text:
My supervisor accidentally forwarded some private e-mail communication to me. What to do?
My supervisor has wrote to another cooperating professor regarding our project and had put me in the loop (CC). But I believe he has made a mistake and had also forwarded some of their previous private important chats and communications. I am afraid if he was willing to share those information with me. Even if part of those are relevant, but one may consider this as sensitive information of these big guys. Is that my responsibility to write back to him and inform him about this? Most of times the sender will notice such a fault, at least after sending the letter, but what etiquette say about this? I cannot say "you have wrongly put me as a receiver," because he had told me "I will put you in the loop," but this was just for the last email, not for their previous communications.

How is this topic specific to academics? It seems more appropriate for the The Workplace, where there are similar questions

I would just let it go and forget you ever saw the other e-mails.  Cut the e-mails that are not meant for you out of future responses and move on.  It's his mistake and he can realize it, or not.

@RichardErickson I believe this question is relevant as the e-mail content  includes information about a project in academia so it is important to know what are the etiquette in this case. Furthermore, I am not sure if I can treat my coworker and my supervisor in the same way.

@Osh - This scenario occurs in all the time, no matter what field you're in. Unless there's something specific to academia that you haven't yet shared, this isn't really on-topic here.

It is professional to let the person know that an email was misdirected, .  - and include your steps (i.e., "I've deleted the email, and will treat the information as confidential, since I assume I was not the intended recipient" and not refer to it again).  If I were a 'student' or relatively junior and it was an advisor, I would likely rather talk to advisor in person, simply so that the advisor can see I'm serious about it. Otherwise, I'd simply contact sender via email (deleting the 'private' text-matter out of the reply email) and definitely be careful not to 'reply-all'!

If it seems likely that your supervisor will accidentally send you more messages that aren't intended for you, then I think you should inform him (the wording suggested in Carol's comment looks good to me).  If, on the other hand, this seems to have been a one-time error, then I don't think you need to do anything except delete the message.

I'm voting to close this question as off-topic because it is not specific to academia.

The most important advice I can give you in relation to this incident is that you should be very careful what you send your advisor, who sounds slightly ditzy, via email, since it could end up getting forwarded to someone else without your permission (or knowledge!).

This happened to me on two occasions, one of which would have been personally and professionally embarrassing to my advisor, or worse.
I had a pretty good relationship with him, and it was very clear the content wasn't meant for me, so perhaps my situation was slightly different, but I said something to the effect of:
'Woah, looks like the horse left the barn on this one. Glad it was just to me!'
In doing this, I admit I understand the embarrassing/sensitive material, but make clear that I appreciate it was a mistake, and also give him piece of mind that I am a safe confidant that can keep something to himself.


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Is it possible to publish 3 papers within 2 years to get PhD?
It has been 4 months since I started my PhD study for two years. My advisor said that to get my PhD I have to publish 3 papers. Is it possible to publish 3 papers within 2 years doing research on insects?

It is possible, at my university there is a legal option on this aspect-you can graduate early. However, I don't know anyone who finished PhD is less than normal time, my peers publish 2 papers per year since the first year at PhD(they have worked also at master within the research topic, so they have a background of 1 year in the research direction before going to PhD).

One data point: I know of a guy who did it in 2.5 years. He was widely considered as very good as well as lucky. 2 years is really pushing it.

Another aspect: Is it wise to rush it? Certain things take time/maturity...

"It has been 4 months since I start PhD study for two years." Huh? Do you mean (1) "I have been in my PhD program for two years and four months" or (2) "I started my PhD study 4 months ago. My PhD program has a length of 2 years"? If you mean the second one, I would say the problem is the unreasonable expectation for anyone to do a PhD in 2 years.

Your advisor wants to push you to quickly publish paper. Getting PhD does not only depend on publications, rather strongly depends on others like your progress, deep understanding of particular topic, also official processing of your dissertation.

The question in its present form currently does not say what your field is. The 'possibility' of publishing X many papers in a given timeframe depends very much on what field you are in. (Even the definition of what a 'paper' entails can vary depending on the field.)
I can't answer your question directly based on the information you currently provide, but I can suggest this: Go online and look up some people in your field. Most academics publish a list of their publications and their CV. You can find out when they did their PhD, and see what they published during those years. You will shortly see some trends.

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How to change PHD sponsored by Marie Skłodowska-Curie Fellowship
I come from an EU country, and I am doing a PHD funded by a Marie Skłodowska-Curie Innovative Training Network (ITN).
The problem is that, after almost a year spent here, I realize that I do not like my subject, nor the professors. I would like to continue my PhD studies, but I need to make a change (professor, subject, maybe country).
I don't know if it is possible to make such a change, while maintaining the Marie Skłodowska-Curie fellowship.
It is hard to find an answer because I prefer not to talk about this with my professors. Also, I asked a Marie Skłodowska-Curie project secretary, and she only told me that I can quit the PhD any time without any financial consequences for me.
I prefer not to give details about subject, the university, or the names of my professors. Still, feel free to ask me if you need more details and I hope I could make my question clearer thanks to your feedback!
Thank you all!

I don't know how it really works, but as far as I understand, the process for Marie Curie Fellowship is the same. Could you, please, offer the link for ERC? I would like to give it a try.

By ERC you mean the following one?  https://www.erc.edu/

When the secretary told you there would not be financial consequences for you they probably mean that you won't have to pay back the fellowship if you quit before completing your PhD.

I am a current MSCA ESR myself. I can tell you this for sure: if you quit working with your professor, you will lose your fellowship/salary. Think of it as quitting your job. You will not owe anything to anyone, but you will for sure not be able to take the fellowship with you somewhere else.
If you have an unproductive relationship with your professor but the fellowship is important for you, you could consider getting advice, collaboration, or even co-supervision from another professor at your school. Be careful though, because your current professor may be sensitive about this.

Since you consider changing supervisors, subject and the place where PhD is carried out, it looks to me that you in fact consider quitting your current PhD and start a new one. You need to check your offer and contract which you signed when you accepted the PhD, but it is very unlikely that you can take this funding with you.
Seeing that you're having difficulties locating the ERC website, it is clear that you were not yourself applying for the funding. I suspect that the University where you are studying applied for ITN and you have got a place in this network. This is technically not your funding, hence you most likely can not take it with you.

The biggest problem is represented by my supervisors. And I am afraid that, because of them, I don't believe in this project any more. The application for fellowship wasn't done by me. I was accepted by my supervisors for this position. So, yes, ITN is my situation.

How much freedom does ITN offer to me? Do I have to pay anything back and in which conditions?

@Newbie You don't have to pay anything back, a MSCA ITN fellowship is one of the best in the world. Actually you don't even have to do a PhD, its more of a research position. The only problem for your professors is that they will have to find someone else to finish the project, but that is their problem, not yours. You can also move into a different topic as long as they agree.

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What level would an assistant professor be hired at, if applying to associate professor position at another institution?
If a tenure-track Assistant Professor who will be coming up for tenure shortly (5th year) applies for a tenure-track Associate Professor position at another institution, and the other institution is interested in making the hire, what is the relative likelihood of the following scenarios:

hired as tenure-track Assistant Professor with shortened tenure clock
hired as tenure-track Associate Professor without tenure, with tenure decision in a few years
hired as tenure-track Associate Professor with tenure

(assuming the candidate's record is tenure-worthy at either institution).

Based on what I've heard and seen, most schools fall into the second pattern, with the first and third happening much less frequently. However, I've known all three possibilities to occur. Ultimately, there is no "most likely" or "least likely" option, as it really depends on the rules for tenure promotions at the individual school at which the applicant is being hired.

I think it also depends pretty strongly on the record of the applicant. A very strong candidate might be offered tenure to entice them away from their current institution.


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Should I give authorship to a senior person whose main role was to connect me to other people?
My former postdoc mentor wants to be an author on a paper I wrote with some other people. Her role was to connect me with the other people (she knew them, and they had access to a specific patient population I needed). Also, my mentor and I talked about some related ideas years back, but never the specific experiment that the paper is about. She thinks the experiment was her idea, but she is mistaken about this: when I first told her about it, it was already completely designed, she gave no input.
Agree to the request?
Pros:

She will support my career more (promote me to other colleagues) if I do what she wants.
If I leave her off the paper, she will probably go around telling people it was her idea and that I'm some kind of jerk. And they might believe her... she is senior and well respected in the field.

