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How long the curse of bad education remains in academic career?
It is understandable if considering the educational record (where s/he has studied and how is his/her transcript) of an applicant applied for junior academic positions such as postdoctoral fellow or assistant professor. BUT, for senior academics, the factors for judging a potential full professor is his/her research, teaching, publications, and other academic achievements.
I read in a few job ads for full professors in Europe (mainly Scandinavia), one of the application materials is unofficial transcripts. It seems that the initial review is substantially based on the applicant education achievements two decades ago.
I wonder how much the education of an applicant affects his/her chance to be appointed as a full professor? Does a bad education (having low GPA at PhD level) always affects someone's academic career, even at highest levels?

@CharlesMorisset of course, it is not critical for postdoctoral, as it is normally hired by principal investigator rather then the institute. However, my question is about the cases where applicant is asked for transcript. It is not always the case.

@CharlesMorisset I also rephrased the question. I am on your side, I also wonder why transcripts should be needed for a job application (particularly at early stage). There are many job advertisements asking unofficial transcripts, but I wonder why it can be needed for senior positions. I just seen the latter in European universities.

@CharlesMorisset: As a counterpoint, when I was applying for postdocs and tenure-track jobs in the US (in mathematics), probably about a third of postings required an unofficial transcript with the application, and I believe almost all require a copy as a condition of employment.  Specific grades and classes never came up in interviews, though.  I don't think it carried a lot of weight; I expect it is mainly to make sure you actually have the degrees you claim to.

@CharlesMorisset I believe NIH NRSA postdoc fellowships (both individual and institutional) require a transcript. That said, I don't know why a faculty position, especially a senior one, would.

@CharlesMorisset: In the US, the diploma is just a fancy piece of paper that you can frame and hang on the wall.  They aren't normally used as an official academic record.  The transcript serves this purpose instead.  An official transcript is mailed directly from the university, in a sealed envelope, on tamper-proof paper.  There's usually a fee involved, so unofficial copies are generally accepted in early rounds.  But there is the understanding that if hired, you'd be asked for an official transcript, and it had better match.

@NateEldredge and don't forget that some US schools still present diplomas in Latin, requiring the extra step of translating them if you were trying to use them for something official.

@user102 I was once asked for middle school transcript!

From a European perspective: the only time I was ever asked for transcripts was for PhD admission. After that, nobody every asked me for transcripts.

Administrative people asked me for a proof of my degree (a copy of the degree itself, without grades, is what I gave). They only wanted to check I was eligible for the position's formal requirements (having a PhD to become post-doc or assistant professor).
Scientists asked me for my publications, my thesis, the list of topics I had taught, etc. They did not care the least about my grades in undergrad or graduate education.

So, I think the ads you saw asking for transcripts, especially for senior positions, are by far a minority. Once you have a PhD, most people won't care about your earlier educational record, since it is not a good predictor of how awesome you will be as a researcher.

Combining the various comments that this question has elicited:
In some countries and at some institutions, the transcript is the official record certifying completion of the degree. When an institution asks for an unofficial transcript, they are really asking for verification that you earned the degree you said you did. Unfortunately, certain events make some institutions feel justified in asking for  proof. You cannot very well mail your diploma!  Unofficial copies of your transcript are easy to come by in the digital age.

they are really asking for verification that you earned the degree you said you did. — But then why don't they just ask for an official transcript?  After all, transcripts can be faked, too.

From Nate Eldridge's comments - An official transcript is mailed directly from the university, in a sealed envelope, on tamper-proof paper. There's usually a fee involved, so unofficial copies are generally accepted in early rounds. But there is the understanding that if hired, you'd be asked for an official transcript, and it had better match.


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Capitalisation of "Section" and "Chapter" in a Ph.D. Thesis
I am submitting a Ph.D. thesis fairly soon and my supervisor has flagged my use of capitalisation in "Section" and "Chapter" as possibly incorrect. I have googled about a bit and I see mixed opinions.
So my question is, when writing a computer science Ph.D. thesis, what is the correct way to capitalise "Section", "Chapter", "Appendix", "Figure", "Table", ... ?
For example, what is the correct capitalisation for the following:

"In Chapter 3, it was shown that..."
"In the previous Section, a method was presented to..."
"The graph in Figure 3 shows..."

My flippant comment about this is to go with whatever your advisor tells you to do, assuming that s/he has given you an answer. ;)

"In Chapter 3, it was shown that..."

This seems correct. "Chapter 3" is the name of the third chapter. Names are capitalised.

"In the previous Section, a method was presented to..."

This seems wrong. "Section" is not referring to the previous section by name, therefore no capital.

"The graph in Figure 3 shows..."

Correct. Same as the first example.
So the rule (I use) is, if it is a proper name, then use a capital. This means, if it is of the form "Section $n$", where $n$ is a number, then it needs a capital.

Exactly.  Section~3 (remember the ~!) is a proper noun, the same rule holds for all words like theorem, lemma, item, equation, section, table, algorithm, etc.  The tilde makes sure that the line doesn't break between "Theorem" and "3" (it's a no-break space character).

(assuming the OP is using a TeX system)

"This seems correct"? Do you have any source for this claim? An answer to this question with no other source that what seems likely to you is next to useless.

@Lii: Dave's answer follows standard English rules: proper nouns like "Section 3" are capitalized; common nouns like "the section" are not. This guidance is thus far from useless.

@aeismail: If he actually stated that this is standard and preferable gave some source for this claim that would be great. But he only writes: "seems correct." and: "the rule (I use)", which is very confusing.

My source is "native English speaker".

Thanks. Any idea about multiple sections, i.e. "as shown in Sections 3.2 and 3.3" vs. "as shown in sections 3.2 and 3.3", or shall I ask a separate question?

@GregKramida Why would that case be any different? I'd use the first version you propose.

The Chicago Manual of Style says that all of them should go in lower caps. Any other Manual of Style I've found is consistent with @DaveClarke . I still have a question. What about "Sections 2 and 3"? I personally don't like it. I would go for "Section 2 and Section 3", but I'm not sure.

"Sections 2 and 3" is fine.

@Rufo: If you till have Chicago Manual of Style, please provide an answer based on that information! That would be much more valuable than Dave's personal feelings.

It is a question of style. The most accepted custom is that given by Dave: you capitalize logical divisions if you refer to them by number.
However, I've never believed that there is any real logic behind that rule, other than emphasis. Identifying things by a number doesn't make them proper nouns: as an example, you don't commonly capitalize “page” as “see Page 10”…

Interesting example with "page".  I see a small distinction between pages and sections: sections are intentional divisions into conceptual units, while page boundaries are much less meaningful, so it's natural to conceive of a section as more of a "thing" than a page is.  However, it's not clear-cut.

A search on Google Scholar reveals that both the forms

in chapter/section 3

and

in Chapter/Section 3

exist in published scientific articles.
For "chapter" the capitalised version seems to be a little more common. For "section" the capitalised version is much more common.

A lot of terrible/incorrect writing gets published and will be thrown up by Google. Doesn't mean it is correct!

@xadu: Note that this search was in Google Scholar, so it only includes published academic articles. That doesn't necessarily make the practice non-terrible, of course, but it does indicate the current usage.

fair point about current usage. That said, Google Scholar does include material which has not been peer reviewed, such as arxiv postings etc. I'll argue that even published articles often have incorrect/inconsistent grammar.

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Can I keep items purchased out of my startup funds?
I am a new faculty in US based university. Surprisingly, when I arrived to my new office, there was no computer in it. I wonder, if I will buy a computer with my startup, would I be able to keep it for myself when I will leave the university?

Hi, Lin. Welcome to Academia.SE. It's considered bad form to ask for different responses based on individual university regulations. I've edited your question to be more in conformance with site policies.

When you will leave?

In general, equipment purchased with university-provided funds belong to the university, rather than the individual faculty member who ordered the items. On the other hand, items procured through individual grants (where the university did not directly provide funding), can often be transferred from one institution to another.
However, it is also true that such property is not normally something that you can normally keep for yourself! The primary exception to this might be if the property has been in service long enough to be declared "obsolete," and no longer needs to be inventoried. Then, the university will typically have some sort of policy on the disposition of such equipment, and that is what you should follow.

that's a bit unfortunate, since previous person took all equipment from my office... and also I have better things to do with my startup: pay graduate students or invite people.

If you had expected the department to provide equipment for you separately from the startup funds, it should have been negotiated as part of your hiring package.

It is as likely that it was not the previous occupant who took all the equipment, but the university or department "reclaimed" it.

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Advanced degrees in two subjects?
Perhaps it is too early to ask this, but I will go ahead anyway, to satisfy my curiosity. I am currently studying Arts in a University, aiming to get a BA Honours in English and German. If I went ahead to get a Masters, would I have to choose one of them, or could I continue with both? And similarly for a Doctoral, if I get that far, does it have to be one subject at a time?

Why would anyone do that? What do you expect as an advantage?

If you're question is:

Can I do a 'double master's' in English and German the same way I can 'double major' in English and German?

