text:
Journal vs conference publications when looking for a job in in computer science
I'm currently a post doc in theoretical computer science and I have a double digit number of conference publications, about half of which are at so called "tier 1" conferences (SODA,STOC,...). Unfortunately I only have 1 journal publication so far, mainly due to coauthors dragging their feet.
Will the lack of journal publications have a great impact when applying for a faculty job in cs-theory at some point, and is it advisable to try to up this number before applying? Or is this fully compensated by having sufficiently many conference papers?

no one cares about journal pubs for hiring. Now for later, that's a different story.

And while the OP is asking about computer science, the answer is likely the same in most fields.

I suspect that disciplines like math and bio care a lot more about journal pubs, since they don't have a culture of peer-reviewed conference papers.

@Suresh: I wouldn't say no one.  The big question that hiring committees ask is "Will this person get tenure?"  A track record of pushing papers through the journal pipeline is one of the requirements for tenure at most places.  It's at most a minor third-order concern, but it's not nothing.

Or is this fully compensated by having sufficiently many conference papers? — This is the wrong question.  If you have sufficiently good conference papers, then the lack of journal papers won't matter.  Quality is way more important than quantity.

@BenNorris: that conference pubs count is a debated anomaly of CS. See for instance this article in Communications of the ACM: http://dl.acm.org/citation.cfm?doid=1536616.1536631. It also discusses briefly hiring criteria and incentives for journal versions.

CS people know that CS conferences count for more than conferences do in other fields, and although they count a little less than journals in CS, this should not be a problem. Of course there are still rankings between the various forums.
The fact that CS rank conferences higher than other disciplines only becomes a problem if you are compared against non-CS people, which often happens when competing for funding and promotions, in my experience.

Actually meant "more than conferences in other fields". I should just stop for today.

Everbody I've talked to agrees that (even high-profile) conferences don't review properly and accept based on interest rather than rigor and substance. It's quite confusing that they are valued more than journal articles, which are (apparently) usually better in this regard.

@Raphael: Having just been on the ECOOP PC, I would have to disagree. Interest is certainly an element, but as there are loads of papers choose from, rigor and substance generally won out. No paper was rejected for being uninteresting (to the people in the room).

Afaik, PC member don't read all the papars closely? You (w|c)ould have been the victim of sloppy reviews without even knowing.

@Raphael: PC members do not generally read all of the papers carefully, but it would be untrue in general to say that they don't read all of their assigned papers closely. There are always cases of sloppy reviews, but top conferences try to avoid these, even if it means assigning someone to review a paper while the PC meeting is going on. Overall, there is some truth to your sweeping statements, but in general, at top venues, they are false.

Let's hope that's true. :)

Since this was a point of discussion on my answer here, I felt this might be a good place to offer an extended analysis (since it also serves as an answer to the current question).
I had stated:

While in some fields, conference papers are akin to talk abstracts, in areas like computer science, conference papers can be very meaty and there is a high churn of papers in conferences. Top conferences can have acceptance rates around 10%, and as such, A+ conference papers are often held in high regard within the community: these venues are far more competitive than many of the good journals. Still, even in the CS area, metric-wise (for hiring, positions, funding, etc.), journals will often still count for more than a conference following the norm in other academic fields.

To which Suresh countered:

the last line of the answer is just not true at all.

and later:

It's based on my experiences (at different levels) evaluating work and people, and watching how others do it, and how people talk about research work. It's not an absolute statement, but CS departments have spent many years in battles with deans convincing them that conferences count for more than journals.

And JeffE:

"even in the CS area, metric-wise (for hiring, positions, funding, etc.), journals will often still count for more than a conference" — Speaking as the chair of the faculty recruiting committee in a top-5 CS department: This is simply incorrect. I don't recall anyone on my committee ever pointing out a CS journal paper in any junior candidate's CV. (For interdisciplinary folks, it's important for research to be published in journals in the other area: Biology research in biology journals, for example.)

This is counter to my own experience in applying for jobs, and in my current department, where journal papers are held in higher esteem. I know there are Computer Science Departments with their own by-laws and policies whereby conferences can be given as much weight as journals, but this is why I said "often", not "always". It is also my experience that such departments tend to be the more famous ones: the ones with enough clout to have their own policies. Smaller/less-well-known departments (which are by their nature more numerous) often have to abide by wider faculty/collegial policy.
In any case, to try to put some meat into the answer, I tried Googling for some tenure-track and hiring criteria in Computer Science. I'll pick out relevant quotes:
1) Department of Computer Science at the University of Vermont: Guidelines for Tenure-Track and Tenured Faculty

Publication of refereed articles in both journals and conferences is very important; in many areas of computer science, publication in top-tier conferences is considered as prestigious as publication in top journals.

2) Department of Computer Science & Engineering, University of Minnesota: Criteria for Promotion and Tenure

A 1994 NRC Committee on Academic Careers for Experimental Computer Science stated “The requirements for good research and engineering in experimental computer science and engineering (ECSE) are different from those of many other academic disciplines” and then added “Because conferences are the vehicle of choice in ECSE for the dissemination of research, well-refereed conference proceedings (as well as work published in refereed private journals) should be given as much weight as archival journal articles in evaluating a candidate's research portfolio for promotion and tenure”. Certain proceedings articles should be weighted equally or even more heavily than archival journal articles when evaluating the candidate's research contributions

3) Duke University, Computer Science Department, By-Laws

[...] recognising the important role played by conferences, book chapters, and other non-journal research documents.

4) University of Stockholm: Tenure-Track Position, Department of Computer Science

The quality of the research should be documented by presentations at well-established conferences and publications in high quality international journals and conferences.

5) Computer Science Department: Appalachian State University: Criteria for Promotions and Tenure

Scholarly Activity
Examples of Indicators of Excellent Performance

Publishes an article in a refereed journal.
Publishes a textbook.
  [nothing about conferences]

6) Wright State University, Department of Computer Science By-Laws

Primary indications of quality normally include, but are not limited to, the following:

publication of research results and of extended scientific and engineering reviews in peer-refereed journals of acknowledge stature (particularly those of scholarly professional societies such as the ACM and IEEE);
...

Secondary indications of quality include, but are not limited to, the following:

refereed conference proceedings;
...

The first two departments explicitly state that conferences can be considered as highly as journals, the next two state that conferences will be considered alongside journals without any explicit ranking, and the last two state that conferences count less than journals.
These are six examples, and are biased due to having "Computer Science" in the title, meaning that they are CS-specific criteria (whereas I suspect many smaller departments would fall under more generic by-laws).
Though many CS departments (esp. the more prestigious ones) have won the battle of giving conference papers their due weight, it is still my understanding that other departments have not, and must fall in-tow with faculty/collegial guidelines.
So to answer this question:

Journal vs conference publications when looking for a job in in computer science

It depends. Though I may not have fully substantiated this here with only two anecdotes, I still hold by the position that in many CS departments (particularly smaller departments), journal articles often (not always) count for more than conference papers by merit of simply being journal articles.
(Some related discussion here.)

The letter of the bylaws is not the same as what actually happens 'on the ground'. I'd argue that if a department (as you suggest) is preferring journals to conference, they are going contrary to the actual practice of research in many CS subdisciplines.

What Suresh said. Also, you're conflating hiring policies with promotion and tenure policies. Your original claim was about the former; your later evidence addresses the latter.

Suresh, I don't disagree. @JeffE, the question is indeed about hiring, but my original claim was not solely about the former; verbatim: Still, even in the CS area, metric-wise (for hiring, positions, funding, etc.) .... The quotes I provide refer to positions, but also refer directly to how research output is reviewed in Computer Science.

I don't think this will be a problem for your first faculty position. In TCS people will appreciate it if you publish journal versions of your conference proceedings. However nobody will expect, that you will do this immediately. Also, imho, having SODA/STOC and FOCS publications is what counts. Other things (teaching experience, grants, making a journal publications out of your conference contributions) are important but secondary criteria.
It is likely that many non-theory CS people are in the hiring committee. In other fields of CS journal publications count even less.


text:
Submitting TeX to ScholarOne
I'm trying to submit a latex document to a SAGE journal using ScholarOne.
I'm having a hard time.
The (poor) documentation says that it accepts tex files, but the pdf it produces says that it cannot turn my tex into a pdf.

Note: The following files were submitted by the author for peer
  review, but cannot be converted to PDF. You must view these files (e.g. movies) online.
response.tex

Is this just what it does with tex files? Should it compile them? I don't know. If it is not compiling, how do I get the error message?

Both the Royal Society of Chemistry journals and the American Chemical Society journals use ScholarOne Manuscripts™ as their web submission platform. In both cases, the system is able to compile LaTeX documents into a PDF file. There are, however, strict requirements about the type of LaTeX document you can use. These are spelt out in a specific help section entitled “Preparing and Submitting Manuscripts Using TeX/LaTeX”.

ACS Authors have two distinct options for submitting work authored in TeX:
FAST Submission: Submit your own PDF file—and provide the native TeX and figures in a .zip file—and your own PDF file will be used for the review process.
STANDARD Submission: Submit a complete and properly styled TeX file, figures, and references using the achemso style package. The TeX files will be converted to PDF by ACS Paragon Plus and used for the review process.