Cons:

It detracts from my record in the sense of making the paper look less independent than it actually is (a fairly minor concern as my tenure application is already under review).
It detracts from the contributions of the other authors who actually worked on the study (also a minor concern because it only detracts slightly for there to be 6 authors instead of 5).
She did not make a scientific contribution to the study, so it is unfair (this is maybe the real sticking point).

I'm not suggesting it's unreasonable to ask for your specific situation, but make sure you've browsed the answers already on the site.  There have been too many questions related to this topic to count, and some of them might have relevant info for you too.

Thanks, I did browse the other answers. But the specifics vary so much case by case, I'm interested in what people think about this specific situation.

It is more typical for me to weigh in on the side of not putting senior people's names on papers when their contributions were borderline or less.  However in this case it seems to me that it probably would be a good idea to include your former postdoctoral mentor as an author.

Her role was to connect me with the other people (she knew them, and they had access to a specific patient population I needed).

That is a contribution.  It sounds like it is not an intellectual contribution, but in signing up with a mentor you probably were hoping to get increased access from her connections...and you did.

Also, my mentor and I talked about some related ideas years back, but never the specific experiment that the paper is about.

That does sound like an intellectual contribution.  You didn't talk about the specific experiment, but that doesn't mean that your discussion didn't contribute to the design of the specific experiment.  In my opinion high-level general discussions can be at least as valuable as specific implementations...especially when they lead to specific implementations.

She thinks the experiment was her idea, but she is mistaken about this: when I first told her about it, it was already completely designed, she gave no input.

Well, you are giving your side of this, and you are aware that her side is different.  Do you have records that would support your version of events?  If so, I would certainly discuss them with your mentor before deciding not to include her on the paper.  If not: if the only thing you have to rely on is your own memory of events, then even if we grant that you and not she are remembering correctly, you still may want or need to act in a way that an external observer would regard as correct.
In terms of your pros and cons: as you mention, keeping a good relationship with your former mentor is a real pro.  You seem to be able to put yourself in her shoes well enough to understand why she would feel slighted and react badly, so in my opinion you need to not let that happen, either by including her as a coauthor or by resolving the different perspectives you have on the situation.
Your cons are not very persuasive to me.  As you say, the paper already has five authors.  I don't know about you, but with that many authors I am going to assume that some have rather minor contributions unless I am specifically told otherwise.  I don't understand how adding a sixth author undermines the independence of your contribution (presumably you will be first author).  You mention that your mentor made no scientific contribution, but that's not clear to me since, as above, you mentioned earlier conversations on the general topic that led to your specific experiment.  I also think that people should not be added as authors for no intellectual contribution...but this is not a very clear case for this kind of principled stand.

I like your answer and agree with your conclusion. I especially like your n+1 argument for co-authorship.

Thanks for your answer. I was leaning towards not including her, but based on your arguments, I am going to include her. I'm not super happy about it, but I think it's the best decision. Thank you for being willing to assume my side of the story for the sake of answering the question. Yes, there is a paper trail as to the origin of the experiment, it's all in email. I could show it to her, but she's not the kind of person who that would make much of an impact on... Anyway, thank you.


text:
What position should a young researcher moving to a UK university apply for?
Having obtained by PhD in Computer Science five years ago, I have been working in R&D projects for the last years. I want to pursue an academic career and I am currently considering moving to UK. As far as it concerns my academic qualifications, very roughly, I have 8 journal publications, an h-index of 8 by google scholar, and a little teaching experience in university education.
The variety of titles in UK job openings is somewhat confusing: (Postdoctoral) Research Associate, (Senior) Lecturer, Research Fellow, etc. And then, there are open-ended and fixed-term contracts.
The question is: what kind of positions would it be best to aim for? In other words, what kind of position would correspond to my skill-set, given that I am interested in evolving academically (research and teaching)? And how could I improve my CV towards this?

Can you tell us a little about your citizenship, or if you have a right to work in the UK.

I don't think it is feasible to make a sure-fire estimation of what "level" you would be considered to be on without knowing many details (and then the question would likely become too localized for SE anyway).
Further, job titles and positions are not standardized between universities or, in some cases, even between different labs within the same university. What's called a Research Fellow in one place could be a Research Associate in another, and simply a Postdoc in the third. However, there are (typically) some "groups" of jobs:

PhD students (which you clearly don't fall into, given that you already have a PhD)
Non-professoral, non-student researchers (postdocs, various soft-money research positions)
Junior Professors and Professors (I'll lump into this everything from lecturers, senior lecturers, and actual professors)

You will likely fall into the second group, maybe you could also hunt for a lecturer position (i.e., the entry-level position of the third group). If you want to stay in research, you should aim to sooner or later get into the third group. However, typically, these jobs are significantly more competitive to get than postdoc jobs.

And how could I improve my CV towards this?

Papers, papers, papers. I think your background in an R&D lab can be sold as a boon ("I have industrial experience, while still not being out of touch with research!"), but at the end of the day, papers are what people really look at.

I'd also add that since this is a question, the papers people are especially interested in are REFable papers -- typically your best 4.

The job you appear to be interested in is lecturer, open ended contract, probably at level 7 (I would guess from your description). You may want to consider the fixed-term contracts as well. Applying to anything above level 8 will be pointless. However, I'd advise applying to pretty much everything at the lower end of things, as the job market in most fields isn't great right now. A postdoc/research assistant position will probably be helpful if that's what you are offered. Hiring in the UK is cyclical, so what's on offer will vary greatly between years.
Source: personal experience

I've now realised this question is old (I can't remember how I reached it), but hopefully the answer will be useful to others).

As far as I see you potentially fit the Lecturer (i.e., Assistant Professor in the US system) level.
This is because you have a PhD, and you are too long after your graduation to become a postdoc (i.e., research fellow/associate).


text:
How familiar should you be with a topic before assigning it as a thesis to an undergraduate?
I am a postdoctoral researcher in a university where undergraduates have to undertake a diploma thesis in order to finish their studies. My professor says we should put in our lab page some short descriptions of 2-3 topics and let interested undergraduates come to us, as it usually happens.
Now, I am expanding my horizons to promising technologies, following the buzz in my domain, and I am confident I will have some personal progress in the following weeks but at the time being I am still relatively a newcomer to these latest technologies.
The question is: should I put out there a diploma thesis description in these new fields, or should I be conservative and go for the things I know pretty deeply? How do you usually come up with diploma thesis topics?

Great question! I edited the title to mention that it's an undergraduate thesis, since I think expectations regarding mentor's familiarity with the topic are different for undergrads vs masters vs doctoral students.

This does not seem to apply to your case (as you intend to explore the new technology yourself anyway), but exploring the possibility of applying a new technology or concept (that nobody in the workgroup is familiar with) to a workgroup’s main subjects may actually be a good topic for such a thesis.

Here is one rule of thumb: You should be sufficiently confident with the topic to be able to guide your student to success.
This means in particular that you should know the topic in which the student is supposed to work in well enough such that:

You are certain that the workload is manageable in the time outlined by the examination regulations.
You know that there is enough low hanging fruit in the topic such that it is clear that even a mediocre student should be able to write a thesis that is good enough for the standards of your field and school.
There are some types of results that a student may obtain during the thesis work that would suffice for the student to write a great thesis, possibly leading to a subsequent publication (given interest by the student).
You think that you can advise the student with the problems that you expect to occur in the scope of the project.
You have sufficient time to actually advise the student and in particular have the time to read into the details of the subject in case the student needs some guidance on them.

Depending on the field, it is debatable whether it is OK to hand out topics of which the advisor has comparably little knowledge, given that all requirements from the list above are fulfilled.
Also, the list above focuses on the minimum requirements. Again, it is debatable whether satisfying all points on the list is enough already (unless I forgot something important).
As far as coming up with new thesis topics is concerned: probably everyone has their own approach for this. One way is to collect the ideas that you have in your own research into idea lists, and after some time filtering them by the criteria above.

You had me cracking at "enough low hanging fruit". It all depends on the Fox's legs length.

@Mindwin That point is actually central. I feel many people can define projects that great students build great theses on. Good advisors are able to also lead mediocre students to reasonable success - and a large part of this is defining a topic that they have a reasonable chance of actually finishing.

So a good advisor has good skills at measuring kits (double meaning intended).


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I want to pursue studying in Social Science. What to do in summers?
I am currently a second-year computer-science student. However, I am interested in pursuing social science after I am done with my bachelor's degree. To be more specific, I am interested in the fields of Philosophy, Anthropology, and Political Science. To be able to do that, I have started practicing and improving my writing skills. Since I do not want to continue studying CS, I will not be looking for internships or any research experience in the field.
In the summer, I want to do things that would help me getting accepted in social science. But I do not know what I can/should do. In engineering, it is pretty straightforward: It is usually an internship in a company or doing research with a prof. What are the equivalent summer positions for social science students?