The answer is not easily. The reason for this is that admissions to master's programs are normally decided by the department, not by the university as a whole. Therefore, admission to one program (say, a master's in English) does not give you the right to get a master's degree in the other program (here, German). You would have to apply to the programs separately. It is also difficult to study for multiple master's degrees simultaneously, since the coursework tends to be disjoint sets, and therefore you would probably need to complete the degrees sequentially (at best).
The doctoral thesis topic would allow you to combine the two disciplines. However, it may be administratively difficult to have two different departments listed on your degree; this is an administrative issue rather than an academic one. There is usually an approved list of fields that can be listed on the diploma; if you want something else, you will have to petition for it, which could be a difficult process.

I am not sure your comment about MIT is correct. I was given a choice between getting my degree from the school/department.

At least in engineering, we didn't have this choice—at least not back when I graduated. In any case, I've edited this to be more generally applicable—it's pretty clear that you can't put anything you want on the PhD diploma—at least not without permission!


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How do I respond to papers that present the authors' views and opinions as scientific fact?
Occasionally I encounter papers in which the authors expend significant effort to either:

prove an hypothesis that I know to be false;
promote a new theory that I know to be fundamentally flawed.

To do this, the authors use methods such as forging experimental results, misinterpreting results or misinterpreting cited references.
As I know that the views presented in the paper are false, I can deduce from the paper that the author must have favored promoting their views over correctness. However someone less educated in the topic might not be aware of this and base their work on this paper as they consider the presented views to be scientifically proven.
Is there a commonly accepted method to flag such a paper, so that future readers will be aware that the presented views are forged and false?

How would you know said hypothesis to be false? Is it something you would necessarily read in some other paper somewhere?

The forum matters. Are these papers appearing in otherwise good-quality journals whose peer review has had a momentary lapse, or in bad journals that everyone knows are crap?

If you believe there are significant problems with an existing manuscript, then you should present these issues to the journal in which the "offending" articles appear. The format this response should take depends upon the nature of the problem.

If the issue is in fact "forging experimental results," then the paper deserves to be retracted. However, this is a difficult allegation to prove, and you would need to have strong justification (not evidence, per se) backing up your allegations.
However, if the issue is misinterpretations of results or previous literature, this does not quite rise to the level of "academic dishonesty" as forging results. It is not necessarily correct to have the paper retracted. Instead, you should consider writing a "comment" or "letter to the editor" or even a longer paper in response to the problems in the earlier work.

Note, however, that if the paper has appeared in a reputable journal, it has gone through some sort of peer review process. As a consequence of this, it will be necessary to present a more "airtight" argument than if the paper merely appears in a repository such as arXiv. In the latter case, however, then there's probably not much you can do beyond the aforementioned "response article," as the paper has not been published, and thus retraction depends on the author "self-retracting" the work.

If the author published their paper with malicious intent, then they will not self-retract the work.

That was my point.


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How to announce a new web-page?
Our lab has recently developed a new webpage; we are thinking of ways to announce it's creation via social media and email:

Is there an etiquette for making such announcements?
Perhaps there are example announcements you could share?

Does it need to be announced? Usually linking to it from your department's site and the lab members' personal sites is enough.

Is the intention of this site (in part) to inform the general public of your research initiatives?

Some social service? Beyond that, I don't know if there is a need.

And be careful not to verge into spamming...

I have removed the link, because it is not germane to this discussion.

Sorry if it seemed like advertising @aeismail the intention was to help to understand our scope of research, but fair decision

The bigger reason why it's not germane is that if you're asking where to advertise your site, then your question can't help others, which makes it off-topic.

In addition to @AustinHenley's point, you might be able to get the webpage linked through a "featured" section on your department website. This will usually have an image and a short description which will be seen immediately by anybody visiting the department site.

If there's a reason for someone to visit your lab's site other than it's new and should be visited, then you could write up a short announcement and post it to a relevant mailing list for your particular discipline or sub-discipline.
Otherwise, the best and most persistent advertising you and your groupmates can do would be to include it as a signature block in your email. People who want to know more about your group can then click on the link. Other methods to generate traffic without purpose will likely tick off more people than inspire them to visit your page.

This is for lab site. Should I add my personal site under my signature?


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How specific does a "Work Package" in a grant proposal need to be?
I'm currently polishing a grant proposal for the ERC Starting Grant scheme. As is typical doubts beset me. There aren't many samples available, and every one I was able to find exists in a niche of its own.
What seems to be a typical pattern is to describe at a very high level the proposed approach: for instance, we will study issue A using method B but they don't go too much in detail. For example, how is this study exactly going to happen?
Where possible I have tried to explain in as much detail my line of inquiry and the expected outcomes. However, especially for a grant with a horizon of 5 years, it's difficult to explain how the last WPs will be studied, as they might depend on the outcomes of the prior ones.
It is highly likely that these proposals I have seen were the unsuccessful ones. If you have any experience of successful ones, how much detail did you give (or make up)?

Try to look at it from the view of a reviewer. You'll have a limited amount of time to estimate whether

the research will have a good chance of success (knowledge generation is success, so negative results are allowed!)
the applicants know the field well enough to work on the topic without stumbling about too many obstacles (e.g. you should say which methods you are using and why)
the work load is managable
the project is well managed.

Every reviewer knows, that you can not predict the future. If you could detail the research you want to do in three years, it would not have been research in the first three years! But you should make clear you know of the risks of your proposal and demonstrante, how you will handle those uncertenties.


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Is there any major problem in applying to PhD program in US after getting BSc and MS in UK?
I'm considering getting my BSc and MS in UK instead in US, since I prefer specialization rather than diversity in education. However, I'm not sure whether or not this choice will affect my chance to attend a competitive PhD program at an American university, since people who get MS tend to stay in UK to get PhD. This route may have the following problems:

I will have to take some extra courses in my grad school in US to make up for classes not taken.
I may be disadvantaged in admission because of differences in the educational systems in the US and the UK.

Considering these problems, should I rather stay in US to get BSc and MS? Or are they negligible? For me, it's the best if the time spent to get BSc and MS will be as short as possible. This may seem strange to people in US, but I want to consider the merits of education in both nations, so I can find the course of education which is the most suitable for me.
(I want to study molecular biology.)

Let me clear up an important distinction between graduate school in the US and the UK:

In Europe, the master's degree is generally a pre-requisite for admission to a PhD program.
In the US, the master's degree is not required for admission to a PhD program, and you normally apply to the PhD program with only a bachelor's degree. You can obtain a master's degree as part of the PhD program, but this is by no means a universal requirement. It varies between universities and even departments within a university.
In the UK, options are somewhat ambiguous. You can apply for a master's and PhD program at the same time, while others may require the PhD in advance.

Therefore, if you are admitted to an American PhD program, you will take courses in graduate school, because that is the equivalent of the master's phase in the UK.
Other than that, there's no inherent advantage of applying or attending bachelor's or master's programs in the US or the UK.

Thanks for your informative advice. I had misunderstanding about structure of graduate school in both nations. Is it also meaningless if I will apply to PhD after finishing BSc in UK?

I don't believe that it is necessarily true that one must have a master's degree as a pre-requisite for a phd in the UK (although it might depend on the subject, I've never heard of it.)

Upon further research, @JeremyMiles is correct: UK programs do allow for admission to dual-degree study programs. However, you should check the specific degree requirements for particular programs before applying.


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Is it reasonable to suggest a PhD thesis topic in an interdisciplinary area in which none of the faculty members specialize?
I think a similar question was answered in PhD Research under guide/advisor of a different department by JeffE. I'm asking a slightly different question. Yet if you find it identical to the above one, you can report it to be 'duplicate.'
I'm interested in both pure math and machine learning, and I chose to apply to math PhD exclusively due to my background. However, recently I've been into (1) developing an algorithm related to proof verification and others for application to mathematics using the state-of-the-art deep learning techniques and (2) deep learning proper without much of sophisticated math involved. I'm certain most or all professors in math department I'm applying to (or anywhere else) aren't working in such an approach as (1), since that's more of a job of professors in CS department.

Though the answer may be case-by-case, is a topic as (1) appropriate for my PhD thesis? I understand that I can have a co-adviser from CS dept., but is this topic likely to get accepted from math department?
If so, by any chance if my interest totally shifts to (2) and has not much to do with mathematics at later stage of my PhD, do I still have to work on something related to math like (1)? (I assume the answer is Yes.)
In fact, one of the programs I got accepted to is quite lenient in letting a math PhD student into its ML PhD program. Is going to this program the only reasonable path for the case that my interest totally shifts to (2)?

Your question is, I believe, out of the scope of this forum, as it is too specific. I recommend that you edit your question to something in the form of "Is it reasonable to suggest a PhD thesis topic in an interdisciplinar area in which none of the faculty members specialize?". In which case it depends. If you are applying to the US, for instance, you don't choose your thesis topic fronthand, but rather explain in your SOP what motivates you and topics on which you would feel comfortable working.

Thanks for your suggestion. I'm applying to the U.S, and I understand how American programs work, other than how they accept thesis topics. I guess I will once again receive the answer "it depends", but anyway I've changed the title.

is [developing an algorithm related to proof verification and others for application to mathematics using the state-of-the-art deep learning techniques] appropriate for my PhD thesis? Maybe... It depends whether this topic constitutes research. can I study this topic in the maths department? Yes, if you can find a supervisor in the maths department. can I study machine learning in the maths department? Again, yes, if you can find a supervisor. (Because you can doesn't mean you should. Perhaps consider whether you should study in the maths department or computer science department.)