The help further states:

When you upload your TeX/LaTeX Manuscript File, the system will analyze the file, and identify additional resource files referenced within the file (such as image files and bibliographic files) that are necessary to complete the document.

and

Manuscript files prepared in TeX/LaTeX (Version 2.02 and earlier) will be used in journal production provided you adhere to the following guidelines:

Use only LaTeX2e. Use of plain TeX and RevTeX is discouraged.
Use generic style files whenever possible. Minimal formatting is all that is required in the document.
Include all sections of the article in a single file. Include the list of references within the LaTeX file. Captions must be created in the TeX/LaTeX document.
References should be cited in text using \cite{}, and the list of references should be itemized using \bibitem{}.
Use \frac to build fractions. Do not use \over or \stackrel to build fractions in displayed equations.
Use \sum_{}^{} for summations and \prod_{}^{} for products.
Use the array environment only to build true matrices, not for aligning multiline equations.
Use characters/symbols in the generic LaTeX character set only. Symbols from other sets may not translate correctly.
Avoid extensive use of \newcommand and `\def .
Some style files (text and bibliographic) that are available in the public domain may be used for most ACS journals, e.g., jacs.sty and jacs.bst; jpc.sty and jpc.bst; achemso. The use of the achemso style package is strongly encouraged. Please note that the ACS does not provide support for using these files.

A further requirement, which is not actually listed, is that all figures should be in the same directory (you cannot upload a directory structure). And, as noted, if you use bibtex, you have to run it manually and include the content of the .bbl file into your .tex file before upload.

So, in conclusion: ScholarOne Manuscripts™ has the capability to support LaTeX compilation. Whether this is enable or not for your specific journal/publisher, I cannot know. In any case, check the documentation! (or ask the editorial office)

I did all of this and still cannot make the site compile my paper. It is a useless piece of junk, and the tech support is so bad that apparently no one there knows what Latex is.

For me, ScholarOne (Wiley submission) did not accept PDF upload and did not convert the latex sources. My solution was to convert the PDF to PS using pdf2ps (GhostScript). This was then properly converted back to PDF by ScholarOne. I absolutely do not understand why they are using such a stupid and confusion submission system, sorry...

[This might be more ontopic at tex.stackexchange.com.]
What you received sounds like an error, but is vague. First, of course talk to technical support if you can get hold of any. These systems are often set up to only accept a minimal set of LaTeX packages. If you are using any non-standard packages, see if you can remove them or include the functionality in the document itself. And of course talk to technical support if you can get hold of any.
See also Submitting a journal article as a single tex file.
EDIT: Peter says the system is not trying to convert at all, and he should know. However, I'll leave this answer here for now. If anyone thinks it should be removed, let me know.

I finally figured this out after about 3 hours. Thing is, even though the system tells you there was an error, it actually HAS uploaded your files. You can see this if you click "Update file order", and here you can download the LaTeX log to see what went wrong. In my case it was because the system didn't have all the figures yet, because it only lets you upload 3 files at a time. Once I'd uploaded all the figures, and deleted all the extra files I'd uploaded in frustration, I was able to force it to compile by clicking "View PDF". Finally submitted. I hope this helps someone, somewhere.
Worst. Manuscript. Submission. System. EVER.

I encountered this problem while trying to submit a manuscript to Publications of Astronomical Society of Australia (PASA) via ScholarOne. When I uploaded the latex source from Overleaf, the submission system complained "Unable to find any suitable files to generate the proof". It is sad that this old problem still exists.
The problem seems to be with ScholarOne's latex compiler. I have found it to be more restrictive than other similar systems and tools like overleaf. The problems are the following:

ScholarOne does not work well with .bib files. Their tech support told me to add the citations directly to the main .tex file rather than putting them in a .bib file. This amounts to replacing the \bibliography{} command with the contents of the .bbl file generated by BibTeX. This is quite surprising since the PASA template in overleaf uses a .bib file for bibliography.

ScholarOne does not work well with \include{} statements. I had to create one big .tex file by manually copy-pasting the contents of the .tex files which are \include-d in the main .tex file.

ScholarOne does not use pdflatex. This means that if you add PDF or PNG images in your manuscript, the compiler won't be able to determine its size. The safe option is to use images in the EPS format. I also had to flatten the EPS files (using Photoshop/GIMP) since their latex compiler can't deal with layers. I also added \usepackage{epstopdf} to the preamble.

File names can't have spaces in them. (Which is in general good latex advice.)

Some packages may not be supported or may not work as expected. In my case, the tcolorbox package did not work.

TL/DR: ScholarOne needs a lot of handholding to compile any decently complex latex document.

As far as I know the Scholar One Manuscripts (S1M) system can convert Word files into pdf, it does not contain a LaTeX engine but will accept PDF files. In the journal I work (which uses S1M), we accept LaTeX manuscripts but explcitly ask authors to produce a pdf of the document for reviewing purposes. It is a mistake or omission by the journal to not explain that the file for review must be either Word or PDF. The LaTeX files can be uploaded but must be marked as "Not for review" which means they are not included in the file sent to the reviewer. You need to check with the journal how they prefer to handle it. In my case, I do not need the LaTeX files until the final revised manuscript so uploading them is of minor use; this, however, might vary between journals.
I do not know of any commnercial manuscript system in use that produces PDF from submitted LaTeX files but then I do not know all journals. In any case, the proper way with S1M should be to submit your files in LateXed PDF format (e.g. PDFLaTeX).

Actually, systems that create PDFs from LaTeX are not uncommon. I've come across more than one. I think initially the journal will accept a PDF, but eventually it will need the LaTeX file(s) to work with. Though I suppose it does not need to be necessarily uploaded through some automated system in that case.

IEEE does pdf compiling. But thanks for the insight about S1M.

It is possible but not journals I have seen at Wiley, Elsevier, Springer, Sage, Copernicus, AGU, IGS.

TeX support is common in math and physics journals.

I'm going through some pains right now trying to submit a latex file to this journal which is published by Springer. So at least the manager by Springer allows you to compile latex files (problem currently is bibliography).

I think I once submitted to one of the ACM journals that had a system that converted PDFs to LaTeX. TOMACS, if I recall correctly.

-1; inaccurately contests the premise of the question. Some major journals that use ScholarOne (e.g. Bioinformatics) in fact require you to upload source .tex rather than output .pdf files.

source: Stack Exchange

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

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

sort: votes


text:
Pointing to problems without suggesting solutions
As a peer reviewer, I sometimes feel there are issues in the manuscript but I'm not sure how they should be corrected/addressed, partly due to my inadequate expertise in those exact issues.
I also sometimes find some words/terms are incorrectly used, but as a non-native speaker I can't easily suggest alternatives.
Should I just point to such issues anyway, or ignore them since I couldn't suggest solutions?

If it ends us as a major revision that comes back to you with changes addressing your issues in some way, how would you decide if they have done so sufficiently?

@ASimpleAlgorithm perhaps that is why some papers have more than one review cycle...

@ASimpleAlgorithm It is much easier to check that a proposed solution is correct, than to come up with it in the first place.

@FedericoPoloni that isn't universally true. For example, the proposed solution may be wrong (hence there are very many extremely easy options) whereas the problem of determining if it is correct may be ill-posed or intractable. But my question wasn't necessarily rhetorical. In the kinds of problems you are thinking of, that knowledge of how to determine if a solution is correct can be used to provide guidance or requirements for the authors then when asking for revisions, rather than simply pointing out a shortcoming.

@FedericoPoloni This is basically what the P vs NP problem in computer science is about. :)

For the first concern, you can say to the authors that the discussion on X is insufficient, and you interpreted it as Z or that it doesn't cover case W.  Request for more information.  Hopefully, they will come back with a version that addresses your concern. You don't have to be exact.  As for presentation, you can outline consistent problems or just say the writing is not up to standard.

Does "peer review" mean you have to re-write the material, or just point out where the flaws may be and the author is meant to sort them?
I suggest it is the latter, so point them out and expect the author to edit / correct or justify what they meant.

I think there is a middle ground between "re-write the material" and "just point out where the flaws may be". I'm not familiar with academic processes but as a general practice the most helpful feedback usually does more than just point out flaws; it steers people in the right direction. This doesn't require doing the work for them. I think your answer hints at a false dichotomy that David Richerby's answer addresses a bit better.

@quant so how does this "it's the authors' responsibility to write their paper" in one of the other answers sit with you? Perhaps the primary function of a reviewer is to point out the issues and a secondary function is to provide solutions. How have you found the review process for a paper you submitted? I found it helpful - especially when discussed with my supervisor.

Let us continue this discussion in chat.

This is roughly my attitude, but:  Sometimes I'd rather (because it's less work) suggest a different wording for a sentence or even a paragraph, rather than see the paper again.  If the author takes my suggestion and the editor sees that, the review process is over.  Otherwise, I get another thing in my inbox.   And sometimes I'm more altruistic; wanting to help a student or non-native speaker learn to make better papers.