1.) What area of social science? Social science is extremely broad.
2.) I feel that the link does not contribute to your question.

I corrected it. But why the downvotes?

Because the link that you had (not anymore) could make some people think you were spamming us.

Also, you still did not include your new field of choice.

How would that be spanning when I just want to show what my fields of interests are via things I like to write about? I guess this is a bad place for consultation

If you read the FAQ’s about this stack, you will understand what types of questions should, and should not, be asked.

Internships and research seem like good choices for social science, especially given your CS background. You will get better answers if you specify which type of social science.

@cag51 I edited it. What do people in these fields do internship about though? Because when I hear the word 'internship' I can only imagine working in a company.

Social science students do internships or research in the summers as well. The focus of your internship might be different, for instance if you are interested in political economy you might look for an internship in a polling company or similar.

My recommendation, if you really want to go into these areas and be standout, complete your computer science degree. There is a real shortage of individuals with strong computational and programming skills in the social sciences. You will likely have potential advisers salivating at the idea of having a doc student who is competent with R, especially so if you are a whiz at the ggplot2 package or tidyverse.
Learn to accentuate your skill set with a strong statistics background and you will be golden.
A strong letter of interest coupled with a strong GRE quant score and a skillset demonstrating competency in programming and statistics...this is an application that many social science faculty dream of having.

Thank you a lot for your insightful answer. But I am now curious, what would the degree that I am pursuing be in Masters, in this case? Or are you suggesting to directly get in contact with a professor and do phd?

@huzo Its probably reasonable to go straight into a PhD. Getting a masters in statistics would be a great asset for the future. Quite a few universities offer 5 year masters/bachelor's for statistics. Its a strong option if you wish to pursue academia. That said, it is not necessary.

In case you want to reconsider getting out of your field, there exists a "field" called complex systems (in some places), where you can combine what you know about Computer Science with social sciences, such as Economics, Anthropology and Biology.
In fact, I am an engineer who pursued a Master's degree in Applied Mathematics and I am now doing my PhD in Social Complexity, where I study social systems using ideas from anthropology.

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Discussing Related Work: Use of the phrase 'the authors'
I just got feedback on my thesis. When discussing related work, I tend to often use the phrase the authors do this and that.
For instance:

In [1] a system is described which approaches problem x by doing y. The authors perform a scalability evaluation showing that their approach outperforms z.

Obviously, my advisor does not like it when I use the authors, because he underlined each occurence.
My question hence is: How can I prevent the use of the authors in the above example?
I talked to my advisor and he said that I should just mention the authors by their names. But I think this is not feasible in my case, because I already talked several paragraphs about the specific related work paper and it would be weird to suddenly start mentioning their names in the third paragraph of discussing it.
It would look like this:

First paragraph about related work.
Second paragraph about same related work.
NameA et al. perform a scalability evaluation showing that their approach outperforms z.

EDIT:
somewhat related: Referring to previous work “by the authors”

It sounds like you have a sensible reason why you shouldn't just replace the phrase "the authors" with the names, without making any other edits.  Introducing the names abruptly would read strangely if it happens several paragraphs into the discussion, since it wouldn't be clear who these people are.
You can solve this problem by introducing the names earlier.  Instead of opening with "In [1] a system is described...", you could use "Jones and Smith [1] developed a system..." or another variant.
There are several advantages to this:

It provides more context for readers.  In particular, it's easier to recognize the names Jones and Smith than a reference like [1], so readers who have heard of this work before can catch on more quickly without having to flip to the references.
It is more generous in offering credit to the authors.  Too much use of the passive voice and phrases like "the authors" could even look like you are going out of your way to avoid naming them.  (I don't think most people would be upset about that, but it could be an issue if the authors are particularly touchy.  I've occasionally known people who were irritated by how they were cited in situations that seemed innocuous to me.)

You may have to edit a bit more to make this work, but it shouldn't require big changes.
One general principle here is that when you have to edit something in a paper, you shouldn't restrict yourself to making only local changes.  Sometimes you can't really fix it without further changes or rearrangement.

I strongly agree with the advantages.  As a reader, I find it quite inconvenient when references are just a number and no names, particularly when there are no hyperlinks.

Also, if someone just writes "the authors" in this context, I would assume it referred to the authors of the paper I am currently reading, meaning that the  cited paper has the same set of authors.


text:
Mental health problems affecting performance in coursework. Who (advisor, professors) should I talk to, and how?
I'm a U.S. student studying abroad in Canada and also an undergraduate student. I believe my question could apply to graduate students in the same situation, i.e. someone who has not had prior mental health issues and who is unaware how to move forward.
Recently, starting a little before this Fall semester, I've been struggling with most tell-tale signs of depression (no motivation, constantly sleeping, gaining weight, etc). I live with my girlfriend off-campus, and she also struggles with mental health issues. I have been struggling to find motivation to work as hard as I was in the beginning of the semester. I was originally taking a 5 course load, but had to drop one course due to not meeting the prerequisite (I was wrongly advised, but take responsibility for not confirming and sitting down with someone before registering in the course).
Of my remaining 4 courses, only one have I truly excelled in all semester (due to the fact that I have worked with with the content of the course before extensively, and it came naturally to me).
I started out well in my other 3 courses (and have also completed all labs and assignments) but have gone downhill, to the point where I am worried I could possibly fail the courses if I don't do well enough on the exams (very bad second midterm results).
I haven't spoke to anyone professionally, nor any advisor at the University about this issue. I feel like if I do not email or meet with my professors soon and explain, they won't take me seriously after the fact my grade has been posted. I wrote one exam the other day and will write the others soon.
What is the best course of action for me to take? Should I email my professors, or meet with them? Should I try to talk to an advisor first? I have read this question but I feel like I'm on a much more limited time table, and of course this is entirely my fault for not taking action sooner.  Does anyone have any suggestions on what the correct steps to take are?

"I haven't spoke to anyone professionally" - do you mean you haven't spoken to a mental health professional? If that's what you meant, why not? Depression is a serious illness, but fortunately, generally a treatable one.

Moreover, in nearly all cases, a professor is going to need to see a note from a mental health professional before making any major adjustments to your grades, deadlines, exam schedules, etc.  Professors are not qualified to judge your mental health status by themselves.  So, in addition to your own well-being (which of course must come first), seeing a professional will also be necessary from an academic standpoint.  Do that first.

At this late date (sounds like you're already midway through final exams), you may just have to do the best you can. At my school there is a process to petition the registrar/academic affairs for a retroactive withdrawal from courses for extenuating circumstances like health issues.

Your institution will likely have a support department with a name like Counseling Center.  Go there.  They can help with a referral and may be able to help directly.

I am fairly confident that your university must have some kind of psychological counseling service for students. These are professionals and also highly experienced in the specific challenges of students. Start there, today. They will be able to point to you in the right direction.
Academically, your college's undergraduate office is very likely to be able to reach out to all your professors and advise them that you have a health issue going on that would necessitate accommodations. Do this as soon as you have an appointment with counseling. They may encourage you to contact your professors for arrangements, perhaps not immediately. You shouldn't need to explain the details of your health situation to your professors--they already have the official heads-up and that is all they need to know.
Bottom line, universities deal with this frequently and have mechanisms in place to juggle with all the aspects; there is no need for you to brave the storm alone.
All the best to you.

It is called student health centers, ( I dont know if they have it in Canada) its is similar like hospitals and health care institution but only patients are students or all staff employed at university. Clinical psychologist are responsible for treating and diagnosing depression.

Step one is to get professional diagnosis of your condition. and after that to ask a consent for freezing a year (if you are diagnosed with health issues)
Rest is up to bureaucracy of your university. my advice, something that I would do, would be to take a break due to health issues, I am not sure if you have this option in Canada, but in many other countries you can freeze your academic status until you resolve your health problem.
by freezing, I mean you can keep your status as regular student, but you are not available to study since you have some difficulties or other external task (military service, student exchange, similar) to overcome.

Don't follow our advice as to what to do (year freeze or whatever): Seek help through your university channels (see my response for details) and then work out a plan for you with them.