Obviously, I can find a co-adviser in other department as suggested by JeffE in the above link, so my question is rather about whether the math dept. approves the topic to be appropriate or not. If you mean this question is equivalent to whether I can find a supervisor in math dept, then it makes sense. Thanks for your answer.

Well, no answer yet? I'll give it a try, even though I'm in CS and I'm residing in Europe. But maybe it helps a bit:
To adress your questions 1-3:

In CS it would - in math it depends on the will of the supervisor.
Depends on your PhD program and supervisor. It might depend who is sponsoring the PhD program as well.
I don't know enough about the US system to answer this one - but you asked for an other option and there is one:
Just quit the program you are in and look for an other one in a CS department! Sounds a bit disruptive, but if this is your research interest, you should follow it!


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Networking in a symposium as a "non-specialist"
I am going to participate to a symposium (or workshop or conference) for the second time. I am a PhD student and I'm not going to present anything there.
I know that networking is very important but I'm so bad at it!
The first time I spent my time mostly with people of my group or directly involved in my project, and occasionally speaking with people I had met before once or twice (but almost exclusively when they were talking with the people of my group/project).
In both cases the conversation was just small talk (I like this buffet, the weather is nice, there is a seminar next week at our institute) or was led by the other people, and I would intervene if directly involved or if I knew the technical topic well (e.g., I am using the same library, I had the same problem...)
I would like to try this so much praised networking, but I fear I will do just the same as before. I've seen the poster abstracts and there is only one directly related to my project, so I am afraid I will not be able to talk anything technical about other issues. I have a master in Engineering as do most of the other PhD students there, but we have different backgrounds and we have focused on different stuff in our research, so I don't feel talking about problems I have studied five years ago to people who have practiced on them until today.
Is it expected to network as a "non-specialist"? I feel like that if I want to talk something to a fellow PhD student (not directly in a project similar to mine), it would be small talk and maybe the daily problems of a PhD student, but this seems like a poor alternative to me.

Is your advisor also going? (If so, ask him to introduce you to people.)

This time not! But yes, I'll follow the advice

Try consider "networking" as a code-word for "making friends". Did wonders for me at conferences where I knew little on the presentations. Also, use commonalities; if there was a venn diagram between you and your speaking partner, start with what's in between the two circles. (Quick social thinking is not necessarily easy so don't feel down about not being able to think of things :)

Let me tell you first that I can sympathise - networking also does not at all come natural to me. However, like most things, networking can be trained. The best opportunity to train is while doing it (or at least trying to), so your symposium should give you ample opportunity to improve.
First, if possible, do as JeffE says - have your advisor or some other (maybe more senior) person introduce you to people. Don't be embarrassed to talk about your ideas or your papers, or just about what you have learned during the symposium. That you come from a slightly different field may actually be an advantage here - the most interesting conversations I had at conferences often started with somebody saying "I, as an XY, find many of the presentations here really interesting, but why is there so much focus on A and so little work on B?".
Second, don't discard "small talk". Networking is mostly about connecting on a personal level anyway - it really does not matter so much what you talk about with people, as long as you talk to them. Talk to them about whatever comes naturally. It does not have to be about their research, even if this clearly is a natural conversation starter among researchers. Other standard conference convo topics (especially among PhD students) are: (1) life as a grad student, (2) difficulty with course work, (3) estimated time to graduation, (4) the ups and downs of the student's relationship with their advisor (although the last two bullets may be a bit loaded on occasion).
Third, try to not fall into the trap of seeing networking as "work", i.e., something that you'd rather avoid, but you know you need to do. This will make it automatically appear unpleasant, and you may end up just going through the motions so that you can say to yourself that you "networked", without achieving much.
Fourth, talk to people that you like talking to, and avoid like the plague people whose company you do not enjoy (for whatever reason). This sounds like a given, but I have seen many people classify conference participants into "important" and "unimportant", and then make a point to always talk to the "important" ones despite not actually enjoying it. This is a bad idea on multiple levels, including the fact that the PhD students from today are the professors and grant co-authors from tomorrow, so there really are no unimportant people in a conference.
Fifth, don't be too hard on yourself. You don't need to spend every minute of a conference networking. Many people, myself included, need a considerable amount of quiet time to function. Give it to yourself. It is ok to spend a few hours per conference day alone in front of your work, or on your hotel room if you feel tired of networking.
In the end, networking is the part of your work where the most important part is really to enjoy yourself. If you find one friend in the symposium, who you stay in touch with over the years, and who you write a grant proposal with in a few years, you networked successfully even if you talked to literally nobody else all week.


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What are good resources on how to carry oneself on a PhD course?
I just started a PhD and I was looking for some guidance on what I could expect in the following years, more specifically, what is the recommended way to progress, how should I allocate my research hours and other responsibilities, and , finally, when and how should I start writing my PhD thesis.
Is there any book written on how to conduct yourself during the course of a PhD? What would be your overall recommendations?

You definitely need to have some (long) conversations with your advisor. He/she will have the best answer for you specifically.

This is potentially a good question, but I will edit it to add a more general perspective.

This depends widely on country and field, making it impossible to answer in a generic manner.

When I first started a PhD program, my professor uncle gave me this: http://www.phdcomics.com/book.htm

If possible, the best person to ask is someone finishing PhD at our place, or a fresh postdoc. When it comes to more general things, it can vary with respect to discipline, university and... your own skills and motivations.

Have a look at this excellent memoir by a recent CS PhD: The Grind by Philip Guo
Although written from a CS perspective, many of his experiences transcend disciplines.

Looks like a nice book, i'll start reading it, as a master's student planning on going PHD in the following months...

I will say though that my experience doing a Ph.D at Stanford is absolutely nothing like his. YMMV

Likewise for me at Berkeley.  Philip Guo's PhD experience was not typical.  Neither, for that matter, was Jorge Cham's (also at Stanford).  [On the other hand, I'm not convinced that a "typical" PhD experience actually exists, so this statement may be trivial.]

Page Not Found, would you mind updating post

what is the recommended way to progress

Steadily.  Make small progress every day.

how should I allocate my research hours and other responsibilities

Consistently.

when and how should I start writing my PhD thesis.

Now, and in LaTeX.  Write down everything you read, everything you do, everything you prove, everything you try that doesn't work, every crazy stupid idea you have.  Write, write, write. Always in LaTeX.
Most importantly: It's your PhD.  You have to hunt it down and kill it.

This bears repeating over and over again: it's your Ph.D - not your advisor's. It's your job to ..well.. finish it. An advisor merely advises.

There is a lot written on the 'PhD journey' but there are some things I learnt along the way that took me across the void (so as to speak!).
I am listing them in no particular order:

Be true to yourself and your supervisor. Keep your end of the bargain. Meet deadlines. Keep your supervisor in the loop (even on trivial matters - the matter may be trivial from your point of view). Respect him or her. Of course you can have friendly arguments. Follow his or her instructions/suggestions/advice closely.
If you don't know, ask. You can ask your supervisor or email other scholars. My dissertation benefited from several prominent thinkers in the field. I simply emailed them and asked for assistance. There is no shame in asking. It is a learning process.
Celebrate your big and little achievements. When you finish writing a difficult chapter, give yourself a treat. Set small goals - you cannot finish your dissertation in a day but you can draft a section of your chapter in a day.
Learn and try to become an expert in your field. After graduation, you would be expected to have advanced knowledge in your field. Be genuinely interested in what you are doing. Think of new ways of addressing the issues. Discuss your approaches with your fellow PhD students. They are often your first audience. Have a network of support.
Most importantly, recognise that there would be some good days and some bad days. Make the most of them both. On bad days, give yourself a break. I think the literature says that most PhD student will start enthusiastically and then lose interest in the middle years and then gain momentum again.

My overall recommendation is to never lose sight of your goal.

the way i see it (i use excel to track my work, but other people maybe use ms gant or just paper checklist , whatever works for you):

set up an excel mini sheet with Everything you need to learn to deliver your final thesis (from literature review methodologies , to coding and statistics with nvivo or spss) video courses or book , whatever fits the schedule , you can divide the day you work on your phd by 1/2, half learning , the other half thesis and research

set up another excel mini sheet with Everything you need to learn to advance your career on your specific domain (post phd) certifications , continuous learning , because pure research jobs are hard to find(we have high requirements in my country) , require at least 2 good papers indexed in high journals(like elite) and at least 3-5 years experience in a lab or similar research environment

If you dont know just ask , if you need a paper you can ask the author , if your stuck you can ask old staff on the lab , or phd team mates ....

want to keep the momentum , help the community , help new phd students, join a sig on latest current problems and help them on the way , also schedule some time off with friends , family , and hobbies

Draft a timeline and either print it and stick it on your wall or keep it on a folder , each mile stone you reach on your thesis you cross it , this visualisation of your objective on a graph timeline helps you keeping focus and discipline


text:
If I notice an error in a figure after manuscript submission, could I be accused of falsification of data during review stage?
I have submitted a paper to a reputed journal (computer science; computer vision to be specific). While i was keenly waiting for the reviews, they were getting delayed. So I began working on an extension of the work.
During that I realized that one of the qualitative figures in the submitted paper might be slightly wrong (a few pixels yet noticeable) due to miscalculation while generating the image. However, the final interpretation and the description of it in the paper still would not change. But, when I critically view the image I think the reviewer may conclude that it could be photoshopped. I checked on the journal tracking system that the reviews have been received.
My questions are:
(i) I am ready for a rejection, but could such a mistake may lead to public shaming or ban from future publications?
(ii) Would it be advisable to write to the editor that I have found a mistake in the submitted paper and explain that it does not impact the discussion. Or should I wait and correct them in the next version?