Yes, you should point them out. You should point out solutions to problems when you know what the solution is but, at the end of the day, it's the authors' responsibility to write their paper, not yours.

A story (and many other intersting ones) I once heard from an editorial board member of Physical Review Letters, who gave an overview talk on the editorial process of that journal at a conference, was that sometimes it happens that the reviewer switches sides and becomes a collaborator of the authors they reviewed initially.
While at first this sound strange (certainly did to me at that time as a young PhD student), I think this is more appropriate then outlining new solutions (which is nice but not necessary) the authors did not think of. I also don't think 1-2 major revisions are a good spot to discuss/recommend in-depth new solutions to a manuscript. It's common to request further data analysis/evaluation or additional measurements. But if there are major flaws in the manuscript/methodology, you should point to it, but personally I would advise/vote then to reject the manuscript for this reason.
Concerning grammar and language mistakes: The associate editor can reject publication of a manuscript, even if the peer reviewer don't vote for further revisions (due to content or language level). It's not your duty to improve the language and associate editors regulary recommend commercial english editing services, when the language level is below the standards of the journal. Personally, if I see a lot of spelling and grammar mistakes, I don't point the authors to every single one, I mention 2 or 3 to the editor and the rest is his job, not mine, especially if the manuscript is multi-authored.

You should definitively point them out, the editor might want to get an additional reviewer on those issues, and the authors can still write a nice rebuttal letter saying that the problem confusing you had been thouroughly addressed half a page earlier and they don't feel responsible for your short attention span or your incomplete grasp on English grammar. ;-)

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


text:
Flow of the Discussion section
Some journals expect the Discussion to have the following structure and order (with some flexibility):

summary of results
strengths and weaknesses
interpretation/context/comparison with previous studies
implications

This makes sense: discuss the study strengths and limitations before interpreting the results and discussing their wider context and implications.
But how about putting the "strengths and weaknesses" after "interpretation/comparison", or even at the end after "implications" (and before the conclusions)? It this less logical/convincing?

I think this mainly depends on the journal, and of course the specific study in question.
While the first order certainly does make sense, the second approach coule also be viable for certain studies.
An example would be a study where a somewhat small sample was conducted, and the results show a significance of some kind. You could go on and discuss the reason/interpretations for the significance, and later mention that to quantify/verify the effect, further studies with a larger sample size should be carried out.
Again, this is highly dependend on the study and the format, so if a journal specifically asks for the first approach, you might want to follow their guidelines.

Personally, I have seen a reasonable amount of diversity (in same journals) in how discussion was organized.  As long as it flowed, nobody kvetched.  Even to the extent of if you want to do Results and Discussion separate or same section (I always preferred same, but if I had a need wouldn't have worried to vary the pattern).
P.s.  If you could tell us the journal and the field, it would help.  Also is your question/concern based on actual experiences of being asked to revise org structure or more conceptual of a concern?


text:
Purpose of IP address and timestamp on open-access full-text article
I understand that some pay-walled journals include timestamp and IP address and/or institution to full-text PDFs to track copyright violations.
However, I also saw an open access journal doing the same despite allowing non-commercial, attributable redistribution and modification.
If that journal grants such rights to readers, then why does it include IP addresses on the copies they download?

Most likely, they are still doing it to track copyright violations. If the document is made available under a license that permits non-commercial, attributed redistribution, then the publisher might wish to collect evidence in cases of commercial or unattributed  distribution.
It's also possible that the same publisher, or even the same journal, also has articles that follow the traditional "all rights reserved" model, and that this information is applied to all downloads indiscriminately.

Note that to give a license on a work you must hold copyright to it. Granting the license doesn't affect your copyright. So the issue is really the same as for more formal (commercial) journals.
The situation might be different for things put "into the public domain" for which you formally give up your copyright. Then the public owns it. But licensed works are still owned by their creators.
If you use a licensed work, the license is a contract backed by the copyright. Without the latter, the former has no meaning.
I can license my own work, but, of course, I can't license your work. It is copyright that makes that clear.
See this, for example:Creative Commons
Likewise, see the discussion of Copyleft at Wikipedia.
Without copyright these could not exist.


text:
Are non-first authors less likely to be invited for peer review?
In fields where the order of authors matters (e.g., health and medical fields), does the order of authors of published papers generally affect how editors choose peer reviewers for new submissions?
Can someone who has never first-authored a paper, but is listed as a non-first author in many papers (with several other authors), be invited for peer review?
Is there any relevant published data?

Depending on the field and area, you might be happy to even find a single person with the needed knowledge willing to review; I don't know how it is in health though.

Certainly someone with no first-author papers (or indeed no papers at all) can be asked to act as a reviewer. However, I think it is relatively unlikely, if only because it can be hard for the editor to be confident what expertise that person actually has (perhaps they're the statistics guru and don't know anything much about reaction pathways in biochemistry...). In contrast, it is a reasonable first assumption that the first author of a paper is broadly capable of reviewing similar papers.
Of course there are exceptions: the editor may know the individual personally; the individual may be recommended/suggested by someone else; they may have a strong reputation in their own right without ever authoring papers (e.g. if they are a specialist lab technician).


text:
What skills can I get during a PhD to be competitive on the job market against non-PhD holders?
Earning a PhD help you learn tools and techniques in your field, and lets you become an expert in a very specific field of science. However, once you get your degree and try to enter the labor market, you're competing against people who are younger than you (i.e. recently graduated non-phd engineers) and may have actual work experience (i.e. non-phd engineers with a few years in the market).
There are, of course, some positions in which they cannot compete, including research and teaching position. Those are the minority, though... in most other fields it seems that holding a PhD is not as important as (for example) work experience.
So, I would like to know:

Is work experience more important than having a PhD in the many work environments?
What skills can I acquire/demonstrate during my PhD to become more "valuable" than a non-PhD candidate for the same job?

Thank you for your feedback. Maybe it's because I don't know what can I do once I get the degree, that it doesn't seems broad to me (that's the question I'm  looking for an answer here). But you're right that it's excluding academia.

@earthling - I disagree; this is very relevant to "life as a graduate student, postdoctoral researcher, university professor". The majority of PhDs end up leaving academia, so they probably care about this very much. Given all the edits (including my own), I'm reopening the question... please flag if you think it should still be closed.

What skills can I get during a PhD [...] ? The skills the student tries to get and the ones related to his major. The question still seems too broad to me.

This question is too broad, but I have a feeling it's a commonly asked one, so I'm going to try to answer it anyways.
To address (what used to be) your second question first: holding a PhD does not make a job candidate any more desirable for the vast majority of positions. Indeed, it can be a factor against the candidate, as they will be perceived as more expensive. For positions where a less-qualified candidate could also fill the role, being overqualified is rarely a good thing. Jobs that are specifically looking for a PhD will typically state that in the requirements. For example, "Masters required, PhD preferred" is a common one in certain parts of the banking sector. However, for entry-level positions (data entry, lower-level analyst roles, etc), you may be at a disadvantage.
Regarding your first question, though, you're being overly harsh on yourself. The process of earning a PhD is significant work experience; indeed, that's your main selling point when looking for your first job. Depending on what you did, you will have some or all of the following experience:

Identifying, clearly stating, and figuring out how to address a problem - this alone qualifies you to be a consultant at any large firm; this is all they do, all the time, for different clients
Project management
Advanced technical writing - your thesis, academic publications
Communication skills - working through the peer-review process
Public speaking - presenting at conferences
Experimental design - your research project
The art of researching - the simple knowledge of how to properly find articles, sources, etc
...

Even better, you've been doing all that for four years. You should be selling every single one of those points as hard as you can when you move to industry.

EDIT: The above answer stands for the edited second question as well; as a graduate student, you will want to learn all of the above if you wish to enter the workforce. More specifically, though, almost industry positions seeking PhD candidates will apply to value the following three above most else:

Self-starter - shown in that you got your work done
Collaborative - demonstrated through successful collaborations with other researchers (successful = researched together, published together)
Good communication - demonstrated through publications, public speaking, conference presentations, teaching, etc.

During the PhD, aim to do those things, and during your job search, emphasize all those traits in your resume and during interviews.

I don't think these skills you have listed are necessarily gotten during a PhD period. A PhD student and an engineer, both can get public speaking, communication skills, etc even during their professional careers, BSc internship programs or even by registering in some general social classes. Even almost every MSc student and an engineer with masters degree has learned how to do research by attending a research methods class. The user is looking for skills which are gotten specially by studying PhD.

+1 for You should be selling every single one of those points as hard as you can when you move to industry. You should always see the skills you have that others don't - and good communication skills is no so common for most engineers (at least the ones I have worked with).

@CharlesMorisset Who needs academic writing/research skill in engineering industry?

@CharlesMorisset of course, but I think any employer may pay more for a PhD graduate just to handle his report writing tasks.

@EnthusiasticStudent - (1) See Charles's comment, that was my point. (2) I cry to see your comment regarding writing. The most important thing you will learn is how to communicate. There are hundreds of thousands, if not millions, of skilled engineers. There are far fewer skilled engineers who also know how to communicate.

