-author.

As far as I can read from the tone of your question, you appear to trust the PI ... why not go directly to him/her with your concern?  Let the PI decide how to handle it, or, if you're not comfortable with that, why not approach a neutral third-party professor who could understand the work and give you a candid assessment?

I would like to achieve this in such a way that does not negatively impact my relationship with my PI, as grad schools require reference letters.

Ultimately, it does not hurt you to have co-authors on a paper, as long as they have actually contributed to the intellectual merit of the work.  However, if, even after impartial third-party assessment, you feel that the work is rightfully yours, fight for it wholeheartedly and directly.  Tell the graduate student and the PI what you think, and insist that you should be the sole author.
Academia is a place where you have to fight for your ideas, or be trampled by the herd.

I don't see how one could discuss a project weekly over a long period of time with somebody and then claim that they didn't contribute to it and therefore don't deserve to be a co-author. It's one thing to have a couple of chats with somebody about something and then go do the rest of the project on your own, but weekly meetings is a definite research collaboration.

It depends on the field.  I have taken myself off co-authorship on papers where I felt I did not contribute sufficiently (although I did get an ack).  Not all discussions are intellectually meaningful to a paper.

Something to keep in mind, Academia involves politics and some things cost you little.
Your PI wants his grad students to do well too.
That means getting their names on research papers.
Even if he's annoying, you said yourself: he's contributed.
If there's 2 other names following yours then that's fine.
3 or less names on your paper doesn't hurt you in any way.
Getting published as an undergrad is already great.
Your only concern as the person who did the majority of the work is that your name come first. That's it. First name in the list is what you want. That is your one and only goal.
If it makes your PI happy to give a little boost to the career of one of his grad students that is perfectly reasonable (also, other people you'll want him to recommend you to will want to know you're easy to work with and willing to play the game of politics because they're all doing the same).

You make it sound like the grad student is simply being added to help his career. Whatever the reasons were for him assuming the adviser/collaborator role, the fact is he contributed and so deserves co-authorship. Politics has nothing to do with it at this point.

sure, but even if the phd student was a numpty who was quite totally useless and contributed little that was worthwhile it would still be in OP's best interest to go with what his PI wants.

Start writing the paper now, make a preliminary draft and send it out to all of them. In the draft, put yourself as first author, add the phd guy as second and the PI as senior author. If at one point the phd guy thinks he should be first author, you can ask why he thinks he deserves it (do that in front of the pi). Then tell him that you respectfully disagree.
These kinds of things happen but as long as your, rightfully so, first author, everything is ok. I heard of people being removed from author lists even when they had done the majority of the work.

If this is copyright infringement, or intellectual theft then get a lawyer. At least call one, consultation is generally free. In fact, the lawyer will know more than the school as to how to proceed here anyway... Good luck.

I'm going to go out on a limb here and say that, if the OP gets a lawyer involved, s/he can kiss letters of recommendation from their advisor goodbye.

Where did you see accusations of copyright infringement or intellectual theft in this scenario? Nobody is saying the OP doesn't deserve authorship, or otherwise plotting to steal his/her work


text:
On writing a review (i.e. summary) for a problematic (published) paper
I am trying to write a review on a published paper for Mathematical Reviews. The paper proposes a generalization of K-theory. Its main definition is fundamentally problematic. So the rest of the results are worthless. Therefore, I cannot write a brief summary of their results, because it means that I did not understand the mistake. On the other hand, the abstract of the paper is very concise and misleading, so I cannot recommend it as the review to MR either. Besides, I do not want to spend too much time to explain all the mistakes and errors in the paper (it is not my duty as a reviewer!). Therefore I was thinking to write to Mathematical Reviews and let them know about the situation and deny writing any review for this paper. But before doing that, I was wondering if there is a better solution for this problem?
P.S. For those who are not familiar with Mathematical Reviews, I should add that MR asks mathematicians to write brief reviews on papers (book, etc) that are already published and these reviews are available at mathscinet. So, these reviews are different than referee reports.

I fail to see the problem. Can't you still write up a summary of the main results and then indicate that they don't hold up because of the problem in the main definition? (e.g., "the main claim of the paper is that the Moon is made of blue cheese, but this result is incorrect because the author has not bothered to look through a telescope")

@Koldito: I think it is kind of unreasonable to write half page summary of the paper and then add about one page to show that the main definition is problematic, and so the reader is advised to not take this paper seriously.

"Besides, I do not want to spend too much time to explain all the mistakes and errors in the paper (it is not my duty as a reviewer!)." What?! It is your main duty as a reviewer! (Except for "too much": once you get enough errors to sink a paper, you can stop.)