If you find a mistake, it is good practice to mention that to the editor. It is slightly embarrassing, but not as much as if someone else finds it.

Plagiarism ≠ falsification of data. It seems like you intended the latter, not the former.

@eykanal thanks. Yes I intended that. Updated the title. What should be my next steps

@Captain Emacs Thanks. Should I explain the technical intricacies to the editor that it was due to to a bug in the code. I am not sure what should be my response. O showed it to a colleague and he says the error is minor and probably won't be noticed. I may change it in the next version. However, since.the reviews are over I am not sure if informing editor would be helpful.

@krammer Really, hard to say - only you know how relevant the bug is. If in doubt, inform the editor. Keep in mind that, if your result is of any importance at all, people may be found that will try to reproduce it or may just stumble over it. How much are you going to waste their time? This is - as they say - your call.

To answer your question, it sounds like the difference is so minor that this wouldn't be considered falsification but just a simple (and minor) mistake on your part.  You said yourself: the difference doesn't change the conclusions.
Addressing the issue is what the editor is for.  Contact them and point out that there was a bug that caused the figure to be generated slightly incorrectly (you are not the first person to have done this).  He/she will evaluate it and likely conclude the same as what you have: it is minor, does not affect the overall conclusions of the work, and will have you update it for final publication.
The reviews are complete but it sounds like you haven't gotten the comments back.  It's likely that any discussion you have with the editor can conclude with you rolling this image in with the reviewer comments.
Don't overthink it.  Everyone involved in this process is human, despite carrying titles like "editor" and "reviewer."  Those folks are in those roles because they have experience and know that these types of things happen.

One should note that if reviewers noticed this and recommended rejection, it may still be that the editor rejects the paper even if the authors point out their mistake. But I agree that the more severe consequences indicated by the OP would not happen.

Do not worry at all! This is very common and you can fix it and add a note in the letter to the editor / answers to reviewers in the next revision, clearly explaining the mistake, how you corrected it, and what has changed in this version of the manuscript (figures, conclusions, etc).
As they have already pointed out, reviewers, editors, etc... are human and make the same mistakes than you, or more. Even if it were already published, you could submit a correction.
Falsification of data or fraud is a completely different thing than what you are describing here. Falsification of data is manipulating it on purpose knowing that something is actually wrong to "prove" some claim that benefits you but does not derive from the evidence.
Here you have a recent scandal in Spain: https://forbetterscience.com/2016/03/18/erc-on-susana-gonzalez-suspended-e2mio-grant-peer-reviewers-to-spot-manipulations/

Actually, this exact scenario is not very uncommon. Newer insights into data and mistakes on earlier analysis/data/calculations/etc are found at every stage: before submitting the data, during review and even after publication.
The criterion is as follows: Did you, to the BEST OF YOUR KNOWLEDGE, believe your data & calculations; and conclusions that followed to be true AT THE TIME OF SUBMISSION?
If yes, and if you find a significant change in either the data itself, calculations or conclusions, you can always communicate this to the editors with appropriate explanation.
You fear that reviewers might conclude wrongly that your image/data was 'photoshopped'. You can communicate this fear of yours in your letter and be upfront about it. Most editors will give you the benefit of doubt.


text:
Is it worth doing a poster presentation?
I submitted a paper to an IEEE conference (Computer Science). My paper was not accepted for publication but it has been accepted for poster presentation there.
The conference requires the authors to pay full delegate registration fees as is required for authors of published works. Is it a common practice ?
I was a novice student in the field when I submitted the paper, but have worked a lot in past few months in the area. And I am not looking for any specific inputs into that work anymore.
Is it worth doing a poster presentation in such case ?
EDIT: (some additional information)

It is not a top tier conference
I am self funded

The conference requires the authors to pay full delegate registration fees — I'm willing to bet the conference requires everyone who attends to pay full registration fees, whether they have a paper or a poster or both or neither.

yes, noticed that. I don't have much experience in going to conferences. and as @xLeitix says, probably its worth doing one since the experienced gain would be invaluable.

I have some experience publishing in CS, so I'll give you my point of view.

The conference requires the authors to pay full delegate registration fees as is required for authors of published works. Is it a common practice ?

Yes. In general, every participant is expected to pay in full, no matter what kind of contribution he/she has submitted. You are paying the conference, not your publication. One could argue that this is the main point why many (weaker) conferences even have poster and short paper tracks - to get more people to pay full registrations and attend the conference without having to accept too many papers.

I was a novice student in the field when I submitted the paper, but have worked a lot in past few months in the area. And I am not looking for any specific inputs into that work anymore.

I should comment that this is a somewhat questionable attitude. Even if you are not planning to continue a certain line of research, hearing what others think about your work will help you a lot in future research projects and papers. Also, I don't think that you can go from novice to can't learn anything in the field anymore in the timeframe of a conference paper review process, so I'll wager that some in the audience will still have reasonable input on your work.

Is it worth doing a poster presentation in such case ?

I would say this depends on practicalities. Is your advisor OK with paying your conference trip without a full paper to show? Is it far, will the travel be expensive? Is it a top conference that you want to attend for the conference's (and associated networking's) sake? Have you done many presentations, or will it at least be good training?
That being said, from a scientific point of view, most poster presentations are not very valuable. They don't count a lot on your CV (except, maybe, if it really is an absolute top conference), and you will not get that much feedback, realistically.


text:
Is it normal to suddenly become clueless about your PhD topic and how to rediscover one?
I am working towards a PhD. My supervisor and I decided upon a topic which interested both of us. I did an exhaustive literature survey, and found that there have been heavy work in this area in the past 2-3 years. The problem statement we started with seems to have been primarily solved, and now extensions to those are appearing in top journals and conferences.
Now, he feels that the work remaining in the area is not worth a PhD so we should look for something else, but he still asked me to explore the area. Now, I am clueless what exactly I am supposed to do and where to look for new problems (given that I have already invested my first year into this along with the course work).
Is it normal during the PhD that the problem that you expected to have not been mostly worked upon, already has so much work done ?
Now, in this case, how should one proceed to look for new problems or extensions of the problem that are worth a PhD ?
My area is Computer Science.

Don't be afraid to completely change the topic if you fail to identify interesting venues to explore. The first year of my PhD was spent at looking at something quite unrelated to the main bulk of my work and I hit a dead end. The work I done in the first year was not even in my Thesis. I also know some people who had switched topic halfway resulting in a multipart thesis on completely different topics.

To answer the title question: Yes, this is completely normal.

Don't consider your time reviewing the field necessarily wasted. You say that you've discovered that the research topic that you wished to pursue has already been thoroughly investigated. If this is true, then you are in the happy position of finding this out now before having invested more of your time.
Now, is it indeed true that the topic has been exhausted? Perhaps this is the basis of your supervisor's request that you continue reading around the topic. Is there a line of investigation still remaining that you can work on? Are you sure all the extensions to the primary findings have been looked at? Is there a way of extending into new and unexpected territory?
On this last point, talking to many other people in the field - or closely related fields - might spark off ideas in your head. Discuss with them whether they think all aspects of the topic have been considered. Find people who are not experts in the specific topic, but are conversant with it who might offer a difference perspective. These people might draw you toward research across two fields. Can the results of the research topic you were looking to work on be extended into other, surprising areas?

I second the need to talk to other people in the field. Many academics are very insightful and have interesting ideas for research within their area.

With the vast output of science it is not surprising that more may be done than what might appear at first. Science is about advancing science and so if your original question has been answered the question becomes what is not answered? A key aspect of all research is that new question spring out of answering (or trying to) question. This leads to the point that one must read up on the literature in the field of interest so that you can identify the new questions that emerge. This is one way of interpreting your advisors suggestion.
It will be very difficult to isolate oneself with a question since others will likely arrive at similar ideas sooner or later. Defining a PhD study can therefore be tricky since it means working on some line of questions for several years. "Knowing your opposition" is therefore a good thing. You need to read up on material not only to identify unsolved questions but also to get a sense of what others are working on. Going to key conferences in your subject is one good way to see what is going on.
At the end, I want to add that I do not think it is your sole responsibility to do all this, after all, your advisor should now more about the field and who is doing what among peers. Getting a PhD is about learning to become an independent researcher and to ask too much of you early on is thus not realistic. What you can do is as stated earlier to read up on literature and build your own picture of the (sub-)field. You will need this knowledge under any circumstance.


text:
Adding a faculty as a co-author
I and two other student, did a course project and it has been accepted for publication in an international conference. I am confused now that whether I should add his name as a co-author or acknowledge him in acknowledgements ?
I would like to share that though, the entire implementation and writing the paper was done by us, we were student of his class and the work was produced as a part of course project.
My field is Computer Science.
Edit: As F'x suggests, that I should ask the instructor. What would be an appropriate way to do so given that his name was not added as co-author before acceptance.(We were confident about the work but were not sure about the acceptance. The conference management software was EDAS and it spams email of all co-authors which we wanted to avoid in his case)

Discuss it with your teacher.

The right time to ask this question was before you submitted. But better late than never.