@eykanal You've mentioned Advanced technical writing - your thesis, academic publications. Despite the case that the employer is doing a research project, he doesn't need an engineer who is professional in doing research/writing/conference presenting, etc. MBAs minoring marketing are almost the most skilled presenters and communicators. In an engineering company (for instance consultant engineers) the employer needs a skilled engineer who has experience in industry and who is able to do his engineering work. They are doing engineering project, not conference presentation or academic project.

@EnthusiasticStudent - As an engineering PhD myself, and as a manager of other engineers in an industry position, I could not disagree with you more. Engineers need to be able to not only do work but also communicate that work both internally and externally in a clear and concise manner.

Very complete answer, thanks. So, as a PhD I develop some skills that would be harder to grow in the industry. I hope than in three years from now I read this answer and can see those skills in me.

Only four years!?

I think the answer in large part depends on the kind of job you want to work when you have completed your degree. You mention that you do not know the kind of job that you want to work when you get out of a the program. This is unfortunate. A Ph.D. = specialization, a mistake many Ph.D. students make is to assume specialization = job. In fact, specialization can make it harder to find a job. If you're goal is to enter into industry than I think you have an interesting road to navigate. The job market will be kinder to you if you have a range of skills that you are really good at, the Ph.D. program is going to pull you in the opposite direction. You're wise to want to understand better what it is about getting a Ph.D. that will make you standout in the workforce, but you'd also be wise to look at some skills for your desired positions that you might not develop while in the Ph.D. program, and look to develop those too while you are in the program. For me these skills are computer science skills. For you these skills might be something different.
Unfortunately, unless you are in the hard sciences, and even then specialization can be a demon, having a Ph.D. might not mean all that much when stacked against someone with a Master's, wider breadth of skills and more industry experience when looking for industry job.

I know in which direction I'd like to go, but I'm far from knowing what work I'd like to have. As I said in the original question (not the edited one), during the first years of my bioengineering courses, I didn't knew which were the different posibilites to work in as a Bioengineer. Luckily, I found in the PhD something I like. And beside that, with your way of thinking you need to have your life figured out up to when you are 40, think that I'm not able to do now (neither when I was 18 and I choose to get in Engineering).

@Alfonso Santiago: that's not what I'm saying at all, thank you for putting words in my mouth. ;) What's the biotech industry looking where you want to work? Are you specializing in something that will make it difficult to find jobs in those places? Do you want to work at.  Big company, startup or be flexible enough to do both?

sorry if I misunderstood your answer. For me, knowing what I'd like to do 5 or 10 years from now is almost imposible. Now I'm working in high performance computational biomechanics (HPCB), something very specific, I think, but those simulation skills can be useful in other areas too. I, actually, don't which is the demand of "HPCB simulators" in the labour market, that's something I should answer myself. About in what kind of enterprise I'd like to work, I think that I'm not brave enough for a startup... but maybe my bravery would change three years from now ;)

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


text:
Is using an answer I posted online on Math.SE considered plagiarism?
To expand on the question, I recently (as in yesterday) posted a question on Math.SE and also wrote my answer in the post, claiming that my answer was wrong. One answerer pointed out that I was correct, but simply needed to do a quick deduction step, after which I edited that question with that deduction step.
So if I use this answer now in my assignment, will it be considered an academic offense? None of my university's resources are helpful at all in this regard. I'm a student in the sciences, and all the 'resources' of the university are towards arts students. I'd like a clear cut answer because informing my instructor that I posted my own interpretation of a question on an assignment is really out of the question, since I don't know if consequences exist for that.
I'm already looking for an alternative answer, but I'd like to know if using my current answer would be an academic offense. Thanks.

This has already been answered on http://meta.stackoverflow.com, I believe

I'd like to know if using my current answer would be an academic offense.

It's impossible to determine this without more information about your university and course policies.  If you're honest about what happened, then I doubt you could get in a lot of trouble for this, but of course I don't know the policies and potential consequences in your case.  At my university different courses can have different policies on collaboration (regarding what's allowed and what sort of acknowledgment must be given), but they should be explained at the beginning of the semester.
If I were teaching the course, it wouldn't bother me that you got advice on this problem, since it looks like you did most of the work yourself and learned something from the feedback you received.  However, I would be unhappy that you posted the homework problem and a complete solution online, thereby making it easy for other students in the class to copy your solution if they know about math.SE.  If the grader detects several solutions with nearly the same wording as the one you submit, then you may all be accused of cheating.
If you can't find a clear statement of the relevant policies on your course or department website, then I strongly recommend asking your instructor how to handle this.  In theory that could end badly, but I don't expect it to.  Bringing it up yourself is almost certainly better than letting the instructor discover it, and it would mean you could stop worrying.

The weird thing about this is that the question that I ask is my interpretation of the question asked in the assignment given to me. It is just one possible interpretation, it is not a direct copy-paste of the question wording given to me. Since I'm required to submit a proof, the proof will basically be the same, hence me being worried. But thanks for the advice.

Only your instructor can answer this question.
If you were a student in one of my courses, consulting Math.SE and using the comments/replies you received would be fine, provided you cited them properly and you rewrote them in your own words.  But I believe I am in the minority.  Most faculty in my department would consider consulting a StackExchange site in the first place to be cheating.  You just have to ask.

The offense lies in taking material without consent or proper acknowledgement. In your case, you can simply acknowledge the comment so that it is clear that you received feedback to improve or correct your work. I think this help can be equated to peer review. Hence I do not think consent is necessary as long as the person providing the help is explicitly acknowledged.


text:
Note taking software: referencing text to searchable keywords
I'm looking for software for macs geared towards organizing and referencing the text in notes. I'm currently studying pathology and would like to be able to "tag" a topic/heading within my notes (not the entire note itself) with a keyword that is searchable. For example, if I have Rheumatoid Arthritis, I'd like to be able to highlight it, and tag it with  multiple keywords or hashtags such as "hypersensitivity reaction type IV" or "#hypersensitivityrxntypeIV" and be able to search those keywords and have any of those topics I've tagged show up in the results. Anyone have any suggestions?

Maybe this would have a better chance of being answered on AskDifferent?

I believe this is not an academic-specific question, and would therefore propose it be moved to Software Recommendations.SE.

You may be interested in using MaxQDA, they are just now preparing to release a mac version. Although it is a software geared towards textual analysis and qualitative researchers, it can tag pieces of text pretty much like you say you want to do.

+1. organising and comparing text fragments by keywords is what textual analysis is all about.

MaxQDA and others such as Dedoose are useful and powerful qualitative software packages to tag and sort snippets of text in this way.
However you might want to try the free trial of Quirkos, which also has a Mac version, but is designed to be simple to use and quick to get started with.

For regular note taking, I use Evernote and Google Drive. Both tools are very useful for writing when you are 'in the wild' (e.g. at meetings or observing cultural behaviour). If tagging the specific file is sufficient, Evernote is brilliant for just this purpose.
However, for analysis purpose I have recently grown very fond of MaxQDA. Among a bunch of great features, this tool allows for 'coding' (tagging) paragraphs within notes and transcribing recordings. You can try it for free for 30 days.
I believe in using the right tool for specific purposes and will therefore recommend Evernote or Google Drive for note-taking and MaxQDA for the actual analysis.

Dude, try Evernote. They have a free and payed version, thats work very well. The most incredible feature is that you can search words (or Tags) in a pdf file. Try This.

Can you please say why you think it works well?

I +1 for Evernote. It's available on all major platforms including mobile, and has robust search features. Just take a look at this table for all the ways you can search, including tags, which you mentioned. https://evernote.com/contact/support/kb/#!/article/23245321

I don't understand this answer; could you elaborate? Every pdf reader can search for words.


text:
Finding academic collaborations by location
What is the best way to find academic collaborations between two locations (e.g. Berlin and Australia) occurring within a certain field / topic?  Some variety of massive, searchable, citation / co-author network map would be ideal, but the examples I can find so far seem quite limited.

Not exactly the same thing, but maybe worth mentioning: one can search the ResearcherID database (http://www.researcherid.com) for a specific author, and obtain a breakdown by country or a map of where his/her collaborators and citers are in the world.

You can, to some extent, use traditional publications databases for that. For example, with Web of Science:
(CI=Berlin) AND (CU=Australia) AND (SU=Chemistry)

will give you the list of publications with affiliations listing both Berlin and Australia in Chemistry. You can then skim through the list, or analyze it further, for example here by institution:

Another way to find a destination for your next holidays can be:

Start with a senior colleague you know well

Try to see who he's been working with recently: find papers, sort by institution

Pick your location and ask him to put you in contact with them!


text:
Publishing as sole author on politically charged topic
I have been working on a manuscript on a politically charged topic, I will be able to complete this work mostly on my own so I should be able to submit as the sole author.
However I am concerned to submit as the only author because of the nature of the topic and because I do not have any previous publishing record so my submission might be overlooked. Should I try to get someone else more known on board, or try to publish this on my own since I have done all the work?

Have someone who's an expert in the field review it and tell you whether it's worth submitting. If they say yes, go ahead. If they say no, ask why and improve it. If they give other suggestions, listen carefully; that's why you asked their advice... Seriously, I think that will give you better guidance than asking us here with absolutely no context.