"Its main definition is fundamentally problematic."
You mean you dislike it, or is it ill-defined oo self-contradictory?

@PiotrMigdal: Let $A$ be an involutive algebra. They start with projections on $A^n$ and then consider the direct sum of these projections as new projections on $A^n$, while these new projection obviously belong to $M_{2n} (A)$. In ordinary K-theory, all projections are considered in the inductive limit of $M_n(A)$ and so this problem do not arise. But the authors did not pay attention to these details.

I know of one paper containing a major `result' that was published some years ago in one of the top journals, but where the proof was fatally flawed, and this was carefully explained in a lengthy review on MR. While it makes for rather uncomfortable reading, it has the virtue of saving the time of the would-be reader.

Your review should do three things (not necessarily in this order). It should tell the reader what the topic of the paper is, perhaps including the authors' main "theorem". (This presupposes that the paper is clear enough to have a topic; I've reviewed garbage that didn't have a discernible topic, but I gather from your question that this is not the case here.) It should make it clear that you think it's wrong. And it should give enough information about the error to allow people in the same area to understand why you think it's wrong. (Once you've explained the essential error, it's not necessary to list a lot of other errors, unless you think that doing so would help the reader or make it clearer that the paper is wrong.)
It is especially important to indicate accurately just how bad the paper is.  For example, is it nonsense, or is it just wrong, or does it give a possibly correct theorem but with inadequate or erroneous proof?  You can save potential readers of the paper a lot of trouble by making the situation clear.

Someone once published a paper whose main theorem was the negation of one of my (earlier) theorems.  I was very pleased when a reviewer (Peter Johnstone, if I remember correctly) didn't just summarize that paper but pointed out the error(s) very emphatically.  I can't find the review now, but I believe it contained the phrase "howlers of which an undergraduate should be ashamed".

Your job as a reviewer is primarily to give a summary of the results to help other researchers find the papers they are interested in; you are not expected to evaluate the quality of the manuscript. However, there's the following passage in the Guide to reviewers:

Evaluative reviews. Your review may include a positive or negative
  evaluation of the item. Critical remarks should be objective, precise,
  documented and expressed in good taste. Vague criticism offends
  authors and fails to enlighten the reader. If you conclude that the
  item duplicates earlier work, you must cite specific references. If
  you believe there is in error in the item, please describe it
  precisely in your review and provide evidence validating your claim
  (e.g., a counterexample, an exact reference which supports your
  assertion, or an indication where the error arises in the paper). You
  should bear in mind that the MR Database does not include author
  responses to critical reviews.

This means that a critical review, as opposed to a summary, will likely be more work than you seem to think the manuscript is worth. In this case, there's the "nuclear option":

Two other treatments of items are possible, but should be used sparingly. You may recommend that the item be listed without a published review, or you may recommend that the author's summary be used as the review. If you decide to recommend one of these options, simply put your request in the Review text box (e.g., "Publish without a review", or "Use the summary as my review"). However, in most cases, the mathematics community would prefer an insightful review to either of these two treatments.

If you choose "Publish without review", the paper will be listed as "This item will not be reviewed". For a regular paper, any seasoned user of MathSciNet will understand this as "do not bother to read".
EDIT: This used to be the case; now there's no such remark anymore, but the icon next to the MR number will say "Indexed" instead of "Reviewed" -- less strong of a signal, but a signal nonetheless (especially to people who remember the old remark.)


text:
Is it advisable to hand in a thesis by visiting my supervisor's house?
I have to hand in the thesis to my supervisor, but I could neither find him in the faculty nor contact him, but I know his house.
Is it advisable to hand in a thesis by visiting my supervisor's house?

Did you consider leaving it in a pidgin hole for your professor? Or with his/her secretary?

I think this is a personal, rather than academic question.  If this person has actually been supervising you, by now you should have some sense of their attitudes towards privacy.  If in doubt, I would say no.  If it were my personal advisor, I would say yes.

My answer is no, not only because of his privacy; but because of the fact that he is your adviser not your neighbor to meet him in home. Further more, he should feel responsible for his student and if he is on a long leave; he should previously inform his students. My advice to you is to call him or send him text message, or email and try to contact him by the university office; if you don't find him, leave a message in his office and give your thesis to his secretary. Every connection should be made inside the university. If you don't succeed these ways, you did your work. Don't be upset.

The pink elephant in the room — why is the OP having to "hunt" their advisor down to hand off a thesis?

Because he refused to give his supervisees his contact information. And such questions exist because some members view questions from a Western-perspective.