Regarding “given that his name was not added as co-author before acceptance”: ask him ASAP. Be honest, be apologetic, explain clearly the situation and the reasons you did not want to add his name beforehand, but also be very clear that you realize now it was a mistake not to discuss it at the time, and that you made the mistake due to your lack of experience in academic publishing.

And the vast majority of academics I've met will be happy with this approach.

If he/she supervised your work, and/or read your paper, and/or somehow gave his/her contribution to your paper, I think that yes, you should add his/her name as author.

Co-authorship depends on the person and (sometimes) internal rules. For instance, during my PhD it was common for the professors to consider reading a paper + giving feedback as contribution worth authorship. Some of them even thought that they deserve authorship just because they talked to you about your idea:)
During my Masters (at another university) my supervisor did not only read the paper, but also corrected some errors in the formulas and checked the experimental results. When I put him as a co-author, he asked to remove his name motivating this as "I just did the work a normal supervisor will do".
So, as others suggest - do ask the professor ASAP.
P.S. Many professors will not fund your trip to a conference if their name is not on the paper unless explicitly agreed beforehand:)


text:
How to proceed when advisor asks you to resign?
This happened with a friend of mine and I am asking this question on his behalf.
My friend was recruited for a sponsored research project in the university and offered a part-time PhD along with that. He is currently completing his coursework (2nd semester) which is pretty exhaustive. He has been working pretty rigorously and one of his poster presentation was accepted in a reputed conference within 6 months of work.
Since the coursework in this semester was tough, he wasn't able to give any tangible output in terms of publications or concrete results. Now, suddenly he has been asked by his advisor to resign. This has come to him as a surprise since he was expecting some scolding as his guide is known for being arrogant (and he is very reputed researcher in the field).
He is unsure whether to leave PhD or how to proceed and convince his advisor.
I believe he is pretty new (1 year of coursework) to the domain and since the project is pure research, he does deserve a chance. But I am unsure of how one should proceed in such cases.
EDIT (based on queries in comment)
Part Time PhD: He was recruited as an employee for the project by the university. And also offered a PhD. The stipend comes from the project cost(funding agency) and not from university funds (as is the case for direct PhD recruits in my university).
Advisor being Arrogant: He is very knowledgeable and reputed but known for scolding students frequently.(Some faculty members also agree to this including my own advisor)

I don't fully follow the logic of your arguments. He should be scolded because his guide is known for being arrogant? He deserves a chance because his project is pure research?

I am not familiar with the term "part-time PhD".  In what country is this story taking place?

Related:  http://academia.stackexchange.com/questions/18898/how-do-i-convince-my-professor-to-keep-me-as-his-student

@PeteL.Clark maybe part-time in the sense the friend does this next to his 'normal' job.

@PeteL.Clark: Perhaps what was meant is that a partial stipend was awarded to cover part-time work as an RA?

@DaveClarke I meant the advisor usually isn't very polite to students.

@PeteL.Clark It means that he has been recruited as an employee for the sponsored project and offered a PhD along with the work. (The phd work may or may not be related to the project)

It would actually help if you modified the question to reflect the clarifications, rather than just leaving the unclear text and tacking on an "Edit" block.

This is a difficult situation. Regardless of the facts of the matter, there appears to be have been a breakdown of trust/communication: either the advisor has been sending signals for a while that the person didn't pick up on, or the advisor is indeed pulling this out of the blue, which also signifies a breakdown of communication.
Probably the best first thing to do is for the student to set up a meeting with the advisor to understand the advisor's reasons. It's possible that a face-to-face meeting might allow the advisor to express their underlying concerns in a more productive way that could lead to a concrete plan for activities.
If that fails, or the advisor refuses to meet, the next person to involve is usually the chair of graduate studies at the department (or the equivalent). There is usually someone whose job is to oversee the graduate program and manage conflicts like this. They might be able to mediate a rapproachment between the advisor and student (or even find another advisor for the student). I've had to do this in the past when I served in this capacity.
Bottom line: if the facts are as you outlined, then I think the student deserves a more reasonable explanation from the advisor as to why they're being terminated. Sadly though, in my experience  I've often found that students ignore signals being sent to them, and that advisors are unwilling/unable to give direct and clear feedback.

I generally agree with Suresh and Trylks advice. The relationship between your friend and his advisor is broken. That is a problem that your friend cannot avoid.
On the other hand, it is not only your friend's problem. It is his advisor's too and since he is the senior party, he is the one that needs to do more than your friend to fix it. I also do not get this "resign" thing. Your friend has a contract with the university, not with the advisor. It has also probably been assigned a committee for your friend's PHD that includes other professors except his advisor. If your friend is incapable for a PHD, again this decision is not entirely up to the advisor. It is the advisor that needs to prove your friend failed to meet the requirements of the project / PHD and your friend should not just "roll over dead" just because the advisor is not happy with him. So resigning is out of the question. If he has already a poster  publication, did well in the required courses then I think the advisor will have a hard time proving your friend is incapable.
So, your friend should ask his advisor what he can do better to make things work. He should follow his advice, be extra nice and work extra hard. But there is absolutely no reason for him to resign. If the advisor is right (and as powerful as he believes he is), he can always fire your friend. But he will still have to justify to his fellow professors why he took a promising student such as your friend (otherwise your friend would not be selected for a PHD) and failed to "advice" him. It is your friend advisor's failure as well and both parties should suffer the consequences.
All this advice is based on your "word" that your friend did actually 90-100% the best he could. In any other case, where the advisor repeatedly warned your friend about potential improvements and your friend deliberately ignored him then he should just suck it up, take it like a man / woman and suffer the consequences. But if the advisor failed to effectively advice your friend, then this failure should be fixed by both parties and not simply by your friend resigning.

Maybe "accept responsibility" instead of "take it like  a man" ? I doubt accepting consequences is directly linked to your chromosomal peculiarities :)

@Suresh I think you're deliberately misunderstanding the phrase. The connotation of "like a man" is "and not like a boy, who runs crying to his parents"; it's not "and not like a woman".

next time (or next edit) you can try with "an adult", it's a less ambiguous and more politically correct option.

Situation: FUBAR. I'm quite sorry for your friend. Good thing is: things can't get much worse.
Now he is a student and the professor is reputed, if he resigns then they are both just human beings. These are two different contexts and your friend is, more or least, with one foot on each of them. With the insight of the second context and a potential imminent resign, I'd ask, from a person to another, "why?".
If it's for the lack of results/publications, your friend should check why did that happen and whether that is going to continue in the future. It's not only a matter of doing and finishing a PhD, but also a matter of how worthy a PhD with few publications is in the end, considering the opportunity cost and all the effort and time that it is going to need. It may be a "Pyrrhic victory" and that is something very few people warn about (actually I haven't seen anyone).
Your friend deserves an explanation. Please keep us posted.
On the other hand. This is a failure in communication, as @Suresh pointed. We only have one side of the story, your friend's, through a third person (you), so it's hard to know. But the description you make of the advisor is:

he is arrogant
he makes things suddenly with no prior notice
he doesn't provide arguments or explanations

The best thing to do in such a situation (if possible, usually not easy) is to switch to a different supervisor, because that guy may be reputed and good at research, but he does not seem good (from your description) at dealing with people, managing them and advising in general.
But again, remember, it's hard not to be biased when all the information that we have comes from a friend of one of the parts...


text:
Does the eigenfactor ranking depend on number of articles in a journal?
The eigenfactor is offered by ISI Web of Knowledge as an alternative journal score compared to the impact factor. It is explained on their site as follows:

The Eigenfactor Score calculation is based on the number of times articles from the journal published in the past five years have been cited in the JCR year, but it also considers which journals have contributed these citations so that highly cited journals will influence the network more than lesser cited journals.  References from one article in a journal to another article from the same journal are removed, so that Eigenfactor Scores are not influenced by journal self-citation.

From this explanation, I am not sure whether the eigenfactor depends on the total number of articles that a journal publishes?

Wikipedia’s article on the eigenfactor.org ranking of journals answers your question:

The Eigenfactor score is intended to measure the importance of a journal to the scientific community, by considering the origin of the incoming citations, and is thought to reflect how frequently an average researcher would access content from that journal. However, the Eigenfactor score is influenced by the size of the journal, so that the score doubles when the journal doubles in size (measured as published articles per year).

To give a simple example: the Journal of Physical Chemistry B is the highest-ranked journal in physical chemistry by this criterion… in good part because it carries the largest number of articles. It is a good journal, but under all other metrics it is not at the very top of its field.

Eingenfactor.org summarizes their methods here: http://www.eigenfactor.org/methods.php. A nice summary of this procedure would improve the answer.


text:
Does the new law "zur Stärkung der Berliner Wissenschaft" make postdocs in Berlin de facto permanent?
In the German city-state of Berlin, a new law titled Gesetz zur Stärkung der Berliner Wissenschaft (law to strengthen Berlin science) was passed.  One of the changes has been described as tenure track for all and giving postdocs the right to a permanent position.  For example, see this article in the Tagesspiegel.  But in another interpretation, such as indicated by this article in Forschung und Lehre, it is not quite as far-reaching:

Laut Novelle kann mit wissenschaftlichen Mitarbeiterinnen und Mitarbeitern, die promovieren, vereinbart werden, "dass im Anschluss an das befristete Beschäftigungsverhältnis der Abschluss eines unbefristeten Beschäftigungsverhältnisses erfolgen wird". Bei bereits promovierten Mitarbeiterinnen und Mitarbeitern, die sich auf einer befristeten Stelle weitequalifizieren [sic] – zum Beispiel mit einer Habilitation oder auf einer Juniorprofessur – muss dagegen eine Anschlusszusage vereinbart werden.