@keshlam I have actually already done that and got positive comments.

In that case, what's the hesitation? Sharing the blame won't keep you from being blamed if people want to blame you. If you believe in your work enough to publish it, I'd say go ahead and publish; if it draws flack, get some of your pre-reviewers to send response letters and get a conversation started...

You are a PhD student, right?  So when you begin a piece of work, you ask your advisor about it for advice, especially if you wonder whether it will be worth your time.  What did your advisor say about this?

@PeteL.Clark this work is completely unrelated to what i am doing for my phd and my advisor is not related to it, it is a school project that was done well enough that it might be worth publishing, so i always worked on it on my own with very little supervision.

I want to begin by acknowledging that I am stepping far outside my core expertise by answering this question: as a mathematician, the chance that I would write an academic paper on a politically charged topic is essentially zero.
I firmly believe that PhD students have the right to work on whatever they want in addition to their assigned thesis work and duties.  (In fact, everyone does.)  When I read other questions on this site in which students in the laboratory sciences say that their advisor tries to shut down their side interest in X, I got dismayed.
Being a PhD student requires a great deal of single-mindedness.  I think it's nice for a PhD student to have at least one project or publication which is not directly connected to the subject of their thesis work: that shows breadth.  However, this should not come at the expense of their thesis work.  Sometimes people with very independent personalities put more time into their independent work than their guided work, and this can be a good decision, but they should still get guidance on that decision!
In this case, I am a bit concerned that the OP may be going out too far on her own.  This is a side project which has some difficulties -- including political ones -- to the extent that the OP is wondering whether she needs more faculty assistance.  She also says that she has not published anything previously.  So the OP has chosen in my opinion a rather tough side project.  How much effort will it take to bring this project to successful completion (including publication)?  The OP doesn't know; that's part of the question.
I recommend that the OP talk to her advisor about this project, including the question of how much time to spend on it and whether to try to publish it now, later or never.  If the paper is sufficiently politically charged, then it has an unusual property among academic papers: publishing it may damage the OP's reputation in certain circles.  This is already worth a serious conversation with the advisor.
Finally: adding coauthors solely to increase the chance publication is both unethical and a suboptimal strategy for the solo author.  I have a different idea: if the paper is hard to publish because the author is so junior, the author can just put the paper in her pocket until she is less junior, and then try to publish it later.  (There is also something to be said for not having your first publication be controversial, at least in many academic fields.)  What a PhD student needs to do most of all is complete the strongest possible PhD thesis, and this strategy ensures that the OP is not getting derailed from that.

Re mathematicians not writing politically charged papers: you never know!  See Redistricting and the Will of the People.

@Bren: I did say "essentially".  Also my phrasing was not perfect: what I meant to write is more like "The chance that I would write a politically charged academic paper is essentially zero -- and, to properly understand this, you should know that I am a mathematician."


text:
how much is a typical budget for publication costs in a five-year project that requires open access?
I need to budget the cost for publication for a European grant that requires open access, either green or gold, and I am struggling to figure out the costs over a five year period. Some multidisciplinary journals can have open access fees up to €10,000 and specialized journals between €2000-4000.
When I add things up it comes to a considerable amount, around €100,000+. I find unreasonable to pay this much for publishing when research money should pay for research, so I am wondering how people budget these publication costs in recent funding application. What are some real costs after 5 years?
I know that in some cases the green open access does not cost because the publisher allows to post the accepted version on a repository within six months. But publishers are becoming more restrictive about this.

It would help if you specify the field.

Everything above €500 seems absolutely unreasonable.

@Arno in my field (theoretical biology), I am not aware of any decent journal that has open access fees below (or even close to) €500.

@Theoretician My understanding is that the actual costs of running an open access journal frugally boil down to about €200-300 per paper, based on experience in math/CS. A biology journal might be a bit more expensive if they re-typeset everything, but if that actually costs thousands, the effort doesn't seem worth it.

@Arno Yes, but sadly the journals charge authors way more than what it costs them to process a paper...

@Arno math journals don't grant waivers to authors from developing countries?

@ThomasSchwarz I am in life sciences but I specified the costs of open access in my field. Multidisciplinary journals charge a lot and those include your field as well.

100,000 USD will pay for 25 publications with a price tag of 4,000 USD each. It sounds like you are planning for a major research project. If you are applying for one postdoc and five Ph.D. students over three years, suddenly 100,000 USD for publications sounds like a lot less, no? Also: publication is part of research, so with OA, publication costs are research costs...

Depends also on the country. As researcher at a German university, you could get away with zero publishing costs (for the project budget) if you stick to journals covered by suitable open access agreements (such as project DEAL), or if your university provides open access funding from other sources.

@StephanKolassa, the project is indeed large and over five years. It is not so much the number of publications but if you want to publish 3-4 articles in multidisciplinary journals you are already around the 40k euro mark + all the rest. So essentially the cost of publishing has been offloaded to researchers but publishers still make the same amount of money. So the problem is not been solved really.

Exactly. It's a case of politicians trying to look good ("We will require OA publishing, because that will democratize research" - which of course indeed is good), usually without increasing the budget for funding, so researchers now need to pay for this out of the same amount of funding.


text:
Is participating in open peer reviewing good or bad for early career scientists?
I see a few questions about open peer review (OPR), as more publishers move towards open access and open review.
As an early career scientist I wondering if publishing my name as a reviewer is a risky business as I am usually very thorough in my reviews but also try to be as fair and friendly as possible.
So I know that being a reviewer doesn't really count that much, it seems that publishing my name has potentially more pitfalls than advantages. I don't like to make "enemies 'among my peers as I respect their work, so I am afraid that my comments might be taken the wrong way and create potential conflicts. This for me would be the only reason not to participate in OPR. In my field people are mostly open and friendly, but of course there is competition.
The only possible advantage I see is that when I am being reviewed I might receive a more fair treatment similarly to the one I have given, but this seems less likely as the pool of potential reviewers is large.
Are there more advantages or disadvantages when participating in OPR?

How early in your career? Student? Assistant Professor?

@Buffy, I don't really think students review papers. But in any case from late Phd until you are not well established in the field.

Note that "Open peer review" can mean different things, not all of which require that reviewers make their identities known. I'm assuming the question here is about the "Open identities" variety of open peer review (in the taxonomy of https://en.wikipedia.org/wiki/Open_peer_review)

My opinion:
I don't see your reasons either for and against as compelling. I suspect it's neither risky nor significantly advantageous.
You should take this on if you think it a good way to contribute to progress in your discipline. You might learn something too.

Agree.   The reputation effects are negligible.

"The reputation effects are negligible." Maybe in the case of a mediocre review. I have received a few reviews in the past that were very so useful that I would consider them as formative for my career, by inspiring significant follow-up work. These reviewers would have received a boost in my recognition if they were known to me. There is also the converse case (see my answer).

@AnonymousPhysicist: you've commented on every (I think) answer here saying that "reputation effects are negligible". Granted that this is a very hard thing to measure in either direction, can you point to evidence one way or the other? (I would guess that we could come up with anecdotes supporting positive reputational effects from a well-received review or political backlash from a badly received one ...)

@BenBolker Sure, there are many thousands of scientists in my field, but the average paper is read by fewer than ten of them.  One can extrapolate that fewer people will read open peer reviews than papers.  Even fewer people will care about and remember who wrote those peer reviews.  Therefore reputation effects of open peer review are negligible.

https://www.smithsonianmag.com/smart-news/half-academic-studies-are-never-read-more-three-people-180950222/ "In the 2007 study, the authors introduce their topic by noting that “as many as 50% of papers are never read by anyone other than their authors, referees and journal editors.”

Keep in mind that your peer reviews cannot be targeted to the people you want to influence as that is an unethical conflict of interest.  This is why a third party editor picks the reviewers.

In the majority of cases, the net outcome for you is probably positive, assuming that your reviews are indeed fair, and most people have the necessary judgment to recognize that.
The tricky part is the minority of cases in which you might have to write a fair but negative review, and (some of) the authors have a personality that cannot deal with criticism. This definitely applies to a certain percentage of people. The ugly part is that such authors might have a tendency towards retaliation behavior, and dealing with that you might want to avoid, at least until you have tenure.
In the best case, the reviewing system allows you to reveal your identity in the case of good news, and conceal it in the case of bad news for the authors.

Risk of retaliation is negligible.  If the person has power over you, you should not be peer reviewing their work anyway as there is a conflict of interest.

@AnonymousPhysicist I think you significantly underestimate the number of people who at some point will have power over OP. The person could in the future review some of OP's papers and grant applications and may be involved in a hiring decision that is relevant for OP.

Highly improbable.  And none of those decisions are made by a single person in academia.

If the author is an influential senior, it's more likely than not that they belong to the pool of potential referees. In the case of a grant proposal, a single "meh" review can break your neck. In a hiring case, a single person can try to steer the decision, which is bad enough.

@AnonymousPhysicist A single bad review is easily enough to doom a project. And could be even for tenure if it is not a stellar one where the bias would be obvious to the committee.

