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Are there any PhD scholarships for 3.5 CGPAs?
I have recently thought of pursuing my PhD. I have managed to make a research proposal. I have done part time MS (i.e. struggle after working hours) with thesis and managed 3.5 CGPA (85%) out of 4.0 and I managed to have one publication in an IEEE conference.
While corresponding to supervisors, I feel some of them like my proposal but it always comes down to availability of a scholarship. For example, I started a correspondence with one supervisor in New Zealand who was willing to supervise me but he won't give me go ahead for university admission because I haven't secured any funding and he thinks that I have no chance to win any university scholarship with this GPA. I told him that my average is 85% and I have over 5 years of relevant work experience. I asked him the minimum % to win a scholarship, to which he replied "100%". He says work experience is never a major factor for scholarship award.
Now as it seems that my GPA is a barrier to even have an admission in a university let alone win a scholarship as most of them don't want to waste their time on a candidate who won't be able to fund himself.
Situation for me looks bleak. Can't bring back the past to work hard and get better CGPA or should I start thinking of doing MS again? As for now it seems that PhD scholarships are only for the applicants with Gold medals and 4.0/4.0. Any ray of hope? Is there any chance that I'll be able to have a scholarship?

You mention scholarships, but I'm not very familiar with that funding route: most folks I know (in engineering fields, in the US) are funded by graduate research assistantships (GRAs). Your GPA doesn't sound that bad, either.

I think a 3.5GPA for graduate school is not bad at all. Though it really depends on where you are applying from. International applicants usually are scrutinized further, especially due to the shear number of international applicants and fewer funding sources for non citizens. I think it would be best to talk with professors from your university or alumni who have pursued graduate school about locating funding and which universities/programs will already have funds for students.
The other thing is the professor may not actually be that interested in you. Professors often will take almost anyone if they are free, but once they have to use their research funds, the standards increase.


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Administrative recognition of frequently-cited unpublished manuscripts
This is not a question about academia per se, but about the academia-administration interface.
When I was a postdoc, I wrote a paper that started to be cited quite often (by the standards of my particular subfield) as soon as I uploaded it to the usual public repository. These were largely good citations, along the lines of "this is a really neat idea" rather than "this author doesn't know what he's talking about". Eventually, I decided against submitting it to a journal, mostly because the unpublished manuscript had already become relatively popular and it wasn't really worth going through the extra work of the journal publication process for essentially no additional benefits re: the visibility of the paper or my reputation in the field. I've been listing it in my CV as a "frequently-cited unpublished manuscript" and everybody has been happy about it.
Now that decision is coming back to bite me in the ass. I am applying to a tenured job and I have to submit copies of representative publications. However, I can't submit a copy of this paper specifically because it has never been published in a journal. I have enough quality publications that this is not a problem, but it annoys me because I'm quite proud of this particular paper, which is as representative of the quality of my work as any of my papers in top journals.
So the question is, those of you who have similarly popular unpublished manuscripts, how do you convince administrators that a paper doesn't have to have a journal DOI attached to it to count as a representative piece of work?

If Grigori Perelman is reading this, "my unpublished work earned me a Fields Medal and Millenium Prize" is not something that applies to me, unfortunately.

That's a really interesting question. That being said, I would remove the derogatory "bean counters" from the last paragraph - it's not only stupid bean counters that you will need to convince of the value of your unpublished manuscript, but also smart professors from other fields.

Also, I should note that even people that fully understand the scientific merit of your manuscript may take you not sending it to a good journal the wrong way. Think about a dean who manages a department - I don't think a track record of not sending strong material to peer-reviewed journals to avoid the hassle will be a point in your favor in the eyes of a dean.

@Koldito This paper belonged in a journal. Revise, perhaps adding more directions for future work and everything the community has added as feedback and send it NOW. Then you can include it under "submitted to..."  and "preprint available at.." and problem solved.