My translation:

As a novelty, it is possible to agree with research scientists, who are graduating (getting a PhD), "that a permanent employment will occur as a follow-up to the fixed-term employment".  For already graduated employees, who acquire additional qualifications with a fixed-term employment — such as a Habilitation or a junior professorship — a commitment to a permanent follow-up employment must be agreed.

That rather sounds that it does not apply to the majority of regular postdocs, but that only junior scientists who qualify for a Habilitation or junior professorship must be offered a permanent position.  For PhD students, it merely says kann (can), which means there is no right at all.  For postdocs who aren't acquiring formal new qualifications (the large majority?), it doesn't say anything at all.  However, the Tagesspiegel article also quotes the actual law:

„Sofern die wissenschaftliche Mitarbeiterin oder der wissenschaftliche Mitarbeiter bereits promoviert ist und es sich bei dem Arbeitsvertrag genannten Qualifikationsziel um eine Habilitation, ein Habilitationsäquivalent, den Erwerb von Lehrerfahrung und Lehrbefähigung oder um sonstige Leistungen zum Erwerb der Berufungsfähigkeit (…) handelt, ist eine Anschlusszusage zu vereinbaren.

My translation:

„When the research scientist has already graduated and if the qualification aim, as mentioned in the work contract, is a Habilitation, a Habilitation equivalent, the acquisition of teaching experience or other performances to improve the professional skills (...) then a permanent follow-up contract must be offered.

Which sounds broader: it would appear that not only a Habilitation or equivalent, but any teaching experience or even other performances that strengthen the CV (maybe proposal writing or publication writing?), would entitle the junior researcher to a permanent position.
Who exactly are entitled to a permanent position as a follow-up to a temporary position, under the new law in Berlin?  Would it apply to a large majority of postdocs, or would just a small, relatively senior subset benefit?
(Of course, a different question is if this will actually make a big difference in practice, but that is beyond the scope of this post.)

NB: someone better versed in Behördendeutsch and with more experience in German academia than me, please feel free to improve my translations.

If a university wanted to get around that rule, the obvious way to do that seems to be to not mention a qualification aim in the work contract. I believe that my postdoc work contract in Germany (not Berlin) didn't mention any qualification aims.

One important piece of context for an international audience: German universities already have permanent non-professorial scientific positions ("akademischer Rat"). Unlike what "tenure track for all" suggests, it's not that the new law would give postdocs a route to automatically become full professors (or even any kind of professor), it's more meant to prevent universities from stringing together time-bound postdocs without ever committing to permanent researcher positions. (IANAL, my outsider understandin)

@lighthousekeeper: May I ask whether your position was funded by a grant or whether it was a regular position funded by a federal state ("Landesstelle")? I'm asking because one of the issues here apparently is a follows: By federal law in Germany (the so called "Wissenschaftszeitvertraggesetz", which can roughly be translated as "Law about non-permanent positions in academia" - kudos to Mark Twain!), regular positions ("Landesstellen") which are not permanent must necessarily include qualification targets. [...]

[...] I'm not a lawyer, but combined with the new law in Berlin, it seems that this implies that, in Berlin, regular positions ("Landesstellen") for postdocs can no longer be filled by given people non-permanent contracts. For if a postdoc is supposed to take such a position with a non-permanent contract, federal law requires the contract to include qualification targets; but if the contract includes qualification targets, Berlin state law forbids the contract to be non-permannt.

(By the way, I just noticed that's a really nice real-life example example for a proof by contradiction - unfortunately, my first year students are probably not interested in laws about regulation of academic work, so there's no benenfit of using it in class... :-) )

@JochenGlueck Couldn't your students model academia, in particular the mobility of early-career scientists, as a dynamical system? ;-) (NB: the point you make about federal law requiring German Landesstellen to include qualification targets is important, and I was not aware of this)

@gerrit: I'll keep this in mind for an ODE course. :-) But for the time being, I'll be happy if I succeed in explaining to them what a vector space is. ;-)

@gerrit: Just in order to provide a reference for the requirement of qualification targets by federal law: It's the second sentence in §2 (1) of WissZeitVG.

If so, I foresee the number of postdocs in Berlin decreasing…

@JonCuster Universities and parliamentary opposition went to court to block the law on competency grounds (arguing this is an exclusive competency of the federal government), so it might not happen after all, depending on how the court rules.

The first quote simply says that a permanent position can be negotiated, but not that it must. In practice, few universities will want to do that for more than a handful of people because it greatly constrains their future ability to hire someone else for that position.

@WolfgangBangerth It says can for PhD students, but must for postdocs.

Oh, I see now. I wonder whether the intent is just that the question of "Anschluss" simply has to be spelled out in the contract, but without stating what the conclusion is supposed to be (either affirming that there will be an "Anschluss", or declaring that there will be none).

@WolfgangBangerth: From what I've read in the media, the law is definitely meant to force the universities in Berlin to provide permanent contracts for postdocs if their position is not funded by a grant. (But obviously, the law will fail miserably - for the reasons you have already mentioned, and also since Berlin apparently found it a good idea to pass this law, but not such a good idea to provide more money to the universities for additional permanent positions. One of the universities in Berlin has already frozen all hiring processes for now.)

@JochenGlueck My position was indeed funded by a grant. Your explanations for the case of a "Landesstelle"-funded postdoc make sense. In my field, it seems that grant-funded postdocs are much more common, but that might be different in other fields.

Short answer: When a post-doc is hired by a university in Berlin (i.e., not with third-party funding), their contract must contain the conditions which, if met, will lead to them being offered a permanent contract. These conditions should be tied to successfully acquiring the skills that are the goal of the post-doc. This applies to about 2/3 of post-docs in science and art, but not to medical doctors receiving specialized training.
Longer answer...
This law was finally adopted in July 2022. The relevant part of the law states:

(6) Mit einem wissenschaftlichen Mitarbeiter oder einer wissenschaftlichen Mitarbeiterin auf einer Qualifikationsstelle kann vereinbart werden, dass im Anschluss an das befristete Beschäftigungsverhältnis der Abschluss eines unbefristeten Beschäftigungsverhältnisses erfolgen wird (Anschlusszusage), wenn die bei der Anschlusszusage festgelegten wissenschaftlichen Leistungen erbracht wurden und die sonstigen Einstellungsvoraussetzungen vorliegen. Mit promovierten wissenschaftlichen Mitarbeitern und Mitarbeiterinnen ist unter der Bedingung, dass das im Arbeitsvertrag benannte Qualifikationsziel erreicht wird, eine dieses Qualifikationsziel angemessen berücksichtigende Anschlusszusage zu vereinbaren.

My translation:

For a scientific employee in a qualification stage, it can be agreed, that upon the completion of the limited-time employment relationship, a permanent employment relationship (consecutive commitment) will be offered if the specified academic achievements and other employment requirements are met. With PhD-holding scientific employees, such a follow-up commitment is to be offered, subject to the condition that the contractually-named qualification goals are reached.

In other words: offering a follow-on contract to PhD students is optional, but it is required for positions such as post-docs where the primary goal of the position is for the employee to acquire certain skills, and those skills are indeed acquired satisfactorily.
The (potential) problem with this is obvious, and is indeed specified in the article from Forschung und Lehre that you already linked:

Die Landesrektorenkonferenz der Rektoren und Präsidenten der Berliner Hochschulen hatte deshalb...vor einem "massiven Ausbau unbefristeter Beschäftigungsverhältnisse in Forschung und Lehre" gewarnt..."Würden die jetzt vorhandenen Stellen in kurzer Zeit sämtlich besetzt, so bliebe auf Jahre und Jahrzehnte kein Spielraum, künftigen wissenschaftlichen Talenten eine vergleichbare Qualifizierungs- und Beschäftigungsperspektive zu bieten."

which, roughly translated, means:

The state conference of university rectors and presidents of higher education institutes in Berlin had therefore warned...of a "massive increase in the number of permanent employees in research and teaching...if the currently-open positions were all filled [with permanent employees], there would be no space for years or decades to offer equivalent training or employment opportunities to future scientific talent.

Now you specifically asked about who this applies to. The law itself defines this: some of the sections (not reproduced here) define "scientific employees" and make a major distinction between those employees required for the normal functioning of the school versus those whose primary goal is to further qualify themselves for academic jobs. But of course the law does not estimate how many employees that might apply to. For that, we turn to this article:

So rechnete es auch Hochschulexperte Tobias Schulze von der Linken vor: Von den 12.245 wissenschaftlichen Mitarbeiter:innen an Berliner Hochschulen seien 5000 Postdocs und von ihnen wiederum ein Drittel Drittmittelbeschäftigte. Die verbleibenden 3354 haushaltsfinanzierten Postdoktorand:innen, um die es in §110 geht, machten jedoch nur fünf bis zehn Prozent aller Beschäftigten im Mittelbau aus.

translation:

Hochschule expert Tobias Schutze from der Linken [a political party] estimates it as follows: of the 12,245 scientific employees in Berlin's Hochschulen, 5000 are postdocs, and of these, a third have external funding. The remaining 3,354 university-funded positions, to which Paragraph 110 [this law] applies, therefore make up only five to ten percent of all mid-career employees.