I am not sure if student counselors are appropriate for treatment of depression @Prof.JoséF.Martínez usually, they dont have this jurisdiction

Who will ultimately help him/her manage his/her potential depression is something they can help him/her with later; he/she needs someone to step in and get things going, student counseling is the right place to start.

yes, I agree, except OP will fail a year, there is no other way than freezing a year ( in that way OP will avoid paying tuition again)


text:
Publish own work online, ethics and platform
My question is similar to this. If someone wants to publish his work in the medical field, for free but without a review process, how is this seen by the academic world? Are there any online services or platforms that provide this service? Is this usually seen as a problem by the institution in which one may work?

Look up all the referring to arxiv.org on this site - it is a major platform for this type of services. The answers to these other questions also mostly answer your question.

I see arxiv is based on non health related science, i'm editing my question, thanks for the hint

In general, academic research that isn't peer reviewed gets far less attention than research that is.  Also, for the medical field in particular, I would wonder about ethical oversight.  You generally can't publish in a peer-reviewed journal unless your research was conducted with the oversight of some sort of independent ethics board; if your work didn't have that kind of oversight, it's probably going to be impossible for anyone to make use of it.

Why do you want to publish specifically without peer review? It might help people answer your question if they understood more about what you are actually looking for.

For example: If you want to publish without peer review, you could just keep a blog and publish whatever you want on it. Does that suit your needs? If not, why not?

I was inspired by a discussion in researchgate (i can't find it now) were they talked about an hypothetic method of publication which was uncontrolled by the big literature firm. Also now the publication of a paper is very delayed in time and there's also publication bias. By publishing it in a platform you could partially avoid these problems and also get a feedback from other experts in the field which is a sort of "peer-review" to assess the validity of a study. A blog is something too much decentralized in my opinion for this kind of work. I hope my comment is clear!

how is this seen by the academic world?

Generally speaking, as inferior to a peer-reviewed paper. But the 'academic world' is made up of a lot of different people. Assuming you have conducted a high-quality study, the extent to which a reader would consider your findings valid or robust or believable really depends on how they feel about the value added by peer-review. Given the growing evidence of the inadequacy of peer-review, the academic world may increasingly see this type of publication as acceptable. But I would suggest that we are not there yet. A more important question for the context of medical research might relate to how the clinical world would see it.

Are there any online services or platforms that provide this service?

Yes. For example, PeerJ Preprints.

Is this usually seen as a problem by the institution in which one may
  work?

In terms of medical research I would say it definitely would be seen as a problem if used as an alternative (rather than a complement) to publication in a peer-reviewed journal. At an absolute minimum, your institution would probably expect your research output to be indexed by PubMed. If, however, you use the preprint route as a complement to publication in a peer-reviewed journal then it should not be seen as a problem in itself. It could become a problem if your target journal does not accept papers previously published an another form.


text:
How can a new PhD Student objectively evaluate how well they are doing?
I'm a relatively new PhD student, and I'm faced with a new (for me) situation. Before, I always had grades and the likes to tell me how good or bad I was doing: if I was at or near the top/bottom of my class, if I passed my exams or not... were all more-or-less objective indicators to tell me how I was doing.
But now that I've started to do research, I have none of that anymore, and it's quite discouraging. It's not that I need constant validation to boost my self-esteem, but rather I'm afraid that I'm not working hard enough, not learning enough... and that it's all going to crash down on me at the end ("welp, your funding has run out and you've produced nothing good enough, no PhD for you"). I sometimes find results, but they always feel rather insignificant. And the fact that I used to be good as a student whose only job was to learn about well-established topics from good professors doesn't mean I'm good enough at research, either.
I've read several Q&A's here (How should I deal with discouragement as a graduate student?, “I've somehow convinced everyone that I'm actually good at this” - how to effectively deal with Imposter Syndrome) and they've been helpful, but simply telling myself that maybe it's just the impostor syndrome talking isn't helpful – maybe I'm really an impostor, too...
Of couse I can ask my advisor from time to time, but if I start asking every month I don't think he's going to appreciate it, and if I ask that bluntly he may not want to hurt my feelings and tell me the truth. So how do I, a PhD student, can evaluate how well I'm doing?

If you are genuinely looking for objective criteria, then submissions such as posters, conferences, papers etc. can be long-term targets. Grades are usually obtained on a semester-wise basis, but you might not be able to have publications every semester (of course, that depends on your field). I would think that having short-term targets such as "finish X this week", "make setup for Y by month end" should help quantify your work.

If you are an experimentalist, than there should be some plan for what experiments to do, what you expect to see, and if things are actually getting done. Note that seeing something unexpected (and not bogus) is kind of the exciting part. But, measurements get done, data gets analyzed, slides updated, there is something to talk with your adviser and colleagues about. If more theoretical, well, there is a reason I didn't go in to theory...

Number of papers written + number of years left. Larger number is better.

The reality is that it’s impossible to evaluate how you’re doing in an entirely objective manner once you progress beyond the stage of doing problem sheets with well-defined answers. Once there’s no objective right and wrong, it becomes a question of what is valued and who assesses it. For example, people try to assess PhD students in terms of all kinds of things:

How many papers they’ve published.
Where their papers are published.
How many people have cited their papers.
How much impact they’ve had on their field.
How often they’re invited to give talks.
Where they’ve worked.
How successful their collaborations have been.
If they teach, how successful their own students are.

The reality is that all of these things measure something, to some extent. Different people will value different things, and assess them in different ways.
If you want to go into academia ultimately, and you’re asking because you want to know what the people who will assess you for academic jobs will value, a good place to look is at academic job specifications - they’re often very detailed and make it quite clear what they’re looking for. You can also ask your supervisor, who will probably be able to give you a good idea of what’s involved.
If you want to go into industry, they may be looking for very different things - again, you can find out by looking at the job specifications, and the skills of the people who work at the relevant places.
Ultimately, this is a good point in your life to realise that now you’ve moved beyond standard taught courses, you’ll never again have the same kind of “objective” outside feedback that you once did. Thus far, you’ve been optimising towards someone else’s objective function; from now on, you have to find your own. Other people can tell you what they value, or even what they think you should value, but no one can decide what you value but you.

+1. It's really a short-term/long-term process. First, decide what you want to have done in, say, one year. (Get your supervisor's input on that.) Then set up a plan how you actually want to reach that goal, with SMART weekly action steps, as per @varun's suggestion. Finally, track whether you are meeting your weekly goals. Adapt if you feel over- or underwhelmed.

As PhD student, your supervisor is the key. He is probably the person that will have a higher stake at your final evaluation as a PhD candidate, both scientifically and bureaucratically. Therefore, he is the key person to talk to.

Of couse I can ask my advisor from time to time, but if I start asking every month I don't think he's going to appreciate it

Of course, but that does not mean that you cannot evaluate how he reacts to your meetings. As scientist (and any other carrear path), you are expected to understand what other people think of your work. This starts during PhD and will continue to happen on your career.
It is also by his judgment, and the judgment of your peers, that you will start to be able to auto-evaluate your performance. And again, this is also expected from you at a later stages of both scientific and non-scientific careers.

and if I ask that bluntly he may not want to hurt my feelings and tell me the truth. So how do I, a PhD student, can evaluate how well I'm doing?

If you suspect that he is not telling you the truth, then you have to fix that. Either on your side (e.g. he doesn't feel you can take the truth), or on his side (he is not able to tell you the truth),
having this fixed is something that both will profit from.
Disclaimer: I am a PhD student and this is purely knowledge that I gathered as a PhD student.

+1 for If you suspect that he is not telling you the truth, then you have to fix that.

Only as a partial answer: most grad students (in mathematics, in the U.S., my experience...) do not fully appreciate that their very admission is a strong vote of confidence from the admitting department. Further, although it would be wonderful if for any given person everything "clicked" and they were incredibly lucky and did something super-amazing ... this would be a ridiculous standard. Even at the most elite places, for all but a tiny fraction, a PhD is an apprentice-ship. What is a successful apprentice? Well, rarely glamorous, ...
Bottom line is that if you stay engaged, and still care about your studies/work, you are almost surely "successful". Successful enough... because now it would be non-sensical to think about "beating" other grad students, both because the notion is far too vague, and because the population of grad students in a reasonable program is heterogeneous in many senses that make comparisons unreasonable. Not to mention that as one is selected into ever-more-elite groups, "being the best" or even "being in the top half" (if that had a sense) becomes ever less likely (and/but, mercifully, ever less meaningful).
So, again, if you are staying engaged and working, you are doing fine. Period. Yes, your advisor should be able to confirm that. Yes, you may disturb your advisor by asking once-a-month... but that's probably ok. Your advisor may not have the insight/communication-skills to respond appropriately, which raises the possibility of misunderstanding... thereby upsetting you...
That is, once people have managed to get into graduate programs in the first place, they have adequate talent/capacity to finish PhD's, if they care and work hard. For most people, "lifetime accomplishment" is very hard to predict at the grad-school stage, yet that is what we should care about. Often, the most "obedient" apprentices give a good impression, but will not have the energy or imagination to do much on their own. Meanwhile, apprentices who had some difficulty making themselves "stay with the program" eventually make very valuable and original contributions.
(Paper-count, grades, all that stuff, ... is pseudo-objective, sure, but only loosely correlated with real-life success, ...)
So how does this answer the question? The answer is that you're doing fine, if you are working hard and staying engaged. Any attempt at finer pseudo-objective evaluation is probably nonsense. Even having trouble with "preliminary exams" (or whatever they're called locally) results far more often from misunderstanding (and mis-communication) than from incapacity. And I'd be remiss to not remind you that the gossip/opinions of other grad students is very often not merely inaccurate, but very wildly so. Even faculty often do not directly communicate the belief system that is the true basis for action, but, rather, quote standard professional mythology.