@HifaMo: most users have a Western perspective. My observation has been that on this site you will mainly get answers specific to US academic culture, unless you ask otherwise, with a few from Europe thrown in for variety. If you want answers specific to the academic culture anywhere other than the US, then you at least have to give a clue where that is :-) Although I'd guess that in any culture, if someone won't give you his phone number it's probably not because he wants you to come to his house instead. I may be wrong.

@Jessop: My idea is that if one has no means of contacting a person, they are compelled to seek his house.

"Because he refused to give his supervisees his contact information."  Are you saying that your supervisor does not have an email account that you have previously used to contact him?  If the answer is really no, then please add more identifying information, including geographic information.  In all academic departments I am familiar with, faculty are required to have an active email account through which they receive important (and unimportant) information regularly.  If the advisor is not answering his emails or says "Don't contact me via email" you need to let us know about that.

@Clark: That's exactly what I meant. The professor said to us, his supervisees, "You don't need my email; I prefer that you hand me hard copies." Upon asking for his phone number, he said, "Why do you need it," meaning do not insist. Patriotism prevents me from mentioning the geographic location, sorry. Maybe, because we are undergraduates.

@HifaMo: You should edit that information into your question.  In all the academic contexts I'm familiar with, not giving any email address to your students would be rather unreasonable behavior. "Patriotism prevents me from mentioning the geographic location, sorry." I don't understand what you could mean by this.

If you do not provide information critical to the answer to your question then (i) I myself am not so interested in answering it; others will be, but (ii) if you leave out key information, the answers that you get may or may not be applicable in a way that could be hard for you to evaluate.  In order for you to confidently judge the applicability of the answers, you would have to have a good understanding both local and global academic culture...which seems to be more knowledge than would be necessary for you to know what to do in your particular situation.

To follow up on Pete Clark's comment: In the academic contexts I'm familiar with, the university and department publishes email addresses of all faculty, and the university uses that email address for all but the absolutely most formal communication.  Even Don Knuth has an administrative email address.

@SteveJessop: "if someone won't give you his phone number it's probably not because he wants you to come to his house instead" - I see a significant difference between "coming to someone's house" (implying entering, or at least talking at the door; certainly privacy-related) and sending a letter (not that different from a phone call, rather less direct).

@O.R.Mapper: maybe that's what the questioner means, although given how shifty this supervisor seems to be, getting a receipt might be in order ;-) Anyway if you are just going to put it in the mailbox of the house then I'd expect an academic to have a mailing address at the faculty that would do as well.

@PeteL.Clark: "patriotism". I've encountered something like this before on Workplace. Occasionally people don't want to state their country because they don't want a bunch of foreigners concluding or saying, "the standard practice in your country is appalling". Of course in this case it means that the questioner can't get an opinion on whether this even is standard practice, and there's a standard response to it, or if this supervisor has gone off the rails and the response is to go up the hierarchy.

Going to his house without prior notice (agreeing some specific time to meet by email or phone) is too close to harassment, from my perspective. Besides, I guess he is not at his house at all times, e.g. my "supervisor" is out this week (with all family -nobody in the house) due to vacations, going to his house would be a waste of time, greater or lesser depending on my patience waiting at his door. Meetings should be agreed before at least for this reason.

"Why do you need it," "I need it because I need it to arrange a appointment time with you Prof, you certainly don't want me crashing into your house without prior notice, I presume?"

Most of the professors in my university have regular office hours, where they set aside the time to be in their office for any students that have any queries. This is usually published in the university website or the professors would tell it to the class at the beginning of the semester.

@HifaMo: Does your professor has a secretary? Even if you definitely want to hand over your thesis in person,  you can ask the secretary to arrange an appointment in the professor's office.

I have to say that this appears to be a rather strange university if the only means of contacting your supervisor is to go to their office (not even having a departmental administration office).  One wonders how such a university would deal with a formal complaint from a student about poor or inadequate supervision!  Or for that matter, with a student claiming to have submitted a thesis that was later lost.  IMHO, the fact that your supervisor has discouraged you from contacting him in any other way, I would suggest that even posting the thesis through the letter box would be a bad idea.

Assuming that by handing in you mean the “final submission” of the thesis, I am surprised that you directly give your thesis to your supervisor and not to some examination office (which then distributes it to your supervisor and potential other reviewers). Even if this is not the default way at your university, such an office may still exist.

I find it unusual you have to hand in the thesis to your supervisor. The practise I know is to hand in the thesis with a department or university office (or even the jaintor when submitting at 23:59 on the last day), who will make an official note that and when it was submitted, so you have a proof of this fact for later reference.