So, it applies to about 2/3 of all post-docs in Berlin. It also applies to similar positions for artists, but not to similar positions for medical doctors.
Now there is still some ambiguity. For example, can universities simply make the conditions equivalent to: "become the type of world-class researcher we would want to hire anyway"? Or must the conditions indeed be so achievable that the current generation of researchers will almost all get permanent positions, to the exclusion of future generations? Time will tell.

It'll be very interesting to see what universities will write down.  "The university shall hire the post-doctoral research associate on a permanent contact if the research leads to at least two nobel prizes."

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


text:
Do online recommendation systems ask specific questions about the PhD candidate?
I am applying to fall 2014 PhD programs in computer science. I have heard that the online recommendation system in place at most universities asks the recommender to answer a series of questions about the student in addition to a place where the letter can be typed. What kind of questions are asked?

As a graduate applicant, why should you care? Your only decision is a judicious choice of folks who will write you strong research-y letters of recommendation.

Take a look at this:

They pretty much ask the same sort of questions (mostly in a Likert scale).

FYI: the candidate name and program aren't quite blurred enough, I can almost make them out.  (Though maybe they are fake anyway.)

It is probably fake. I took it from Oregon State's website: http://gradschool.oregonstate.edu/help/docs/34#

I doubt if anyone's name is really "New Applicant".


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Gnuplot in thesis and articles or not?
I'm doing an astrophysics thesis with a lot of programming in Python. I'm currently using gnuplot for my plots, but I wonder if this is actually looking quite professional. Are there other options which look better and are still easy to use?
Here an example of a figure in my thesis:

The vertical line I got with the following command:
set arrow from 4861.3,-1200 to 4861.3,2000 nohead lc 2

I know it reaches out of the figure, but I use this command for all of my script and I know only at the end what the upper and lower boundary of the y-axis will be. Every peak is different.

I do not think there is anything wrong with GNUPlot, it is probably more important how you design the plots within GNUPlot, see for example http://academia.stackexchange.com/q/10282/4394

Do you have an example of a typical plot in your thesis? If you do, then you can probably post it and ask, "What can I do to improve this plot?" and solicit specific advice rather than just asking about alternative software packages that may or may not help you.

@Irwin: editted the question.

@JanosBraem Questions "Is GNUPlot able to generate publication-quality plots?" and "Is this plot (generated by GNUPlot) publication-quality?" are very different. And the later may be unsuitable for StackExchange sites as "too localized" or "off-topic" (as it is about tweaking plot, what has a lot to do with other sites, SE sites, but not - academia).

If you know where the peak is, how come you don't know how high it is?  Why use an arrow without a head instead of plotting a new line of data with two points?  There are problems with the graph--legends should be larger than tick labels, line width could maybe be a bit thicker, having stuff like u($1/(1.9072)):2 (or even the file name) is not very professional-looking.  But these are all fixable with a bit of effort without using something other than Gnuplot.

@RexKerr You're right, a new line with two datapoints would be better. thx

@PiotrMigdal The focus is on the first question. But with the hints and tips here I'm convinced that with some approvements Gnuplot also suits for publication.

See my comment here.

StackOverflow has a gnuplot tag that would be helpful for making your graphs more "professional" looking.  In this instance, just using GPVAL_Y_MAX/GPVAL_Y_MIN for the y-limits of the arrow would help to keep the line in the frame of the axis. Alternatively, GPVAL_DATA_Y_MAX contains the maximum y-value of the data line. See, for example: http://stackoverflow.com/questions/7330161/accessing-gnuplots-autorange-values

If you do the programming in Python, you could also do the plotting in Python with matplotlib. With a little adjustment of the plotting parameters, it is possible to produce publication-quality plots with this software.
Alternatively, if you need fancy annotations etc., I can recommend the pgfplots package for tikz/LaTeX. You could export data from your Python program to a csv file, and then use that as data source for plotting with pgfplots. If you are also using TeX for the main text, it allows to to produce graphics which nicely fit the formating of the text.

With matplotlib you can also generate figures with LaTeX text and formulas in them

For the plot you've shown, I have a couple of suggestions to make it look more "professional".  (Maybe you're already doing some of these in the actual document.)

Use a vector-based file format; your lines will look smoother, up to the resolution of your printer.  I suggest set terminal pdf.
Set a meaningful title for the curve: plot "tkrs.txt" using ... title "Dilithium flux density".  Or omit it completely: plot "tkrs.txt" using ... notitle.
If plotting a mathematical function (rather than a dataset), set samples 5000 or something similarly high for your final output.
Try to choose a font for the labels that matches the paper's text as closely as possible.  See help term pdf for more info, and other interesting tweaks.  You can also use non-ASCII characters (e.g. Å instead of angstrom).
Set the plot to a size and aspect ratio that fits nicely on the page, preferably so that your word processor (or LaTeX) doesn't have to rescale it.
For your vertical line, you could cheat and use a parametric function, so that it will be clipped to the boundaries of the plot.  It's a little tricky because if you make the line extra long, by default the plot will be rescaled to fit all of it.  But there is a way to avoid this:
set xrange [ ] writeback
set yrange [ ] writeback
plot "tkrs.txt" ...
set parametric
set trange [-1200:10000]
set xrange restore
set yrange restore
replot t, 4861.3 notitle

Thx a lot for the hints, I'll try them all next week.

It is difficult to produce professional-looking output from Gnuplot (even harder than it is from Matlab, which I also wouldn't recommend).
Since you're already using Python, matplotlib is the obvious choice.  You you can even make a decent attempt at producing full figures, not just one panel.
Typically astrophysics doesn't have much reference to astronomy these days.  However, if your thesis does, you might also want to check out APLpy which adds on to matplotlib.

@MarcusAntoninus - What is the difference between "difficult" and "with care"?

@MarcusAntoninus - Just for reference, I view the graphs in http://www.phyast.pitt.edu/~zov1/ as borderline in terms of publication-quality.

@RexKerr could you go into more depth as to what is wrong with the plots in the link you gave, they look basic, but essentially functional. I've seen worse in publications.

@PaulHiemstra - All of them are badly aliased.  In the first one, the axis labels are too small--all the text is, really--and the erf label is too close to the border.  In the second one, the tick labels are not helping anything and the arrow looks cartoonish.  The third one is good; only the tick labels are too long.  The fourth is just ugly; you need less space and wavy lines not just slashes to indicate space, and you need it on the graph line as well.  The fifth has bad axis label spacing (including tick labels), and the smoothing has introduced a shift in the data.  You get the idea.

@PaulHiemstra - That said, I've also seen worse, but the nice-looking ones don't look easy, and the easy-looking ones don't look that nice.  And the examples don't cover things that gnuplot doesn't do that well like line symbols (e.g. setting line width of your box symbol).  Then again, sometimes you don't want your figures to be a work of art but just to get the point across, and then you can usually get something acceptable without changing too many defaults.

The choice of plotting choice will depend on several factors. First, it is important to state that there are many options, from GNUPlot, through commercial plotting packages such as Grapher and Origin, plotting capabilities of Matlab and R to plotting using specific packages such as pgfplots (LaTeX) or graphics packages accompanying programming languages (e.g. PSPlot). What you chose will depend on other factors such as what your peers use, what you may have become familiar with and perhaps what you can afford (thinking of open source vs. commercial).
My personal experience has been that there is no single software that can do everything and so for me the key has been to identify what I need done and to minimize the number of software I need to accomplish it. This has led me to choices that are not common to my peers and has also left me to find my own solutions, not dreawing so much from other pesons experience (thank heavens for sites such as stackexchange)
So stick to what you know as long as it can do what you want but always keep an eye out for new solutions and try to figure out what others are doing that may impress you.


text:
Present journal paper at conference or the same work at multiple conferences

Possible Duplicate:
Under what circumstances can one republish a conference paper/presentation?

I have recently completed a Masters of Science which I pursued to fill a personal goal and to advance our development of a regional tsunami warning system.
Having read the thread on multiple publishing and presenting I am still confused as this is a new issue for me. Coming from Government we present on special projects or findings any number of times.
If I wish to publish my findings in an academic journal am I precluded from presenting at any conferences?
If I present at a localised scientific conference without published proceedings, am I precluded from presenting at a global one?
Can I focus one on localised context and the other on the global implications, then cite having presented at the local level?

There are a number of very similar questions, perhaps duplicates. See the links in my answer below.

The exact answer depends on the topic, but normally:

Publishing finding in an academic journal does not preclude presenting at conferences (except in computer science!). In fact, it's quite common to first publish a paper in a peer-reviewed journal, then go to one or even several conferences to advertise it. Just be sure to mention it at the conference, because if there are proceedings, there may exist conferences with different ideas, depending on the field.
Presenting at a local conference does not preclude presenting at a global one, certainly not if the local conference has no proceedings, because then there is not really any publication at all.
The answer to your third question is most likely yes.

To be 100% sure, contact the organisers of the conferences.
See also:

Publishing the same results at multiple conferences
Submitting the same research to multiple conferences
Journal publication and acceptance to competitive conferences
Under what circumstances can one republish a conference paper/presentation?