In universities and in general in life, an external sincere evaluation is the strongest tool you can have to assess if you're doing well or not.
Many PhD programs include an yearly internal evaluation of the student's work, but sometimes it's not enough. My suggestion is to ask an informal external evaluation to someone outside your institution. He/she might be someone who knows you a little or someone you don't know in person, but he/she must be someone expert in your field.
Once you found someone who is expert in your domain and is available to informally review your work, you should write down a technical report about your activities since you started your PhD program, and then send it him/her asking to evaluate it.
If he/she's a serious person, in a couple of weeks he/she will reply to you including his/her assessment of your work, and some suggestions on which directions to take.
If you were able to find more than one informal external reviewer, that would be even better.
G-luck!

This is an interesting idea in principle, but I wonder how effective it would be in practice.  Have you had experience with people who actually do this?  I would wonder whether a random external expert is going to have the time or motivation to evaluate the work of random grad students.  I would also wonder about political considerations.  If the external person gives an opinion of the work that is much higher or lower than the advisor's, that seems likely to lead to tension between the two of them - and academic research communities are often small...

So I'd wonder whether the external person would really feel able to give an honest opinion.

I must say that I would not agree to doing such external evaluations of grad students at other institutions than my own. For one thing, the "external, objective" aspects of grad students' work (in math, my field) do not typically reflect their eventual course... The key things are intangibles, and that's why everyone has trouble "objectifying" what's going on...

To expand on Stuart's list of what different people may find interesting

What courses have they taken and how fast did they complete them? How relevant are they?
(If teaching) How good they are at teaching, grading exams and producing teaching material?
Have they had main responsibility of any particular course or lab?
Have they participated and gotten experience writing applications and documentation?
Have they gotten practice co-supervising graduate and/or undergraduate theses or (individual or group) student projects?
(How well) have they learned to make presentations / explanations of their work tailored to a particular audience?
Have they acquired practical know-how of independently working with the tools they use, and are those tools useful in other fields or industries outside of academia?
Can the results be applied to solve any problems in their own, or other fields or industries?

In my experience, it is very hard. If you do not already have self-confidence in your progress and skill development (and the fact that you ask, indicates you do not), you will need to accumulate experience to find out how to judge yourself; whether you are over-optimistic or undervaluing your work. A supervisor can help, but need not. They may think in different categories.
What you could do is, that, after accumulating a bunch of results, you ask your prof whether they can constitute a paper, e.g., for less dominant results, a conference. That externalised feedback is likely to be better and more specific than if you ask about your own progress.
Don't worry too much about impostor syndrome - it is the hallmark of conscientious students and signals that you care; it's ok to take that into account, but don't let it take over. Also, don't forget, if you compare yourself to the stars, you are not going to win - there are absolutely brilliant people out there which are able to do amazing things. So, forget them, and compare yourself to what you want to achieve and your progress in view of that, of course, with regular feedback from the scientific community, via talks, papers and the like. On the PhD level that's all that counts.

As a Ph.D it really is simple:
1) Have a plan when to graduate and communicate that expectation to your advisor
2) Figure on publishing in referred journals three times - use these as your progress milestones
3) Don't get married
4) Don't have children
5) Live in the lab/library
Notes:
In re: 1) if your advisor cannot give you a timeframe - GET OUT FAST
2) Different disciplines have different expectations. If you are publishing, you will graduate and you will have what you need to get a job.
3) & 4) Dissertations are very jealous mistresses
5) If you ain't doing the work; the work ain't getting done.
And remember most of all: You are the only one who cares if you finish. To your advisor you are cheap labor.
Ed Ph.D, PE

This is altogether a bad advise. To your advisor you are cheap labor OP never mentioned a remotely close statement leading to this.

This may be how you got your PhD, but to say this applies as a general rule for everybody is terrible advice. (Even with your disclaimer with respect to #2.)

This opinion is merely an incompetent rant, and is very bad advise, in any case.

Your research has an ultimate goal. You divide the long way to the goal to X stages. Then you complete each stage, moving from one to another. Your success can be assessed as Y/X*100% where Y is the number of successful steps.

Can you please expand a bit on how you think this might be possible in general?  There are a lot of unknowns in research.

I don't understand your question. When you get a grant you get it for some final purpose. Also, you present your research plan to the money-giver. Full-fulling the steps in the plan shows your advancement. Usually nothing goes by plan so you change it accordingly. But again you remain with the plan which you are going to complete. Also, negative results are valuable results, too.

"Usually nothing goes by plan so you change it accordingly."  And thus "3 of 7 stages" isn't very meaningful to a graduate student with little experience in how to evaluate such things.

It was meaningful for me. But researchers are different, yes.

Only low-level, automatable non-research "research" can be done so mechanically, and evaluated mechanically, I suspect.

@paul
there was time people did not believe that computer will win Garry Kasparov. But finally auto mat perfectly outwits human champion. I think you can automate your research and evaluate it not worse than computer evaluates chess position. On the other hand, I understand that researchers should convince grant-givers that it's impossible to evaluate advancements. It's very comfortable.


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What does potential PhD adviser want to see from a candidate that is applying for a second PhD/restarting a PhD?
I'm about to (not) graduate from a grad school. I've put "(not)" intentionally.
This is my situation. I started working on a project that was new to our research group. The new topic only remotely related to what has been done before in the group and by the supervisor. The project was presented as a hot topic where I can "make my name" and graduate fast.
As far as I now understand, my supervisor didn't have much experience in this field although he's been around for some time - he is not a new professor. At the time when the project was assigned to me, my supervisor was trying to bring a new faculty (who has extended experience in this field) to the department but it didn't work out - this person didn't get the position, although he did help me with the initial experimental setup and some consultations. I'm really grateful to this person for that.
The topic turned out to be pretty well developed, not much room for wandering around in hope to bang into something big. Besides that I was left completely alone to work on the topic - no relevant classes, no seminars, no advice from my supervisor, no one else in the university working in this field. I ended up making my own experimental setup, fabricating samples, running simulations, writhing data processing scripts and looking for the objective for the project completely on my own. The supervisor's approach was to find something interesting but his planning didn't go any further than that. He never showed in the lab during my PhD.
When I raised my concerns about the direction of this activity he would just either mention some irrelevant anecdotal stories or say that others working in the field have better tools but we have ideas and that's why we are better.
During our latest conversation he just said "I cannot help you with that." The funding for the project was over and I had to TA classes that are not related to my undergrad field or the current project - getting some knowledge in the subjects takes additional effort. I had to RA initially.
My work resulted in several papers (not with me as the first author) that were from side projects. I also spent one summer doing an internship at a big company. Trying to overcome the circumstances I put more and more work basically working 80 hour weeks (no weekends or holidays). But I find it extremely difficult to reach a goal when this goal has never been even discussed. My productivity went down. When I asked my supervisor about what the objectives of the project are his response was: "to find something interesting." I feel utterly unsatisfied.
I feel completely drained right now, and in a pretty bad mental state. I applied for several post-doc and industry positions without much success. I feel that I have to compete with the applicants that didn't have to reinvent the wheel every time to get something done. One rejection was due to the lack of the first author publications.
During my PhD work I steered the project towards more fundamental research. Right now I'm applying for another PhD in more fundamental field that I studied by myself. It is rather remotely related to the current PhD topic.
Defending where I'm right now is quite doable even with what I have and my current supervisor is willing to write a good recommendation letter for me. My concern is getting a second PhD and funding issues related to this. What would be the best way to approach potential PIs for the second PhD? If a professor reads this post: how does he/she perceive this situation and what he/she would want to know/get cleared before considering an applicant like me?
I'm currently in engineering and looking to continue in physics. Changing the project doesn't appear as an option to me. I raised my concerns about the current project several times and it didn't result in anything. Besides, this is my 5th year and I should graduate (or not). On top of that, the situation as a whole must be changed, I'm not happy staying here.