I wouldn't find it okay if someone would come to my house because of that. Work and personal life should be separate and it would be inappropriate to visit the supervisor there.
Does he not have an office? If nobody can tell you where to find him, then you should call him or write an email and ask for an appointment.

The supervisor should also have a mailbox and people at the office who know how to contact the supervisor.  Leave a copy at the office as well as a message about where the copy is.  Keep a backup copy in case the supervisor wants you to drop by the house anyway, (but let them suggest it: it is less appropriate for you to offer anything other than "how shall I get it to you").

You are over-generalizing. In my institute, professors call students to their home occasionally.

@user13107: Visiting someone's home because you've been invited by them is much different than dropping in on someone's home unannounced.  The idea that it is potentially invasive to make an unannounced visit to someone's home is not particular to academia.

In my opinion, vocabulary such as "coming to my house" and "visiting someone's home" is blurring the issue. Unless the supervisor's house actually doesn't have a mailbox, we are talking about dropping something into someone's mailbox (= sending a letter) here, aren't we?

@O.R.Mapper If this is the official submission of a thesis, the timely receipt of which will decide about the student's career, it would be careless to just drop it into a mailbox, wouldn't it?

@StephanLehmke: I am not sure what is careless about leaving a document in the mailbox of someone's private home, which is about as direct as the submission can become short of ringing and handing it over in person (and actually even more direct than sending it via mail or having someone place it in the supervisor's office). That said, the OP is talking about their supervisor, who - unless specified otherwise - is not necessarily the professor grading the thesis. Likewise, the OP does not specify whether this is about the final submission of a thesis (which, depending on the place, ...

... may involve a lot more than handing over the document, namely some registration of the submission process with the database of the institution, for example), so all we know for now is that the OP wants to "informally" hand over a copy of their thesis to their supervisor, possibly for proofreading or advice or any other supervising activity related to a thesis.

@O.R.Mapper Ah, Ok. I missed that detail (non final submission). Quite confusing situation.

@StephanLehmke: To be clear, I agree if this is indeed about the timely recept of a final submission. However, at least in the institutions I am familiar with, thesis supervisors generally would not want to burden themselves with checking, and possibly formally certifying in any way, the timely receipt of any submissions, as centralized student databases are much more suitable for tasks such as keeping track of who started what on what date and who has to finish what by what date. Least of all, they would keep track in their head, or any other means readily available in their private home.

As a faculty member, I value my privacy. Home is home and work is work. Unless I suggest this myself, I would be displeased by a student coming to my house unannounced.

This is exactly right. I would be incredibly ticked off by a student showing up unannounced at my home, unless either I invited the student (unlikely) or it's an absolute emergency (which I hope is even more unlikely).

That said, we don't know how long the supervisor's uncontactability has lasted, or how hard the questioner has tried. If he really is so flakey that he isn't visiting the faculty or taking phone calls or checking email, and hasn't told colleagues where he is, for a protracted period, then the questioner is entitled to be displeased already ;-) And on a sombre note, someone should go to his house eventually, albeit not the questioner. He might be dead.

@Steve Chances are then that they won't be at home but in Aruba.

@RoboKaren: the road trip movie about a student who needs to find his unexpectedly turned-on-tuned-in-dropped-out professor to hand in an assignment before the end of spring break, practically writes itself.

I assume you will still let people in emergency enter house, even if it's unannounced.

Sure, but emergency is if someone's physical being is in risk, not if I haven't responded to their email.

I should mention that undergraduates in particular don't seem to understand "emergency." For them, emergencies seem to include band practice, death of their roommate's great aunt, and watching the world cup. :-)

Following on from a comment by the OP that this supervisor has refused to give his supervisees his personal contact details, I think it's important to say very strongly that no, in this case it is entirely inappropriate to go to the supervisor's house.
To even ask it is creepy and weird. If a student actually did this, after I'd refused to give out my personal contact details, I'd be talking to the university administration office; and, depending on their advice and whether or not this had happened before with this student, the police might get involved too. Based on previous experiences, when a student with this sort of serious boundary problem starts creating these sorts of issues, it's important to act decisively and quickly to close things down before they escalate into really serious problems.
So no, don't go round to your supervisor's house, given that they've already refused to give you their personal contact details. To do so would be creepy and weird.
Ask the department administrator how you should hand in your thesis to your supervisor: they will either take it on their behalf, or point you at a suitable location to leave it, or provide other guidance.

Questioner specifically states they don't have the supervisor's email address. I think the supervisor is weird, and possibly negligent of their teaching duties. So I certainly agree with going to department administration, the supervisor is causing students problems, and the department might want to put a stop to it.