Dear gerrit and aeismail; Thank you so very much for your quick and informative responses and the additional links. Once I get over the first time gitters it will be ok but I appreciate folks like you who are willing the mentor. All the best and happy holidays - Lis

Publishing finding in an academic journal does not preclude presenting at conferences — Except in computer science.

In fields outside of computer science, publishing a paper does not normally prevent you from presenting your work at a conference; as gerrit points out, the two go hand in hand quite frequently, and many people will speak about just-published research in a presentation. (I know I have!)
However, what publishing a paper can do is change the form of the presentation, int he sense that the journal may place some restrictions on how you can reuse the material that has been published.
For instance, you may need to provide citations when including figures from the paper in your presentation, as well as citing any text that is taken directly from what has been published. For many journals, however, you may do so without asking prior permission, so long as you include the appropriate citations.

Publishing a paper does not normally prevent you from presenting your work at a conference — Except in computer science.

@JeffE: Why does CS seem to work so differently from every other major field of academia?

You have to start with the understanding that conference proceedings are the primary publication venue in CS, and work backwards from there.  Presenting at a conference is simply a perk of publishing a paper in a conference proceedings.  But if you've already published a paper elsewhere, you can't publish it again in a conference proceedings — no double dipping! — so you can't present it at a conference either.

@JeffE: That I knew. What I don't understand is why only CS seems to have this model. What are the differences in CS's evolution compared to other academic fields that would lead to this radical paradigm change?

The standard fiction is that even in the 70s and 80s, the field moved too fast for journal papers (which typically had a several-months-long review cycle) to be useful.  In some subfields, a six-month old paper may as well not exist.  Computer scientists were relatively rich, flights were relatively cheap, and there was no internet, so conference proceedings filled that gap.  [Other fields have responded to the same pressure by imposing fast review cycles and page limits on their journal papers, but CS has (largely) resisted the urge to abridge our archival publications.]

Also, computer science grew out of a mixture of mathematics and electrical engineering (with occasional bits of physics), which gave us a healthy(?) disrespect for the scholarly traditions of other fields (and our own). So what if everybody else does it differently?

Well, for one thing, it can make it a lot harder to evaluate personnel for an interdisciplinary position. One candidate comes in with 5 or 6 high-quality journal publications. The other comes in with a bunch of conference proceedings (which could also be very high-quality). Guess which one the non-CS people on the panel would likely prefer?

The one with the more convincing recommendation letters, of course.  (Ha ha only serious.)

Here in Germany, the letters of recommendation come after the finalists are selected.

A question please: what if the journal and conference were submitted at the same time ? We had this issue before. We could not cite any of them because none of them were published (even at the phase of revised journal and camera-ready conference). This issue raised a lot of opinions. What is your opinion please ?

Not sure exactly what you're asking, but outside of CS, it's OK to present a work at a conference while the journal paper is under consideration. Citations are tricky, because, as you said, there's nothing formally published to cite; however, in the conference presentation, you can always "cite" the paper as "submitted to Journal X."

@JeffE, for me the weird part is to understand which authority dictate this rule in computer science? I posted a full question http://academia.stackexchange.com/questions/61547/which-authority-dictates-regulates-that-in-computer-science-a-journal-paper-cann


text:
How can/should I indicate that it's okay to use open access content in a paper?
Suppose I want to reuse some substantial piece of content - say, a figure1 - from someone else's paper in my own scholarly work. If the other paper is under a traditional license, I'll have to obtain explicit permission from the copyright holder (usually the publisher), and then when I include the figure in my own work, I can say "Figure from reference [x], used with permission."
However, if the other paper is under an open access license or is in the public domain, and my own work will be released under a compatible license, I don't need to explicitly contact the copyright holder to ask for permission to use their content. When I attribute the figure in my work, can I still say "used with permission"? Legally speaking, I do have permission to use it by virtue of the license under which it is released (or lack thereof, if public domain), but including that phrase makes it sound like I've received an explicit statement of permission from the copyright holder, and I wouldn't want to give a misleading impression about that.
If I shouldn't say "used with permission," what would be a suitable replacement? If it's under a Creative Commons license, for example, I could say something like

Figure from reference [x], used under the terms of the Creative Commons Attribution 4.0 license

but that seems a little verbose. Is there a better alternative?
I'm also interested in how to handle this when the content is in the public domain, or is under a much more permissive open access license (perhaps one whose attribution requirement is merely "you must credit the author"). I understand that I'm not legally required to include any notice saying that I'm allowed to use content under such a license. But for this question I'm more interested in the ethical obligations that a reader might perceive.

1Even though a single figure would often be considered fair use. But let's pretend for this question that whatever I want to reuse is enough that fair use doesn't apply.
This question concerns a similar situation, but is asking about whether it is legal to reuse content at all, whereas I'm asking about how to properly show that it is legal to do so, after it's been established that no explicit permission is necessary.

Read the terms of the CC license it is licensed under. It spells out, more or less, what you should do.

Almost all CC licenses include an attribution clause. As of the 4.0 version, this means:

Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.

Clicking the "appropriate credit" shows some more information:

If supplied, you must provide the name of the creator and attribution parties, a copyright notice, a license notice, a disclaimer notice, and a link to the material. CC licenses prior to Version 4.0 also require you to provide the title of the material if supplied, and may have other slight differences.

So the easiest way to satisfy this is, indeed, to say

Figure from reference [x], used under the terms of the Creative Commons Attribution 4.0 license.

Where your reference should contain the rest of the information, including a link. If you're pressed for space, you can abbreviate the license (CC BY 4.0), or put the text in a footnote.

OK, that helps... but let me nitpick a bit. Sec 3(a)(2) of the license says the information can be provided in any reasonable manner, such as at a URL referenced in the document. The journal page for the paper I'm taking the figure from includes a copyright notice and reference to the CC license etc., so it seems like linking to that URL may satisfy the requirement without me having to include an explicit copyright notice for the figure in my work. If that's true, then what do I need to include in my work to show that I have permission to use the figure?

And if that's not true, here's a better example: suppose the figure is under a different open access license with a less strict attribution requirement - perhaps nothing more than "you must credit the author." Or perhaps it's public domain, so there is no attribution requirement and no legal restrictions at all on its use. What do I need to write in my work to show a reader that I'm allowed to use the figure in that case? That's the question I'm really interested in.

@DavidZ Best practices for attribution gives more info about attribution. In particular, your reasonable manner seems to be satisfied by citing the article in question, as it contains both the author and the source. If you want to avoid naming the license with the figure, and the entire document you're citing is under the same license, you could place the license info in the bibliography as well.

@DavidZ There are no such guidelines for material in the public domain, so anything indicating that the work is in the public domain will do. You should be very careful with this, though. A work's public domain status depends on the copyright law of the country in which it was produced. And in some countries it is impossible for the creator to place something in the public domain before the copyright would expire naturally.


text:
How common is it to work extra with one's professor after getting a M.S.?
I'm in a situation where I am continuing to work on some of my M.S. research work after I have filed and will receive my M.S.
It is fine with me and I think it's good because there were loose ends. This is computer science field, and it involves a programming project we want to improve.
In the back of my mind, I'm hoping we can write a journal article. Part of me, though, wonders about whether this may be risky.  Will my professor make excessive demands on me, even though we're officially finished?  I also need to focus on other demands, such as my job.
So I worry a little about the expectations.
How common is it to continue working after getting one's MS, but without any official agreement (i.e., I just informally meet with my prof and discuss my progress).
Also, in case you're wondering, I'm not currently interested in doing a PhD (maybe later, just not anytime too soon).

What are you worried about? Pay, publication, time commitments? Can you define what you mean by "risky"?

@Ric - Ok, sure I will clarify

Your concern that this is "risky" is somewhat vague, but generally, I'd say that working on something like this is extremely common. I've never "cleanly" finished a project, where it is fully wrapped up, with nothing else to do right as my degree was awarded, I moved to a new position, etc.
I'd say it's extremely common, and if you think that extra work might result in a publication, fairly valuable. There is the possibility of things being too demanding, but generally people are pretty understanding of other obligations that come up, especially if you let them know in advance.

Thanks a lot ! I added a little more, in regards to "risky" comment. But I think I agree - this would be valuable to me if we can get a publication

I must say, overall my professor is very understanding. So, I am more confident now that it would be good to do some more work

As Fomite mentioned this isn't uncommon. With that said, I would like to add to the answer by suggesting a more official agreement. Instead of just working on a project, it's better to actually be part of his lab (even part time). Working in a research lab after you have completed your degree's obligations shows more commitment to research and this can make you a more attractive candidate if you want to consider PhD in the future. This of course depends partly on your time constraints and partly on your advisors decision.

Thank you, this is good suggestion. I will see if my work would allow it (sometimes there are legal clauses about jobs on the side) . thanks !

Definitely! I wish you the best of luck

You mention 'your job', which suggests you've already moved on post-degree.
At the same time, you'd like to write up your work for publication, which is a very admirable and understandable goal.  If the above is correct, then you are trying to balance an academic life with an industry life, and they are seldom compatible. For one thing (and I've experienced this), your academic advisor won't 'get' the industry obligations.
From your standpoint, you've already attained the end-goal: get a job. But, if you wish to continue working to get this publication out, do it now and do it quickly. Your advisor will have no qualms about continually asking for further analyses/models/whatever so long as he/she believes you're invested, because honestly, you're working for free at that point. So get it done!