I think right now your post is not likely to get many high-quality answers because it looks like you're asking whether or not you should stick with your current project or not—which is something we can't really answer for you. However, your question about what faculty members are looking for when someone wants to change programs or schools is very relevant, and can probably get some good answers. You should refocus your question on that aspect (including changing the title!).

Thank you for your suggestion. I'm not very familiar with the rules of this message board, should I start the new topic or edit this one?
Starting the new research topic is too late, I'm pondering graduating this summer.

We're not a message board—but rather a Q&A forum. Go ahead and directly edit this question.

Don't want to be annoying, but it is really a long message for few informations related to your question. Would you mind suming this up a bit ?

You should continue to apply for postdoc and industry positions and not consider quitting or applying for a second PhD.  The things you've described here are not atypical for someone working on a PhD.  It is expected you will work independently and in a self-guided fashion.  As a PI, I have little sympathy for a student who runs out of RA funding and now has to TA.  Being a TA is valuable job experience that you should be proud of and having an RA position is a luxury to all graduate students that you should not play off so lightly (it is very difficult to get soft money in grant funds to support RA's in the first place).  Your description of working 80 hours per week on holidays and weekends sounds very typical of a student trying to finish their PhD (I did that for many months leading up to graduation).  Going back for a second PhD would not necessarily increase your chance of success in finding a postdoc or industry position.  It sounds like your are simply discouraged by your situation and have not searched for positions long enough.  Keep at it and stay positive.  Finish your current PhD.

I would have to disagree with some aspects of your answer. I wouldn't normalize the OP's situation. It seems to me like the supervisor didn't do their job properly. Yes, PhD students are expected to work independently, but isn't it the supervisor's job to provide them guidance and help them get unstuck? I've had a similar experience to OP during my PhD, so I know horrible it is to be stuck with a supervisor who doesn't know anything about your field but doesn't mind jeopardizing your career to "find something new."

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


text:
Is it legal to share an electronic copy of a few book chapters?
I have scanned a few chapters of a textbook (about 10%) and I want to make the electronic files available to my classmates. The reason why I scanned the chapters initially was so that I could print them out and give it to a friend, and that is what I did.
The class of 93 people has an intranet with a chat room. I could ask them to email me of they are interested in getting the files. The folder size is large, so I would need to provide a link for them to download the files off, say, Google Drive, and Google gives the option of restricting the download to a specific person if they have a Gmail account. The other option is to post a download link on the chat room that could be used by anybody. Would that be legal and/or ethical? If I do share the files individually, would it be fine to send a link to an individual email that could be used by anybody? The students have access to the book in any case, at the library.
I understand that when my classmates share an entire textbook on the chat room in this way, it is illegal and unethical. But there is a finer line being drawn here because what I want to do is not dissimilar to sharing the files with one or two people.

When you share a file with 93 people, that is very dissimilar to sharing it with one or two people.

I'd have thought sharing with 1 person is technically illegal; the difference between sharing with 1 and sharing with 93 seems like merely a difference in magnitude of the offence.

You will get better answers if you write in which country you live. According to your profile this is South Africa. Legal situation may differ vastly depending on country!

Which country are you in?

@Raphael South Africa

@DavidRicherby The first exam has passed, so only an handful of students from my class will go onto the chat room between now and the supplementary exam. If I choose to send them the folder individually by e-mail (which I think is the best option), then fewer students will actually e-mail me to request the folder (each page is a png image).

@JonathonCowley-Thom Precise laws may vary, but usually there is a distinction between a "private" and a "public" setting when it comes to copyright and distribution. For instance, you can watch a DVD with your family and friends without breaking any laws; but if you wish to play that DVD in a classroom or a bar or any other public setting, the law probably expects you to ask for an authorization (for instance, pay for a license). Sharing with one person easily falls under "private", but sharing with 93 arguably doesn't.

@Stef You're talking about the difference between setting and number of people. Playing a DVD in a bar that only has one other person in it is the same as playing it in a bar with 93 people in it.

@JonathonCowley-Thom No it's not. 1 person is 1 person, and 93 people are 93 people. Those are two different situations. What does "playing a DVD in a bar" mean? If I bring my personal laptop to a bar and put it on a table and watch a DVD with a friend, is that illegal?

@JonathonCowley-Thom What if my laptop has a large screen, so that two customers at the next table can watch over my shoulder? What if I put the laptop on top of a shelf, where every customer in the bar can watch it? You're making an argument as if the world is black and white and there are hard and clear lines drawn in the sand. That's not the case. Boundaries are fuzzy. However, what is clear is that 93 is a much higher number than 1. It's easy to argue that sharing with 1 person is private, but it's pretty hard to argue that sharing with 93 is not public.

In the U.S. the key to this question is whether or not your use is considered fair use. Here is a link that explains more. In determining whether a use is considered fair use in U.S. copyright law, there are four factors:

Character of the use - If the use is personal or educational, it's more likely to be considered fair use than if it is commercial.
Nature of the work - If the material is factual and published, it's more likely to be considered fair use than if the material is artistic and/or unpublished.
Amount of the work - If you use a small amount of the work, or in the case where your use is transformative (you're not just making a copy) if you are careful not use an amount larger than what you need to achieve your purpose, it's more likely to be considered fair use.
Effect on the market for the original - If your use would be unlikely to affect the market for sale of the original work (even if it were widespread), it's more likely to be considered fair use. Factors that help: taking steps to prevent widespread distribution of the work, if the work is out of print or otherwise difficult to purchase, if the work is not available in the format you need (e.g. digital), if you are sharing a small part of the work, if your use is transformative, etc. (Here, the fact that the students already have access via the university's library, which owns a legal copy of the work, helps your case.)

There are no hard-and-fast rules; you have to use your judgement and weigh all four factors to make a determination. This link has several examples of common copyright-related scenarios in universities.

What I want to do is not dissimilar to sharing the files with one or two people.

The scenario in which you copy a small part of a factual published work for distribution to a very limited group of people for personal educational use, who can already access a legal copy owned by the university, and you take steps to prevent more widespread distribution, seems completely fine under U.S. copyright law, although IANAL.
However, distribution to a much larger group (almost 100 people in your class) changes things, because it shifts the balance of the fourth factor away from fair use.
(Again, all four factors are relevant. If you were copying a single page to share with the entire class, or if you were copying 10% to share with one study partner, it would be more defensible - but sharing 10% of a book with the entire class is less defensible.)
As a reference: this sample campus copyright statement says that "making multiple copies of articles or book chapters for distribution to classmates... would most likely not be considered fair use."

"Who anyways have access to the work"... what about when that's not true?

@Mehrdad There are no hard-and-fast rules, only factors that count "for" or "against" fair use, and "all the recipients already have legal access" is a factor "for." Every case needs to be evaluated separately with regard to the four factors.

@ChrisWhite I'm not sure what your point is, certainly "access" is a matter of degree (your comment sounds like a reductio ad absurdum argument.) The 4th factor is if the use affects the market for the work; whether or not they already have a legal copy of the work is relevant. (A similar argument comes up very often in the context of digital music, e.g. in the question of whether a user may circumvent DRM on a piece of music, it is highly relevant whether that user already has legal access to it in another form.)

@ChrisWhite But a library can make one copy of a small part of a work. All four of the factors have to be weighed in determining "fair use."

@DavidRicherby Huh. I missed the part where the OP said "93" - for some reason I thought it was a small group, like I study group. I'll revise my answer.

@ff524 I still disagree that three chapters is a small part of the book but we're on roughly the same page, now.