Amazing that this is what it actually comes down to, what gets assessed or critiqued is a function of personalities and power rather than quality of work or progression of the discipline. But the reality is this is absolutely the case, and those who approach a scientific career idealistically just get burned

@benxyzzy By and large these legitimate factors matter, but there are black sheep in every profession, so it's a good idea to behave in a way that shields against their power.

One thing to be said is that in my reviews I never state "accept" or "reject", and generally try to balance between positive and negative comments. But of course negative comments are more common because it's sort of the point of the review. In any case, not deciding the final fate of the paper means less probability of retaliation, I think.

@lighthousekeeper well overall it seems that there's not really that much to gain and possibly more to lose. I think I agree with your points.

One advantage that you haven't mentioned is visibility/networking/reputation; by providing a thoughtful, thorough open review, you will make yourself known (favourably) to the authors — and to anyone who reads your review, in cases such as Wellcome Open Reviews where the reviews are published alongside the paper.
OPR might also incentivize you to work harder to frame your reviews as constructively as possible, knowing that your name will be publicly associated with them (although this might not matter much given that you say you are already a fair & friendly reviewer).

Ah, but does it sort of force a bias toward favorable reviews? I have to admit to being skeptical here.

It might; that's a disadvantage of OPR in general (i.e., of the system). The OP asked about advantages to them (an ECR) of OPR.

@Buffy Overly positive reviews would hurt the reviewer's reputation too.  But all the reputation effects are negligible.

@AnonymousPhysicist, I am concerned about the quality of the reviews, not the effect on reputation. Junk reviews help no one.

@AnonymousPhysicist fair reviews are not necessarily positive, hence the problem of revealing your name because of people who don't take criticism

Best case scenario: influential members of your research community see your review, and conclude (1) you are a good community citizen and do your fair share of paper reviewing; (2) you are a conscientious and thoughtful reviewer. These impressions result in a small positive boost to your overall reputation.
Worst case scenario: an influential author of the paper reads your review and takes the criticism poorly. They engage in a campaign of retaliation, attacking you whenever the opportunity arises (hiring decisions, tenure, grant and papers reviews) and spread negative gossip about you to other senior researchers.
I think the cost-benefit calculus is clear. Note that I do think there are good reasons to favor open reviewing and that there are many opportunities to improve the peer review process in general, but I would save experimentation in these directions for after you have tenure (or are otherwise confident and secure in your position in your community).

In practice, campaigns of retaliation usually hurt the retaliator.  If the author of the paper has power of you, you shouldn't be peer reviewing them anyway.  It's an unethical conflict of interest.

A campaign like that is indeed the worse case, not entirely unrealistic, but probably rarer than the case of "opportunity retaliation": If the author is invited to review the reviewer's next grant proposal, they might use the opportunity to "pay back". There is zero risk for the retaliator, since they can write the review in a way that is indistinguishable from a regular negative review.

@AnonymousPhysicist I'm not sure how familiar you are with academia, but (1) a great many people (almost everyone more senior than you in your research subarea) have power over you, when you're junior; (2) you will review those people's papers all the time (though usually blinded); (3) nobody considers this a conflict of interest.

You're claiming thousands of people have power over a junior faculty member.  This is just wrong.

@AnonymousPhysicist It's probably closer to hundreds than thousands.

authors: Vladimir F Героям слава


text:
What factors determine application fees?
I have no serious need to know the answer to this question, but I'm mostly just curious (after applying for undergraduate schools 4 years ago and applying for graduate schools now).
What sorts of expenses are institutions trying to pay for when requiring application fees for the applications? Why is there a wide range of fees? (I know Stanford graduate school is $125, and Chicago is $55, and I've only applied to 5-6 schools so far.) Are the institutions just breaking even, or do some of them use their prestige to earn a little extra money?

I suspect some schools (like Stanford) use high application fees to cut down on applications from students who are clearly not qualified.

As for the prestige factor, University of Chicago is also a top institution, certainly not less than "half as good" as Stanford.

In our department, graduate applications are reviewed a committee of tenure track and tenured faculty and one student representative. Nobody is paid extra. This is viewed as "departmental service". I get the impression that high application fees are a weeding out mechanism in addition to being extra money for the university/department budget.

Application fees are primarily there to moderate the number of applications and in the case of universities receiving huge numbers of applications partially finance the application process. There is of course many services for which one can argue to cover costs. This includes personnel to handle applications, personnel to evaluate applications, costs for paper handling (at least earlier including postage if anything had to be handled through regular mail). When looking at the costs for taking in the money and possibly distributing it within a system that likely involve many persons it becomes clear that a well defined cost analysis is not likely done, it is not cost effective. Instead the pricing can be used to signal, for example, prestige and to ward off chance applications. The level of the  pricing will likely be determined by these factors but also include considerations to what levels will be reasonable for the uptake of students visavi ethical and social goals for the university. In short, the pricing is more of a tool "for" recruitment than a precise estimate for the costs involved in the application process.


text:
Are editors biased when evaluating transferred papers?
Certain publishers who manage a large portfolio of journals offer transfer services if a submitted paper is rejected before being reviewed.
I have had mixed luck with transferring papers, sometimes I transferred to a more selective journal and the paper was sent to review, sometimes I transferred "down" and didn't get reviewed.
I have always wondered if editors are somewhat biased by receiving a transferred paper because they might be wondering why it was rejected by their colleague.
Is it a good idea to transfer papers when the format between the two journals involved is somewhat similar? Is it better to spend an hour redoing the submission to avoid some negative bias?
Does a transferred paper bias editor judgment?
Please only answer if you have some direct experience, otherwise this becomes an opinion based answer.

Personally it's no (although I will of course look at the reasons for transfer), but I'm only one person and can't speak for anyone else.

Answers based on personal experience will be opinions.  To get more than opinions, you would need a scientific study of this, and I doubt such a thing has been conducted.

@DavidKetcheson yes I agree, but I rather have answers from first-hand experience rather than someone who "thinks" what editors might like or not.

From my experience with with transfers, both as an author and an editor, I believe that transfer improves chances of acceptance.
When a paper initially arrives, the editor has no way to know if it's any good or not, and they make their decision in as unbiased a manner as possible.
When a paper is transferred, however, that is not the case. Transfers typically involve communication, and they are not automatic. Instead, they generally represent a third option that is between reviewing and rejecting.  When an editor receives a transfer, they are being told "This manuscript isn't right for our journal for reason X, but I think it's not junk and that you are likely to want to publish it."
This is good for you as an author, because the editor is being given a positive review.
This is especially often the case when dealing with a transfer from a "glamour" journal to a more "bread-and-butter" journal, because the rejection from the "glamour" journal typically has little to do with the validity of your work and more to do with how "glamorous" it is. A journal that is more concerned with validity than glamour will often be very happy to publish such "rejects" because if it was actually junk, the glamour journal would likely not have have referred it to them.
Now, there are often bumps on the way, such as reformatting, but even those don't always happen: I've often had transfers sent out for review "as is", and then the reformatting happens during the revision process, when I'm much happier about investing the effort.
Bottom line: as long as you're working with a good and functional publisher, embrace your transfers as good news.


text:
Current position in grant applications when unemployed
I have recently completed a post-doc and am currently unemployed. However, I am doing the same activities as before, mostly writing and publishing papers that resulted from my postdoc. Obviously, I am not getting paid and am not under contract from my previous institution. I am also doing some freelance work, just a few hours a week, for a private company which is however not known in academic circles and is a very small company. So I don't see any large benefit in listing myself as a freelancer for such company. Just listing freelancer people might be wondering what kind of freelance and it would not make sense for academics.
What are my options to show that I am still active in research and that it makes sense for academics reading my CV in a grant application?
Should I list my current position as a "consultant" for my ex-institution? People know that there's not such thing in academia and might be wondering and why I am not a "post-doc".

You should not be working for free.

@AzorAhai-him- Completing one's own papers is not "working for free".

@lighthousekeeper It is if you're not getting paid for it.

Are you writing grant applications in order to be employed again by some university in case of success, or are you planning to continue the way it is now?

@Snijderfrey Obviously I am not rich :), I am writing papers and grants because I want to get a position.

In this case, I would say that having a strong supporting letter from an institution is more important than how exactly you call your current position.

Independent researcher. Under this label, you can summarize the completion of your own papers from the previous job, and the consulting work.

I am not totally convinced, researcher financed by whom?

@HermanToothrot The word independent spins the fact that one does not have a main employment in a positive way.


text:
Literature management for workgroups
We are looking for a solution to manage our literature (citations and corresponding PDFs) in our workgroup (~15 persons). Everybody should have read-write access, so a solution having a shared library would be the best for us.
Which workflows do other groups use for a common literature management? We've checked out EndNote, Reference Manager and Mendeley so far, but are not happy with the "workgroup" options these softwares provide.