I think it's always worth getting papers peer-reviewed, and not only to avoid administrative hurdles like the one you're having.  If I come across an arXiv paper (even as a citation) I will not at first know that it's highly cited.  I do however know from first hand experience that many arXiv papers are flawed.  I'm even aware of a very highly cited arXiv paper that has mistakes that invalidate one of the side-conclusions (not the main point though).  Knowing that a paper is peer-review at least signals to your readers immediately that it's less likely to have mistakes.

To be sure, the issue is not the strength of your application for tenure-track jobs, but pride, since you "have enough quality publications that this is not a problem."
With this in mind, the comments in favor of publishing the paper in question just to get it on CV prior to applying are a mute point, if the heart of your question is your candidacy, rather than ego.
Thus the necessary alternative perspective: bite the ego bullet and do not include the paper in question in your CV. Problem solved, and none created.

One more thought: Delaying submission for publication may make sense strategically, since this will allow you to submit (and add this paper to CV) after you start the tenure job, thus giving you a 'freebie' pub to boost your first-year pub count. Good luck!

@Alexandros : After saying "submitted to" and "preprint available at" should he also add "cited 31872901 times in scholarly journals"?

how do you convince administrators that ...

You don't and you can't, and I endorse Alexandros's suggestion.
The department to which you have applied, if they want to hire you, will try to convince the administrators of exactly this. The admins don't know you and don't trust you, but they might listen to such complaints coming from someone they trust.
In the meantime, in addition to any other benefits, submitting your paper to a peer-reviewed journal will signal to the hiring committee that you are doing your best to make their lives easy.

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Response to desk return of PLOS submission
I recently submitted to PLOS One.  The manuscript was returned before sending to review, with a general comment

Please ensure that your search strategy is adequately described such
  that another researcher could reproduce your experiments. Please
  include sufficient detail to this end. Eg, search strategy/protocol,
  search filters used, the dates of search, inclusion/exclusion
  criteria, reasons for inclusion/exclusion

The paper uses Web of Science.  The search terms and methods are simple and detailed in full.  I am confused if there was something specific they are wondering about, or more important, if they assume there was some additional criteria or method used.  For example, downloading all data with search term "Graphene" using the Topic search box.  I am not sure what else they would think is being done.
PLOS being particularly open access, I understand the extra focus on the methods, but is this a common response?  Is it usual they did not read the manuscript and just skimmed it, and I should reply with line numbers of where it exists?
I don't believe it is really an issue of the manuscript not stating it clearly, as it is its own subsection in methods detailed in each step.

From the list provided, the date of search seems like the most likely to be forgotten. To reproduce your dataset, people need to know which dates the search results should stop at. Did you include that?

@ping I included the dates of the data used for search, am I supposed to include the date that I performed the search as well?

It looks like they ask for that, although it's probably slightly less important if you were already limiting the dates to the past. Changes could still occur if the list of journals they index changes, and I'm not sure how web of science handles things like retractions. All of these things are difficult to deal with even knowing the search date though! Also, if your dates of interest were close to your date of search, some recently published work might not yet have been indexed?

@ping That is all true, but has less than 1% effect on the data.  Anyway, it seems that is a bit weak to desk reject something.

@user1938107 Dates of search are absolutely critical, and must be included.  What if you were performing your analysis using an old data set that had been gathered in 2003?  I'll bet the results for "graphene" would look really different!

@jakebeal They would be different, but not by much, if the results for graphene in the year 2001 was collected in 2003 or collected in 2010.  I would be surprised if there was that many new publications in the year 2001 after 2003

@user1938107 I picked 2003 because the first significant production of graphene was in 2004, and your presentation here confused me into thinking your search was not date-limited.  Perhaps your presentation of the paper analogously confused the editor?

@jakebeal sorry for the confusion.  In the paper it is explicit, such as, 'data was downloaded per year for each year from 2009 to 2013'.  I had mentioned this to ping earlier in these comments " I included the dates of the data used for search, am I supposed to include the date that I performed the search as well"  So I assumed you were still talking about the same thing.