"There are no hard-and-fast rules; you have to use your judgement and weigh all four factors to make a determination." In that case, you might run this by your university's legal department.  Just the fact that you've gotten an expert opinion "helps" you in borderline cases,

@SharanDuggirala: Your remark about acceptance should be directed at ahorn, the questioner, not ff524, the answerer.


text:
How to mitigate bad grade in research on PhD application?
I've just finished my fourth year (out of 5) of biology studies in one of European universities. I have some experience in research and my grades are quite ok (in US scale it would be 3.75, which means I'm in 5% of the best students in my university). This year I'm starting my master thesis and I expect it to be rather successful - I have interesting topic and good supervisor, with whom I have good contact. This year I'm also starting new studies in electrical engineering and I would love to work in biomedical engineering.
There are several PhD programmes I would like to join abroad (mainly US, UK and Germany). However, I have just got my grade for a research project from spring semester, which is really bad (C+). It is my only grade lower than B, but since it's in research (actually, it's my only grade in research), I'm afraid that it might be a big obstacle in admission process. I'm not a kind of person who blames everyone for my failures, but this time I cannot explain it in any other way than bad supervisor who didn't like me. I've learnt many methods during this project and I've done the worst job for the research group. I've also learn a lot about research in general by seeing my supervisor's mistakes. That is why I'm really happy about this experience, but it doesn't change my grade.
My question is: is there anything I can do to make this grade seem less important or to explain it to admission committee? I'm pretty sure that "Supervisor didn't like me" is not what they want to hear.

The admissions committee will still see the grade in the transcript, but the question of whether or not you should spend words in the cover letter on explaining the grade (especially if you're expecting good references from your MSc supervisor) is just as important as what you might say. If you say anything other than admitting it was your fault (even if it wasn't), it could be construed as you making excuses. This would be best answered by someone who has had experience being on an admissions committee, but why not just stay silent on the issue?

@gman There's plenty of questions here about bad undergrad / lecture course grades, but this is about bad research grades. I think there's enough distinction here to keep the question open.

@gman: This is what I call a "blemish" question about ONE bad grade. IMHO, it is quite "distinct" from the other question about a bad transcript OVERALL.

@gman: More importantly, the "subject" in question here is research, and it's widely acknowledged on this board that demonstrated research experience is perhaps the most important factor in graduate admissions.

If this project is your only experience doing research, you are right that any admissions committee is going to look at it. My advice would be to put a couple of sentences about it in your cover letter. Briefly state what the project was about, and finish with something like "I learned a lot about doing research even though the final result was a bit disappointing." That will show them that you did put actual time and thought into the project, and in the end the grade given to you by one unnamed project supervisor will count for a lot less than a good reference letter from your Masters thesis advisor.


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What is the meaning of “In Proceedings Of ...”?
I saw the phrase “In Proceedings Of ...” many times on Google Scholar. What is the meaning of that?
For example, “In Proceedings of the International Conference of ...”. Does that mean that you send this paper to that conference and they accept it?

In many cases, the paper has to be presented (oral - poster) in order to be included in the proceedings.

When it comes to conferences, if there were submitted papers, and they were published as a volume, that volume is called the proceedings.
A paper that was published in the proceedings must have been accepted by the conference.
Sometimes the proceedings are published as a standalone work, and sometimes they are published as a special issue of a journal.
It should be noted that some societies publish a journal that has "Proceedings" in the title, such as the "Proceedings of the National Academy of Sciences" or the "Proceedings of the Royal Society". These should be distinguished as standalone journals and not confused with the proceedings of a conference.

Consider this an extended comment to complement Bill's answer.

Articles published in conference proceedings have lengths that can vary from one page to several or many pages, depending on the conference. Each conference specifies the length requirements. Some conferences do not publish proceedings, but give to the participants a list of short abstracts. This is typically called the Book of abstracts.
Proceedings might be published not only by conferences but also by schools. For example the International School of Physics "Enrico Fermi" publishes a series of proceedings collecting articles and lecture notes from the school's courses.
At least one conference that I'm aware of does not call the published volume proceedings, but digest. This is the Conference on Precision Electromagnetic Measurements (CPEM). I don't know if there are other conferences which don't use the name proceedings.

"I don't know if there are other conferences which don't use the name proceedings." - There are, though unsurprisingly, their proceedings cannot be as readily recognized as conference proceedings unless you know the conference.


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Valuation of existing Systematic Literature reviews before starting a new one
I will start a systematic literature review of my research topic. Before embarking on this venture, I searched for already existing systematic reviews, mapping or survey papers but I have not found any literature review or survey that directly relates to my topic although I have found many surveys which are related to one aspect of my research area but not whole. (e.g. my topic is Methods of Y in Z. I have found existing reviews related to Methods of Y but they do not cover Z.)
I have been taking notes from these papers as I read them. Now my question is: What would be the value of these existing reviews in my literature review? Can I refer these to justify my review with the fact that they do not cover my whole research area? or refer some interesting points raised by existing reviews in my review?

Yes and yes:
"Can I refer these to justify my review with the fact that they do not cover my whole research area?" When publishing any scholarly research, it is important to demonstrate the originality of your work. If you can show that people have done work similar to yours yet not quite on topic or not as comprehensive, then it shows that you are aware of other scholars' work and that you are clear on your unique contribution to the body of related literature.
"or refer some interesting points raised by existing reviews in my review?" Since the other reviews are similar, then certainly you should summarize and quote them on aspects that do have some bearing to your own topic. After all, you probably learned something from reading them that informed your own work; you should present these parts to your readers for their learning as well.


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Does ranking of journals matter in Bioinformatics?
Does the rankings Q1, Q2, Q3, Q4, and Q5 by Scimago Journal & Country Rank matter when looking for post-doc? I am interested to know about Bioinformatics and Computational Biology.

I think this is more regional than disciplinary.

What @AnonymousPhysicist said.

It's unclear to me what you're asking about. Does "looking for a post-doc" mean you're trying to hire a postdoctoral scholar, or that you want to be hired as a postdoc? In addition, what does "matter" mean? Many people will favor publications in fancy, well-known journals during the hiring process, but it's not a great system. Are you asking whether you should try to publish in higher-ranked journals?


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Number of publications needed to get into a computer science PhD program?
I've looked at the resumes of the type of candidates that get into computer science PhD programs at the top few universities (e.g. Stanford, MIT etc.) and a lot of them seem to have multiple publications (2-4) done during their undergraduate years. Is this representative of the entire pool? Or is this just a self-selected group that puts their resumes online.
I currently have one first-author workshop paper (5 pages), and I wonder how this might affect my chances at entry into these top universities.

You don't need any publications to get into a good Ph.D. program.  Publications are often slow, and it's an unexpected bonus for an undergraduate to have publications, not a necessity.
What is a necessity is to have strong reference letters attesting to your potential for research, and one of the best ways to get those is to get involved in research.  Being involved in research, in turn, will also tend to lead to publications.  Thus, you see the correlation.  Research and research-related activities that help a person into graduate school also tend to help cause that person to end up with publications.
In short: publications aren't the key, they are simply dependent on the same root cause.

Concur with jakebeal: no publications are required. I entered the Chemical Engineering PhD program at MIT without a single citation to my name, albeit with a semester of undergraduate research experience.  That said, having publication(s) on one's CV almost certainly won't hurt one's prospects.
One of the nominal purposes of graduate school is to teach people how to do research; and, also, how to then publish it.  An educational system where applicants were expected to possess the full skill set taught therein would be rather ... poorly conceived.

It really depends on a lot of factors, such as field and nation where the PhD program takes place. In the US publications are an added bonus but not fundamental. In Europe it is very helpful to have a publication, especially when you apply to a fellowship. In Australia/New Zealand PhD position are often tied to a scholarship application, and it is very unlikely that you will get such scholarship without at least one publication, so you might get admission to the phd program but without any funding.

From my experience with the Australian system most PhD scholarships in Australia are linked to undergraduate grades. In particular, your grades in your honours or masters research year will count a lot. A publication often gives you a little boost, but it's mostly the grades.

And, from my experience in the UK, almost nobody has any publications as an undergrad so I'm not sure I agree that it's "very helpful" to have one in Europe.

@JeromyAnglim that has not been my experience with NZ and AU universities. In Biological sciences often you have 100 applicants for 1 position and publications make a difference indeed.

@user4050 I guess the difference is between the large university administered phd scholarships and single stand-alone scholarships. For example, some universities might have a hundred of more APA and university-funded PhD scholarships. I find these tend to operate to a formula that heavily weights grades. In contrast, stand-alone scholarships are much more about individual academics who have a grant and are making choices between applicants.


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How to deal with the extreme social hierarchies in research meetings?
It seems to me that academic settings have a very high degree of social hierarchy and I find it very hard to deal with it while being at the bottom of the ladder. Any tips on how to deal with it?
I attend research meetings where I am the newest student in the subject while the other grad students are all very senior students with years of background. This makes it very hard for me to get my ideas or opinions be heard given implicitly how the time is proportioned between everyone. Like if one of these senior students has something to say which could be very silly or trivial or even wrong. he would get more social space to say it than anything I would want to say. Its very uncomfortable as to how much anything they have to say gets so much attention.
I constantly have to find ways to try to severely compress anything I would want to say so that in a few seconds of window of opportunity I might get, I can get across my point. Its like a constant battle for every sliver of time and space.
How do I get myself heard!?