I'll go with group-level Wiki on that one. Give every member of the group read-write access (or IP-based write access), and have maintain lists of references (and attached PDF files) by topic and sub-topic. If you want to include some notes on a paper, create a new page for that paper, and put your notes there. People can add their own notes to the same paper later, by editing the page.
Search capabilities will be important, so choose you Wiki software so it has decent search support. Or export all the PDF files of papers as a read-only network drive, thus allowing for full-text search of the whole database through client's OS (which is what I do myself).
For examples of wikis run by research groups, see for example professor Hero or SklogWiki (on which papers are ordered by topic).

If you run your own server, then there are some open source, web-based reference management tools like refbase, Aigaion or WIKINDX which seem to me most suitable for your purpose:

You can share a reference library plus file attachments (and quotations in the case of WIKINDX) and
all have import/export functions for RIS and BibTeX, so that all users can upload their own references and download the collective library independent of their reference manager of choice.

Swiss Academic Software (I work for them) has a solution called "Citavi for DBServer" where the data is saved in a MS SQL server. The software "Citavi" is installed on the client computers to access the data. You can set different rights (Project manager, author, reader).
It is also possible to install the SQL Server on Windows Azure, allowing cross-organizational collaboration in a private cloud.
Caveat: Citavi is Windows-only (but a platform-agnostic web version is being developped at the moment).


text:
When to submit as a "Brief communication", when as an article?
Many journals, especially in the life sciences, offer the possibility to submit results as as a brief communication.
I'm wondering when to choose this way of publishing. If I don't have enough results for a large paper because it used to be a "hobby project" that should be put to an end, but the results are interesting and I want to publish them, should I opt for a brief communication?
How do I choose between this form of publication and an article?
This includes the question of how small a "real" article can be.

The answer is often that you submit an article, and the journal says "We might accept this if you can make it a brief communication, which means 1 table, and X words".  (Where X is a relatively small number.
Write the article and see if it naturally fits into their criterion for brief communication. If it does, submit it as such, if not, submit it as an article. The length of a 'real' article depends on the journal, but I've had a lot of papers rejected and this only happened once because the article was too short.

I've heard of the situation happening in the reverse as well, you submit it as "note" (or whatever) and the journal asks you to write a full article. The prior editors of Criminology would not publish notes.

The Journal of Neuroscience has this web page
Brief Communications
It does explicitly say,

Brief Communications are short research articles intended to present exciting findings that will have a major impact in neuroscience. Brief Communications are limited to 4,500 words. . . . may include no more than 4 figures, tables, multimedia, and/or 3D models, . . .

Please ask the editors of that journal for more details.
Also, the Wiki page for that journal says,

some issues of the journal contain articles in the following sections:
   Brief Communications . . .

I guess it means not every issue publishes brief communications.
Disclaimer: My research area is not life science and I am not affiliated with Journal of Neuroscience.


text:
What is the etiquette about the length of a visit when giving departmental seminars?
If you are invited to give a departmental seminar and the department offers to put you up for up to two nights, how long should your visit be? I find it a little rude when our speakers arrive an hour before and leave an hour after the seminar. Do you have to spend a full day at the host department?

In my opinion, it is not rude to make only a brief visit, especially if you accept with, e.g. "I would love to come, thank you, but I'm afraid I can only come there for the afternoon - I hope that is okay?"
Certainly I agree that it is as great idea to stay for the whole day if you can.
I've noticed that perception of etiquette seems to differ a lot from person to person. Whether or not it is okay to recommend a taxi from the airport (as opposed to picking up the visitor yourself), whether or not to take visitors out for a late drink (or karaoke!), whether to put them up in a hotel or your house, how long to encourage them to stay... these are all aspects where I've seen things done differently. But a small minimum of communication beforehand and flexibility during the visit seems to suffice to guarantee a good visit.
If you're the one visiting, I would certainly recommend at the very least hanging around the department some and going out to dinner with your hosts (assuming they invited), but it's more or less up to you.

Think of this as an opportunity, rather than an obligation.
Find people in the department who are doing interesting work and try to organise a short meeting with them. Volunteer to hang around after your presentation to talk to PhD students (and ensure that your presentation has some appeal to keep people around). Ideally, try to have a fairly full schedule to maximise the benefits gained from the opportunity, though avoid having every minute planned so that you can have spontaneous extended discussions with people, should the opportunity arise.
Planning ahead is probably key, as not everyone will be able to accept an unannounced visitor for a lengthy discussion.

People who give invited seminars are quite busy. It is frequently the case that they may have to come late or leave early. However, unless the guest is local, it is usually considered normal for a guest to spend a day visiting the department. The reason for this is that many times there are people who wish to meet with the visiting speaker, and thus an extended schedule is necessary. Cutting the visit short may also deprive you of meeting people who might valuable future collaborators for your work efforts.
However, in circumstances where the visit does need to be curtailed due to length, the more important it is to communicate this with the host organization in advance.

If you are the one organizing the trip, telling the visitor that you are covering one or two nights' stay is enough of indication that the department wants to host a long enough visit that would allow meeting with other faculty, post-docs, and possibly grad students. If the visitor does not take the hint, you may have to ask them, "So basically you are refusing to meet with our department?" -- and you can actually take it to the chair and ask whether it would make sense to withdraw the invitation, as this visit is the event that is supposed to benefit the department, not just hit the financial bottom line. Basically, whoever is paying for the trip should be fine with an abridged visit. If the department is paying for it (the round-trip ticket will be a fortune for the same day trip), it has all the rights to have the visitor to themselves to ask questions and promote the young researchers of the department. If somebody's grant is paying for the trip, then let have them waste the money. I ran a department colloquia series for a year, and never had an issue like that with any of the visitors, including some biggish wigs. (We are sort of ways away from big airports in a US midwestern college town, so there is little physical opportunity for the visitors to escape; it's not like you are taking a train ride from one university in Boston to another.)
If you are the one visiting... well, if you don't take the hint, you will lose respect of that whole group. If you are a young researcher, that may be a big hit to take: people talk, and in a year or so, the rumor may spread to half of your discipline about your rudeness. If you are a named prof with $XX million of external funding, you don't have to give a s$%t about anybody, and by now everybody else in the discipline knows that much about you already.


text:
Paying for page charges after a grant ends
Often publications resulting from funded research are published after the grant ends. It seems nowadays more and more publishers are requiring fees (submission fees, page charges, and open access fees). How does one pay for these fees after a grant ends?

You did the work, choose a journal that do not charge the authors!

The way it works here in Japan, is that each professor has an amount of money called "discretionary spending", from there, they get money for these kinds of things. And is usual that if a professor has his name in the paper , he should use part of this money to pay for the submission.
That money does not comes form a grant, but the University's endowment, so I guess it depends on that.

I refuse to publish in a journal that charges me for publishing my years of sweat and labour for their financial gain and asks me for money as well. Its against my principles.
Once I was asked to pay 500 dollars for color pictures. I asked them to revert them back to black and white and just have them in colour online.
Open access is a different story and I see it as being legitimate on their part to ask for money for it. It you don't have the grant money => no open access. Put a preprint somewhere and publish somewhere that allows preprints or at least turns a blind eye.

This may not be viewed as an option. If a given field recognizes a particular journal as prestigious, then it will directly hurt the researcher's professional standing to abstain from publishing because of moral stance.

There may be prestigious journals in a field that have this kind of behavior. I don't know I have academically been raised to refuse to accept such practices and I believe in the principle. I have seen two of my mentors reject such practices and that has affected me as well. If I have to make the choice between the more prestigious journal (I doubt that all of them have such behavior in any given filed) I will choose to stick to my principle.

While I may not personally want to support such publishing policies, I think it is unfair to my funders to not publish in the place that will have the largest "impact" (and I don't mean impact factor).


text:
Is it possible to be known in academia by a different name?
I am currently a Canadian grad student about to publish my first paper. However, I really dislike my real legal name, to the point where very few of my real-life friends know my real first and last name. This is mostly because I come from China, and my legal name is a difficult-to-pronounce transliteration of my original Chinese name, which itself sounds very tacky and funny in Chinese. Even my parents are embarrassed at how they named me and use a totally unrelated nickname to address me even in Chinese. (to use an English analogy, I go by "Jake" when my real name is "Alexander")
Is it possible to publish consistently under a pen name that has no relation to your real name? I am not seeking to use it as a throwaway name for a single publication, but rather to simply be known as a different name. I don't even intend to hide my real name - it'll likely end up being in parentheses on my personal webpage or something. I just don't want to see a name I'm embarrassed of on every single thing I publish.

I see no problem with this.  Is you search "name publication" in this forum, you will find many similar questions.

Why would you be ashamed of "Alexander"? Having said that, I think I saw few people using some nickname for their first names, usually from foreign (i.e., non English speaking) origin.

@PsySp I was just using an example to illustrate that the nickname I go by in Chinese is phonetically unrelated to my "real" Chinese name.

@user54609 Ah ok, I see. It seemed like "Alexander" is a name to be ashamed of. I get it now.

@NateEldredge I read that question as asking about using a pseudonym for a single work rather than changing your "academia name" semi-permanently.

My answer to another question applies equally here:

Regardless of what your ID card says, you can publish your papers under whatever name you want. Some people use pseudonyms. Much more common is that many women continue to publish under their maiden name when they marry and change their surname.
There's no reason you can't publish papers as [Jake].