Check if you have covered all the details that the editor has mentioned. If you are very sure that there is no scope for adding any other detail, you can write to the editor, providing a point by point explanation of what you have done, with page numbers and line numbers as evidence. Since the manuscript has anyways been rejected, you do not stand to lose anything by doing this. However, ensure that you maintain a polite and courteous tone throughout your email. Your email should not give the impression that you are refuting the editor's decision; rather, it should seem like you are seeking more clarity on the weaknesses of your paper, so that you can work towards improving it.

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For graduate admissions, focus on bachelor thesis or other research publication
Given a student coming to the end of their undergraduate career working on both a thesis for their bachelor degree as well as a separate research project in a research lab, which would hold more weight towards graduate admissions in US schools.
The main questions started with; in admissions, do people read the bachelor thesis.
I never have, but can't be sure of a standard.  If the student is working on a research topic that is set to be submitted for publication, should they focus on that paper and not worry about the bachelor thesis, vice versa, assuming time is constant and the bachelor grade remains the same.
My first thoughts were, a bachelor thesis is not peer reviewed, so any peer reviewed article would be much more likely to be read or at least glanced over beyond the title.  No one expects much out of a bachelor thesis, so it will be hard to convince someone to read it, maybe without some two page overview summary linked to the application.

Im not saying not to discuss one or the other. Im saying the importance of time to invest before finishing either.  Is it worth lowering the quality of the bachelor thesis in order to publish a paper in a conference or journal.

Assuming both are closely related to your subject for graduate studies, either could be more important.  Even if you have a published paper, graduate admissions committees are not likely to truly read it, though many people may take a quick look at it, to get some sense of what level it is at.  (Though if this is a joint paper, just from looking at the paper, a committee will not know how much is due to you.)
Here committees will form an opinion largely based on your letters of recommendation, so if you impress someone in the research lab or your thesis advisor, you should definitely ask for a letter of recommendation.  If your thesis advisor is well known, a strong letter from that person can make a bigger impact that one from your research lab.  On the other hand, if you don't do a good job on your thesis, you may want to think twice about asking that advisor for a letter.
So, ideally, you should try to do a good job on both, and get letters from both.  Presumably you have some tacit agreement with both the lab and your thesis advisor for how much work they expect from you, and you should try to meet both of those.  If you can't, this means you are overcommitted, and you need to have a conversation with one or both of these parties.  (The same goes if you are unclear on how much work is expected of you and you are having trouble balancing these projects.)

Im a little confused, you are saying graduate admissions do not care about having a peer reviewed publication?

http://academia.stackexchange.com/questions/13500/importance-of-independent-under-graduate-research-in-graduate-admissions?rq=1 both comment and answer seem to allude to the publication of importance (given it is good quality)

@user1938107 No, having a peer reviewed publication is definitely a plus.  But just having your name on a joint publication (since you're working at a research lab, I'm guessing your work there is joint) does not necessarily mean too much without letter writers clarifying your role.  And an impressive thesis can be more impactful that a mediocre paper.  (This is at least true for pure math, but I would guess many other fields as well.)

The student would be first author, and contributed most of the work (its not me who is the student).

@user1938107 Then can you clarify where you fit in in the situation?  It seems to me that neglecting work on your theses to do something else should be agreed upon by the student and the thesis supervisor.

The student can't finish the thesis after graduation, but s/he could prepare the journal submission afterwards.  So, if the student is interested in doing both, perhaps the initial priority should be on cranking out the thesis.  Hopefully you (as advisor or mentor) can help the student keep the thesis from getting too big or ambitious.
If it's not feasible to do both (one after the other), and if the planned thesis is non-research-oriented (for example a literature review), then I think the article related to a research project would make the application more attractive.


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Average time alloted for manuscript review across disciplines
I am asking this question because I've always had the impression that manuscripts submitted to a journal in my field (theoretical linguistics) take an insanely long time to get published, and sometimes I get the impression that this is because, most of the time, nobody other than the author cares about getting things done within a reasonable amount of time. Some examples from personal experience follow.