Some academic communities are more receptive to new voices than others. One thing to do is look for the parts of your community that are less status-conscious.

May I ask which country this is because at least in the US and the Western European countries I'm familiar with, this sounds alien? I've seen questions on this site about countries in other locations where I could see this happen - and as you run into established cultural barriers, I find myself at a loss how to suggest help. If it's in the group of countries I first mentioned, I cannot imagine obvious "errors" bring shared to a nodding audience just based on seniority...so I wonder if maybe there would be some social interaction issues you, too, might want to consider working on.

This in US. The steep preference to experienced people makes logical sense but its not clear how a newbie is supposed to get heard here.

It sounds to me as if the research meetings you're asking about are meetings of the students of one professor.  If so, does the professor also attend these meetings? If so, I'd suggest that you take your concerns to the professor.  If I were the professor supervising several students and if the whole group had meetings, then, as a matter of principle, I'd want everybody to have a fair chance to talk, but, in practice, I might get so involved with the content of the discussion that I don't even notice that the newest student isn't getting a chance to talk.

@guest How, exactly, is discussion in the group mediated or facilitated?  Who, precisely, decides how much time people get to speak, and in what order?  And who sanctions anyone who speaks out of turn or goes against the established norms?

Some more detail about the context of these meetings would be helpful. What is the purpose of this meetings? To discuss a project or projects? If so, are these joint projects that you are involved in? What are they a meeting of, exactly? The department, a particular research group?

There is no order really - its all about body language (1) to whom the prof turns to speak when airing ideas (2) who gets the prof's attention when speaking - thats where the hierarchy shows up!

@guest this sounds like a vicious cycle. You don't speak up, so unconsciously they don't expect you to talk (maybe they think you are too shy and want to be nice). The solution then is to start  speaking your mind,  trying to make sure you are heard.

I think the previous answers make some assumptions that I am uncomfortable with: they describe how academia should work, but not always how it does work, especially for people who are from disadvantaged groups.
For a basically healthy academic community, I think the advice in the other answers is pretty good about essentially how not to block oneself.
A lot of academic communities are so not healthy, however, and often in ways that are not readily visible to their privileged members.  For example, I have female colleagues who have frequently had the experience of having their ideas denigrated and dismissed for apparently rational reasons, then hearing the exact same idea readily accepted when spoken by a man.  Or there may be a power-clique and anybody who isn't "blessed" by the clique may have a much harder time being heard.
Some academic communities are also simply downright toxic and not good for anybody.  I have seen groups where any sign of weakness meant students and postdocs would start verbally attacking one another, trying to gain favor in the eyes of their professor.
I think the first thing to do, then, is to try to get some perspective on what type of academic situation this really is.  Find some more experienced friends or a faculty mentor outside of the group that you can trust and who is generally "good at people", and talk to them about your experiences---not your feelings, but the actual words that people are using.  That person can then help you figure out whether the problem is in the group or in yourself, and what the best path to take is, whether it is changing your attitude, improving your standing, or simply finding a different group.

I partially agree with blankip's answer that you must improve your attitude towards the group and the ideas expressed there. It is very important to stop seeing people within your group as competitors and instead accept them as colleagues and partially mentors (at least initially). So, ask for advice when needed (outside those meetings) and listen carefully (by temporarily shutting down your ego) to listen to their suggestions and ideas, even if you think their ideas are silly. Being a researcher is about being open minded to different ideas and alternatives and you must only disregard those ideas when you have 100% solid proof that they cannot work. Otherwise, your opinion about how silly they sound has absolutely no weight.
On the other hand, you should not be intimidated by the same group either. Although you will always learn more from listening than talking, do not be afraid to say your opinion when you have valid reasons to believe your idea will work. Even if you are shot down in flames, you will have learnt why your idea was not good and that could save you months of work. In this context, the bruising of your ego will be helpful towards your research. Moreover, in academia you must learn to grow a thick skin for rejection, otherwise you will not make it. One harsh comment on a lab meeting is nothing compared to the rejection of your first paper in which you have invested many months of work.
You must also should not care about these imaginary social hierarchies. Those senior graduate students are also in the same bottom as you in your fictitious hierarchy structure. Many of them may probably have many years doing a PHD without their PHD being any closer. At least you are at the beginning and that means that the sky is still your limit. For many of them, even if they are getting close to their PHD, their limits have been already set for them.
Also understand that in Academia having a big ego is part of the game. We all partially believe (one way or another) that our contribution will advance the human state-of-the-art and promote the boundaries of human knowledge. You must really believe in yourself to actually embrace such a concept and insisting on doing research despite of the inevitable rejections. In this sense, in Academia you will meet many people who are full of themselves. This is partially normal and expected. You do not have to be like them. But you must also not allow yourself to be intimidated by them either. After all, we are all judged by the magnitude of our research and not by our magnitude of our egos.

Like if one of these senior students has something to say which could
  be very silly or trivial or even wrong. he would get more social space
  to say it than anything I would want to say.

Have you ever thought thought that this is a group that has met for a while so they like to have a little levity to the meetings?  It is likely that most people on the team understand that the person saying the silly or trivial thing is just trying to have a little fun at the mundane meeting.

Its very uncomfortable as to how much anything they have to say gets
  so much attention.

You need to have a better attitude about your group.  You just joined and you are already making judgments about how others should act.  It is likely that this group has a dynamic that they like to have a little fun.  Even if you are 100% correct and the group just has dumb ideas... Well first maybe the group appreciates hearing ideas without being shot down.  And then secondly maybe they aren't that dumb and the ideas come with a bit of history of the project/research.  There are a lot of things I could say in a bubble that I wouldn't agree with myself but might be perfectly fine given X, Y, and Z.

I have to like constantly find ways to try to severely compress
  anything I would want to say so that in a few seconds of window of
  opportunity I might get, I can get across my point. Its like a
  constant battle for every sliver of time and space.

If you are handling it this way, chances are you are just making it worse.  If you are just providing slivers of ideas then there is a chance that the group thinks that you are scatter-brained or can't form an idea.  This could actually make others want to cut you off even more.
How do you overcome all of this?

make sure you don't have body language that senior members ideas or conversation is "dumb".  If they feel this they will want to tune you out.
when you do talk have well formed ideas and continue talking until they are understood.
have more communication with the team outside of these meetings.  To gain acceptance faster you need to share your ideas/wants outside of the meetings.  If there are a few people you are closer with, talk with them first and run things by them.  If you bring something up via email that is a good idea there is a good chance someone will give you a good amount of time to explain it further.  Note that this might not be the amount of time you wanted, but will be more.  There is also a good chance that a senior team member will take over your idea, but this is how groups work.

Your status with this group needs to be earned, that is apparent.  Incrementally showing your worth and also showing appreciation of others is key.

But given how severely time constrained the profs. seem to be, its a huge competition to get to hold their attention for a minute or more - unless I have something really good to say immediately then the prof will just tune out! Thats where it gets competitive to get the profs' time and attention. (emails are worse because they are even easier to ignore!)

@guest - It is about quality.  Make sure when you say something it is good.  Don't get offended if people "tune you out".  At the same time, don't mind repeating yourself if you think you have a good idea that was tuned out.  One of two things will happen eventually.  Your group will appreciate your idea or they will eventually tell you why it doesn't work.

Also email isn't good if you are sending one email to one professor about something and this professor is usually busy.  Either send the email to people in the group that will respond or send it to the entire group.  Even if they don't respond, if you have a good idea and they read the email, then they might be looking to give you more time.

Here are some ideas:

Bring along an ally who has some interest in the material.
I was going to say, follow up after a group meeting, with an email to all the members of the group, but I just discovered you tried that but they ignored the email.
Ideally the group should function with a talking stick.
Visit some other groups to see if it's just your group, or if it's the general climate at the institution.
When you get a turn to talk, if possible give them a little outline of what you're going to talk about.  For example: "I have two comments.  First, ... (develop this one as extensively as you like)... My second comment is (this one should be the shorter one -- in fact it can be extremely short -- it was simply designed to buy yourself some uninterrupted time)."  If you get interrupted anyway, do assert yourself.
Jot down key words and phrases of the things you'd like to talk about, 5 minutes ahead of time.  It can be nerve-racking to try to speak when you keep getting interrupted.