Sir C.A.R Hoare published many papers under the pet name Tony Hoare (of course not legal name). There is no problem for him, DBLP doesn't get confused either.
I know some Asians add English first name when publishing papers. For example, if his name is Xiaoli Feidao (embarrassed enough???), and he publishes papers under the name Lee Xiaoli Feidao (or even Lee X. Feidao). That way it is still easy to claim authorship without explanation, and people can just call him Lee.

Lee sounds chinese enough :)


text:
How much more work should I put to my master's thesis?
I have been doing my master's thesis for a year now. I was quite productive during the past months, so I already managed to publish one paper on the topic.
Now, the productivity seems to have drawbacks too - I have already fulfilled every requirement there is for a thesis, and even more, but I haven't described even half of the work I did during the past year.
So, I am now left wondering should I return the thesis tomorrow for evaluation, or use two or three more months writing (I'm a terribly slow writer). I would probably like to apply for a PhD position, so I guess I should make the decision from that point of view. If I have a very comprehensive master's thesis, does it add any value for application? Having the one paper would already opens all doors in my home country, but I don't know about the others.

How did you advisor answer this question?  (You did ask you advisor, didn't you?)

Yes. No clear answer. (might be because he's new at the department)

Ask him for a reasonable timeline to completion/deliverables and a plan of action that he would like to see from you. Having a strict, measurable objective usually helps in such cases.

So how did your advisor's senior-faculty mentor answer when you advisor asked this question?  (Your advisor does have a mentor, doesn't he?)  It's your advisor's job to give you a clear answer.

Having a paper published on your own work, while doing a Master's degree (i.e. in a relatively short time) sure is a good point of your application to any graduate program. Having a paper submitted for publication is always a plus, but having one already published is a strong plus for you.
Regarding your thesis: the quality of the thesis itself will probably not matter much in admission to a PhD program, unless it is visibly bad, in which case it will sure hurt. Otherwise, chances are noöne will read it through when you apply. Thus, if you are strongly confident that your thesis can be accepted/graded/defended (I don't know what the detailed requirements are for your program) in its current state, don't overdo it.
Don't get me wrong: you don't want to be seen as the guy who did the absolute bare minimum to get away with it. That looks bad, and may leave a stain when people ask for references. Otherwise, if you think your thesis is of good quality, just submit it. The extra work it requires to get it to “perfect” or “awesome” is probably not worth it. The only exceptions I can see are:

if your Master's program has a ranking system, and getting a good rank (or even 1st) can boost your future applications
if the writing will also be useful for new papers, in which case you might as well include it in the thesis


text:
Are there still teaching professor positions in Western Europe in Biology/Env Sciences?
It seems that I can't find any evidence of just teaching positions in universities across Europe, aside from the temporary position for a semester or two. I am mainly interested in Italy, France, Switzterland but let's make this a bit more broad so it applies to more people.
Every job ad I have seen requests publications and then asks to have a strong research agenda, raise funding, etc.
Do those positions still exists in Biology/Environmental Sciences and related fields? Or perhaps positions with minimal research pressure?


text:
How to pay for or avoid publishing cost without research funding and without limiting journal choice
I am wondering how can someone publish a manuscript without having any money to pay for the publication costs. I am aware that there are some journals that do not require a publishing fee, however by limiting the choice to only these journals it leaves very few options given the specificity of most journals.
Can the cost be shared among co-authors? Is it common for the first author to ask money to the co-authors to pay for the publishing costs? A previous answer to this did not explain if this is a common practice.
Are there certain journals that might waive the publication fee given the financial circumstances? There was a previous question regarding unaffiliated researchers, but what if someone is affiliated but is publishing research from done at the previous institution which does not have money to cover the publication cost.
My field is biology and I am from a developed country, so the option of applying for a publication fee waiver for developing countries is out of the question.

Can the cost be shared among co-authors? Is it common for the first author to ask money to the co-authors to pay for the publishing costs?

It is not common to share the fee of one publication. However it is common to ask for a collaborator to pay the full fee if he has a funded project and then you pay for other publication in the future.

Are there certain journals that might waive the publication fee given the financial circumstances?

Yes. I am from a country which suffered several cuts in science due to the 2008 crisis and my research center was left without funding for several years. Due to the lack of fundings my supervisor started to ask for fee waiver and he got several waivers from Open Access journals, such as: PlosOne, Plos Computational Biology, Nature Scientific Reports, etc.
In the PLOS journals he is used to get 50% of discount and in the Scientific Reports he got 100%. The Sci.Rep. staff asked for the research center budget in order to deliberate if they would give a discount or not.
Usually you can find the waiver policy in the website of each journal.


text:
Version control for research and teaching statements
Every time I apply for a job I write a new cover letter, research statement, and teaching statement. While each statement is personalized for the specific job, I tend to do a lot of cutting and pasting and little new writing (yes I have a whole collection of past statements). This seems like something that might be useful to keep under version control. how do people manage the different versions of the cover letter, research statement, and teaching statement?

Maybe branching may help (I haven't tried it for CV, but I intend to try it one day); see. http://nvie.com/posts/a-successful-git-branching-model/ or http://pcottle.github.io/learnGitBranching/.

@PiotrMigdal I specifically left dealing with a CV out as I think it is a very different situation. Branching might be the way to go, I just don't see how I would ever merge the branches together.

(I don't know why I've written "CV"; perhaps my minds was not awake when writing comment and I got a hint by "While each statement is personalized for the specific job, I tend to do a lot of cutting and pasting and little new writing" ;).) In that case (i.e. rather variants than updated versions) I think that version control might be not the right tool (except for typical versioning of LaTeX file).

I think that we now have a large number of “What is good version control system for X?”, with X spanning a number of common academic tasks, and to which all answers run among the same lines. And no definitive answer in any case. These are really not the best questions of Academia SE :(

In addition: in its current wording, this is a poll question (“how do people manage…”). At the very least, it should be edited (or closed).

@F'x see my meta question about if this is a poll question and is on/off topic. As for the version control comment, I am not sure I am even looking for version control software ... If a VCS is the right way to go, I am sure SVN, GIT, HG, etc, can all handle it and I don't want a particular product recommendation.

My research and teaching statement have a lot of commented text (I write in LaTeX). This is because I amend each document specifically for each job application - as you do.
The detail in which I describe each topic changes depending on what job I am applying for.  I comment out text which is too detailed for the job to which I am applying. However, for other job applications, I might like to have that text put back into my statement, or write new text, to be perhaps commented out in a future application for a different job.
I now have documents with a lot of phrases from which I can "pick and choose", depending on the specific job to which I am applying, and amend appropriately. It isn't really version control, I know, but I find it useful to have a selection of wordings to choose from in one place so that I can compare and contrast things like the level of detail and the tone. This isn't particularly onerous as these documents do not total more than 2 - 3 pages in my case.

I am in the middle of my job search and I do the following to keep myself organised:
Directory structure: ('#' for comments and '/' for directories)
/Interested
    /<deadline>-University1
        #job ad and README.txt in here
    /<deadline>-University2
/Not Interested or Expired
    /<deadline>-University3
/Submitted
    /<deadline>-University4
        /Application Materials #pdfs, copied over from git repos
/RS-git #git repo
    #possibly a generic Research Statement in here
    /<year>
        /University4
            #Latest Research Statement in one of these
#similarly for TS, CV, CL
/TS-git #git repo for Teaching Statements
/CV-git #git repo for CV
/CL-git #git repo for Cover Letters

For each job ad I have a directory for the ad, a readme with notes to myself, and a directory for the application I am building/submitting.  I then create related directories in each of the RS, TS, CV, CL directories, so that I can quickly start the application without affecting other concurrent ones.  Importantly I never have to pull an earlier commit or mess around with branches to switch between job applications.  This last bit is important because I often work on two applications at the same time, either to copy-paste between them, or simply to meet simultaneous deadlines.
One last note, my  are in ISO format, so they appear in order of submission deadline.

Your notation for the directory structure isn't easy to parse. Are you using -> as a directory separator and // as a comment marker? The standard directory separator character is / (or \ sometimes), so this is confusing.

While I keep my correspondence in version control, I don't have the same document for cover letters that go to different schools.  I simply prepend the name of the school to all of my correspondence for that school, and/or file everything into folders with the school's name.
As you point out, you end up personalizing almost everything (even CVs), so we aren't talking about one document for which you need version control.  You want version control for all the documents, but each document has its own identity.
Now, if you do have a unique document that will be sent to different schools, you would want to create one document, and then create a symbolic link (or an alias) from one original to each school folder where it will be sent.   Then, when you update the original, all the symbolic links point to the same file.
Finally, you may want to consider using a word processor that has the ability to use templates, but I find that is sometimes just as much work as simply duplicating a file and changing the duplicate.

Presumably your commit logs are something like "added application to X". When making a new application, how do you pull the bits from all your old applications merge them together?

Copy/paste, or duplicate.  It's generally not a drastically different document, so the changes tend to be incremental, or I'll change the same paragraph in a number of different letters.  I'll probably pick the closest one to what I want it to become, and go from there.