For the last paper I submitted before getting my PhD, I had to wait nine months from the submission date to get reviews back from the referees.
Last week I got a review request from a journal I had never reviewed for previously. The review deadline is March 15 (almost four months).
In early October, I submitted a manuscript to a journal that I know asks reviewers to return reviews within 6 weeks. I checked the status of the manuscript online and it still says "with editor".
Earlier this year, I was about to start writing a review when my wife went into labor. By the time we came back from the hospital, I had forgotten about the review, so I missed the deadline. The editor didn't contact me to ask about the review until two months after the deadline.
Late in 2013, I was asked to write a survey chapter for a handbook. The expected publication date of the handbook is summer 2016.

All of this is not me being unlucky with editors and referees. In private conversations through the years, many colleagues have confirmed that it is virtually unheard of to get reviews back within 3 months of submission; 5 or 6 months seems to be a good average, but in some cases it can take longer (see my first point above). In general, everybody seems to have accepted that the submission-to-printed-journal process is going to take a bare minimum of one year, and that's assuming that the manuscript is accepted without revisions. If revisions are required, two years is not out of the question. Also, it's not like our papers are ridiculously long. I've reviewed about 100 papers so far, and the longest one was about 50 single-space pages; 30-35 single-spaced pages is closer to average.
I remember that, when I was a postdoc, my astrophysics housemate mentioned that in his field the entire submission-to-printed-journal process took only three or four months. I really can't see a good reason why theoretical linguistics shouldn't operate on similar timeframes, other than the fact that everybody seems to have grown used to things taking way longer than they really need to. What are the wait times in other fields? How do you manage to get things done quickly?

Being in the same field, I can confirm everything said in this post. What's strange is that linguistics journals typically have a quicker turnaround that books and proceedings. I submitted a paper for a proceedings volume in 2010. Even without peer reviews, it still hasn't appeared.

This question is not only discipline-dependent but also journal-dependent. For example, in my field (metrology), review time can vary from one-two months to many months - almost one year, depending on the journal.

Great question. It always bothered me that the review process at (respectable) physics journals,  takes 3-6 months, while in CS/EE you usually don't expect to see the first round of reviews before a year has passed. I'm also bothered what is the reason for such a discrepancy across (quite similar) scientific fields.

@RanG. I work in CS, and I was furious the one time the first review round of a journal took more than 6 months. So no, I certainly expect reviews in less than a year.

This seems like a poll question, which are generally frowned upon. As answers will not only be field, but often publisher/journal specific, I don't see how it is going to be valuable enough to make an exception.

@Sverre - Journals tend to have a much better worked-out workflow than book proceedings, which are often organised on an ad-hoc basis by a workshop organiser.  So your observation is what I expect.

For mathematics, here's the latest survey done by American Mathematical Society:
http://www.ams.org/notices/201410/rnoti-p1268.pdf
You can find median times from submission/acceptance to acceptance/print/electronic print for various math journals as well as other statistics like the current estimate of waiting time for each journal. Not surprisingly, the median time from submission to acceptance in 2013 varies greatly; some take only a few months and others nearly a year and a half.
They do this survey every year. For instance, here's the one published 2 years ago:
http://www.ams.org/notices/201210/rtx121001473p.pdf
The worst offender that took the longest between submission and acceptance that year was Annals of Mathematics (which happens to be among the most prestigious math journals), and the median was 24 months.
I don't know if there is data for other fields. But American Physical Society occasionally makes statistics for their journals available, e.g., pages 14-17 of this PDF slides:
http://www.phys.nthu.edu.tw/~colloquium/2009F/T2.pdf
From my own experience as an author and reviewer as well as from what I hear, it appears that math journals typically take longer than physics journals. But probably things are drastically different across subfields even within one discipline (e.g., theoretical vs. experimental).
In any case, as the fact that they publish statistics indicates, both disciplines seem to take turnaround time very seriously. But for some reason, it appears that review tends to take more time if a journal publishes more mathematical papers. This seems to hold true for electrical engineering, too; the journal I have published in most frequently belongs to electrical engineering but is known for being heavily mathematical, and, lo and be hold, it's notorious for its slow, slow, slooow review...