I have myself handed in a thesis by visiting a professor's house. But I had contacted him beforehand.
You need to answer -

Is it really urgent to hand in thesis now?

If the answer is no, don't bother with going to house.

Give it to the department secretary and ask them to time-stamp the cover. Now it's no longer your responsibility.

As mentioned previously in comments, this answer really depends on the culture of where in the world you are. Within my country, South Africa, I am positive that none of my professors would mind in the slightest if I tracked him down at his home for any query at all. I'd say he would invite me in for coffee while we discussed the issue at hand.
Of course there are exceptions to any rule. There are probably some professors in my institution that would indeed take offence. It could also depend to some small degree on the professor's specific attitude towards the student in question.
I'm talking about an environment where the amount of students any single professor would supervise is small enough that he would know each student personally at least to some degree.
To recap, in my institution I would and have tracked professors down at their homes if I have any queries, even if the reason is not considered particularly urgent.

As another South African, I can say that if I had showed up an my supervisor's house she would not have been happy to see me. However, she always made it clear how to get hold of her -- when she would be in her office, which days she didn't check email, etc. -- and would respond to emails or notes left in her pigeon hole promptly.

How do you know your advisor is at home? What if he is on vacation? What if he is out of country?
The purpose to hand in your thesis is to let him read it and review it? right? If he is not home, how do you know he will get your thesis and read/review it?
You need to find his whereabout first. Then contact him and ask him how and where to deliver your thesis. If he tells you to hand in the thesis to his house, do so. If he wants to get it at his office, do so. It's your responsibility to make sure he gets the thesis and read it.


text:
Must I reference resources for definitions I express with my own words?
I am writing a master thesis. When must I cite a resource I used ? Most of the time, I read a definition in a given book and express it in my own words: must I mention the book in question for this particular case ?

Definition of what? Give us an example that concerns you. If it's an extremely well-known concept like the definition of a derivative in mathematics, unless that definition is core to your work, it can probably go uncited. However, if it's a relatively unknown concept, you probably need to cite a source for the definition.

@BillBarth for example the definition of drive-by download attack (in computer science). You can know it only if you are in the field of security. But it is not a strange notion for people who are in this field.

That's probably worth citing. I don't think that's in common enough parlance across a wide range of even CS disciplines to not need a citation.

@BillBarth Ok, thank you very much for your 2 answers.

Related question: http://academia.stackexchange.com/questions/14427/citation-to-well-known-results-and-reference-to-user-manuals

When referencing a definition, you are not only providing the reader a place where he can check that you did not made a typo in writing the definition, but a place where you can have obtain some background on the topic. Also, in some fields, with a definition comes a corpus of theories.

If you recall a definition which may be unknown to your users, it is always a good idea to refer to a book/article from which the notion originates. Do this even (actually, especially) if you choose to rephrase the definition in your own words. Remember, references are important to navigate your readers and put your work in a context. Definitions are no exception.

This requires judgment. You do not generally need to cite things which are considered common or general knowledge.
Example 1: If you are mentioning Brownian motion that you observed in particles on a petri dish, you might not have to cite  Brown's original 1828 paper, but if you are discussing the motion of black holes due to macro scale Brownian forces you might want to cite the relevant recent literature.
Example 2: In the social sciences, there are various lineages of even basic concepts such as "resistance." In these cases, it's good to note which intellectual thread you're following.
TL;DR: If you are writing your thesis, you generally want to err on the side of having too many citations rather than too few. It prevents faculty from scribbling "where the hell did you get this from" in the margins.


text:
Writing a thesis: Is it a good practice to use personalized lists?
I am writing a master's thesis using Latex. I am attracted by pifont package that allows to use personalized lists as the ones this picture shows:
My question: is it a good or bad practice to use such symbols as personalized lists ?

Are you considering using planes, hearts or religious symbols? ;)

@PiotrMigdal No, I want just those different arrows, hand shapes and check symbols.

Related: Is use of unconventional design elements or layout something frowned upon in academic context?

The advantage of using a simple round bullet is that it's such a familiar device that people don't notice the symbol itself. The brain recognises that it's a list structure, and immediately starts reading the items.
If, on the other hand, you use a less-common symbol, the reader will notice it, and possibly be distracted by your icon choice. That's not what you want.
There are some cases where it could be useful to distinguish the items on the list in some way. For example, you might have a list of features, and use checkmarks and Xs to indicate which are supported. But even then, I would use better icons. Most of the ones you've shown look ugly and old-fashioned, in my opinion.