In biology, things are much faster (although it can vary for different journals). From my experience, reviewers usually get a deadline of 2-3 weeks to submit their review, although many reviewers fail to meet this deadline. So the typical time of getting back the first review is around 1-2 months, depending on the journal.
Since speed is often an important factor, some journals make a point of advertising their typical review/decision times. For example the journal Genome Research states their average turnaround time for review is 30 days. The journal eLife gives the following median times: 3 days for initial decision (editorial decision whether to send the paper to review), 29 days to post-review decision, 90 days submission to acceptance.
How this affects the quality of reviews, especially those of interdisciplinary work (e.g. combining math and biology), is a completely different matter...
However, one way to explain the difference in speed from a theoretical field like math, is since biology is an experiment-based discipline, the reviewers basically evaluate what the authors report about their experiment - they cannot, and are not expected to, reproduce these experiments on their own. Once the paper is published, other labs will eventually try to reproduce its results.

As a linguist and former editor, I would say that your problems are on the outer edges of experience, which may have something to do with the journals you are submitting to, but not beyond belief. No names, but there are a couple of well-regarded theory journals that are known to have this problem. The main explanation is that reviewers take forever, and editors only have a limited power and willingness to nag: they are willing to wait another 4 months rather than drop the reviewer and get someone else. This problem is somewhat ameloriated by submission software which is now popular that automatically nags reviewers. The ultimate solution, I'm afraid, is that authors need to email the editor with a status query with a week after the supposed deadline (if the journal says when they expect to return a decision). A significant contributing problem, IMO, is that there is nearly no infrastructural support for the editor.
Handbooks and the like are another story. Expect a 4 year delay from invitation to appearance.

I guess an important consideration here is how quickly a field evolves.
My field is condensed matter, and usually the paper stays with the editor one week or less, with reviewers one month and depending on recommendation this will be cycled until acceptance, although subsequent reviews tend to be faster. Then you get proofs/the paper appears online in overall a month or less.
I say that how fast the field evolves is important because for a hot topic many people will be working on the same problems simultaneously (think graphene a few years ago) and getting publication delayed by even as little of a couple of months might mean being the second, rather than first, to report a result.
I would imagine fields like History, literature and so on evolve much slower than say molecular biology or materials science. Then fast publication of research is not equally critical in every field. This doesn't mean of course that times couldn't ideally be reduced across disciplines.

Contrary to what RanG reports in a comment, I have the feeling that (applied) CS is comparatively fast in terms of turnaround times. Reviewers typically get ~ 1 month of time for review (+ a few weeks of slack, realistically), and most journals aim to come back to authors for revisions in a time frame of 4 to 6 months.
That being said, the time from initial submission to when a paper actually appears is usually still multiple years. A big contributor is that, at least in my community, there is a pattern that most (including very good!) submissions go through a lifecycle of Submission -> Major Revision -> [Major Revision] -> Minor Revision -> Accept -> Publication, with each step taking about half a year. That is, even very strong papers are often forced to "go through the motions" of some iterations of pseudo-revisions that don't really add anything substantial to the papers.
Of course, in CS, we primarily publish in conferences anyway, so most people don't really mind so much.

Theoretical CS, on the other hand, is closer to math in my experience.


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Disappointed about workshop, are all like that?
I submitted an article for an IEEE congress in the field of Software Engineering, the congress was categorized as a type B congress according to the Australian ranking (I do not remember the exact name).
I went to the workshop sessions because my article was accepted for one of those, but not the main conference, and it was pretty lame. The reasons were the following:

some people were given a presentation of topics not already finished it up, with a lot of holes in their respective research
some people were introducing their doctoral research proposals, which were in a a very initial developing point; I have been also a conference review and I would rejected those works straight ahead
people attending were no caring of what has being said there, also some of the people in charge were almost sleeping during some points of the presentations

I suppose that a workshop was for sharing ideas between the academic community, and not just for the sake of accepting some bad made papers to get money while other researchers want to do the things right.
Also I forget to mention that in one session, the chair of the workshop was the lecturer in charge of one of the lame papers; I do not want to think bad, but it seems like he influence the acceptance of that paper.
In any case I am really disappointed about this type of congresses, I cannot imagine how lame it could be a type C conference.
It is always like that?

Is your question actually "Are all workshops bad?" Or is there something else you really want to know.

I wasn't suggesting that you change the title to "Are all workshops bad"! I just thought you might want to understand why a workshop might be organized like the one you attended, or what the value of such a workshop might be, instead of just knowing whether all other workshops are organized the same way.

I have a habit of picking the bad talks to see at conferences much less workshops. There are always lesser presentations at these meetings, including, possibly, one's own. I find such events better for reconnecting with your best potential collaborators and old lab friends than actually seeing new work.

I understand your frustration, but workshops are not for seminal research. It is usually for hosting / presenting papers that cannot make it to major conferences or provide a venue for very small and specialized areas of research. This is not a bad thing. Especially in CS, papers that are technically correct and well-written sometimes get rejected in major conferences, due to the high rejection rates. In this cases, workshops provide a alternative venue to patent those results and lower the authors' sense of rejection.
Also, many research projects (in EU but maybe this applies to USA as well) have the obligation to organize workshops during the duration of the project. In those cases, it is normal that most of the submissions are from project partners. This explains the little "inbreeding" you encountered. Also, since each workshop has a minimal number of papers that should be presented, in cases of low number of submissions, it is inevitable that some less-good papers get accepted. Also, although peer review is still formal (and not blind to bad papers depending on their authors, as you imply) on those workshops, the requirements for presentation are less strict than major conferences and marginal papers might actually make it.
Are all workshops bad? No they are not. It is actually easy to tell them apart (most of the cases).

Are they co-hosted with major conferences
Do they take place for many years
Who are the PC chairs (this year and previous years)
How good are the papers that got accepted in the previous years?

All these four criteria are a strong indication of the quality of the workshop.
A general advice. Many researchers (not excluding myself) tend to overvalue their research in comparison to others. Since your paper also got rejected for the major conference, that also implies that it was not that seminal or exceptional (which is of course OK). To someone else's eyes the comments you make about the "other" papers might also apply to yours as well. So, talking about lame papers and workshops (especially if you express those ideas publicly) will not make you a lot of friends and academia is really a very small world.


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Advice for preparing a virtual presentation
I have a paper that has been accepted for a conference abroad, but because I have been put on administrative duties on my university I will not be able to make the presentation. So, I have spoken with the PC of the conference and has given me the option to make a presentation and send it to him to present it in the conference allotted time. For me is the first time that I will be doing this, so I would like to know some advice on how to do this presentation:
For example, should I make a simple Powerpoint and just recording my voice? or should I make a presentation like those that are on the MOOCs courses? As silly as it sounds I have no clue on how to prepare a presentation in this format.
Any advice?

If I were in your situation, I would check with my college's video support office, to find out what can be done and how much work it would involve.  They did a great job for me, when I was too sick to travel to campus but able to teach my class from home by video-conference plus slides  (I wouldn't even try to combine power point and voice recording on my own, but perhaps you're more competent in that area.)

Andreas is on the right track. There are a large variety of video services available these days. Most laptops have a webcam pre-installed, though the quality of such cameras is often not the greatest. It is certainly possible to give a presentation over the internet. Your image can be on a big-screen TV, and you can see the audience in return. You can even take interactive questions. A variety of service providers allow such video for low cost, or even no cost. Though, in some cases, you should be aware that there may be people other than your intended audience watching.

By the way, whatever the reasons for you being "put on administrative leave" you should probably inform the conference of sufficient details for them to make an informed decisions about your participation. Not saying you need to tell them every detail, just enough that they won't feel misled.

First of all, you need to know the specific requirements from the conference host. Do they have a specific file format that they want you to use? Otherwise, you might want to do a screencast recording. There are free software available such OBS (Open Broadcaster Software) where you can record your screen and microphone at the same time. That way, you can go through your powerpoint presentation while recording both the screen and audio. Make sure you use a good microphone when recording and try to minimize as much background noise as possible.
Good luck with your presentation, I'm sure you'll nail it!
PS: Let me know if you're struggling with getting OBS to work, it's fairly easy and straightforward so there shouldn't be any issues (also many guides available on youtube).

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Open access journal for long-form publication
I am currently working on a paper in the field of image reconstruction, or computational biology if you will. Now matter how I slice or dice it, it is one of these stories that cannot be told in 3500 words or so. Not only are there several equally important methodological points that need to be discussed to get a complete story, there is also quite a bit of background required to point out the subtle flaws in the currently popular ways of approaching this particular problem; and it takes some words to clearly point out what may appear to be a subtle problem from a distance, especially while making sure to be fair to everyone.
I don't intend to butcher what I feel is a solid and profound story for the sake of cramming it into some word budget. I am no fan of needless verbosity, but I really am going to need about 20 pages to do this right. I strongly prefer to publish in an open access journal. And I would imagine that an open access online journal does not have as much of an incentive to be stingy with word counts, no? PLOS computational biology would be a logical choice, yet they do have a restrictive word count. I can't find any open access journals that appear to be sympathetic to my plight.
Am I missing something? Or should I just write the whole article first, make that into the supplement, and then write a 3000 word teaser with nonstop references to the supplement to substantiate my claims? I am somewhat afraid that people will actually miss the point without an explicit disclaimer at the start of the 'article', along the lines of 'hey, if you want to read the actual story with a good flow to it, you need to start reading the supplement. this is basically just a drawn out abstract.'. If you are referring to the supplement, the convention is to refer to a figure of secondary importance; not to three pages of text you kind of have to read first to understand the rest of the article.
Does anyone have a helpful perspective on such a situation?

20 pages is not a particularly long journal paper.

I know; longer papers have been published. But as for my field, which journals would you suggest? I don't know of any that will take it.

20 pages is suspiciously short to be the longest format a journal is willing to accept. Are you sure the restriction in PLOS Computational Biology applies to you? Having read their author instructions, the 3500 word count only seems to apply to software articles. Alternatively, can't you move parts of the article to supplementary files?

Plos One do not have an explicit word count limit, and computational biology should be on-topic for them:

There are no explicit restrictions for the number of words, figures, or the length of the supporting information, although we encourage a concise and accessible writing style.

For further info see http://plosone.org/static/guidelines
Also, have you seen that Plos Computational Biology has two types of articles, Research articles and Software articles, and that the 3500 word limit only applies to the latter (see http://www.ploscompbiol.org/static/guidelines). For Research articles they only say:

Although we have no firm length restrictions for the entire manuscript, we urge authors to present and discuss their findings concisely.

thanks; that is very helpful information. I must have read their info page too rapidly. Plos One is also a good match for my target audience and has an impact factor which I think matches well.

Have you considered arXiv? They are open-access and handle quantitative biology e-prints. Here's an excerpt that may interest you from their "Oversized Submissions" help page:

If you have trouble submitting a very long paper, such as a long review article with many small figures, or a thesis, AND you are sure that you have efficient figures, then contact the archive administrators to ask for an exception (be sure to quote the automatic rejection identifier and to explain the large size).

I have considered arxiv; but I would like to publish in a peer reviewed journal. Many good non-biologist scientists I know are perfectly happy to publish only on their personal website; and so would I. But biology as a field is VERY conservative in this regard, and my coauthors wouldn't have any of it. sum of impact factor == grant money; at least that's the perception.

I don't suppose your coauthors have any ideas either... :\

A colleague today suggested journal of microscopy. Indeed it appears they would take the subject matter and length; although it isn't a big step up from self-publication, impact-wise ;)


text:
Should Figures and Tables follow a certain order or be at a specific location in a document?
This is a topic I constantly think about when writing a document.
Often after I complete a document in LaTex I would go through the document to make sure that the figures are where I want them to be (I want you here, not there!) and this is a very frustrating procedure.
My question is: How important are figure locations in a document, e.g. if the figure you refer to is not on the page where you are referring to it, perhaps even two pages after.
I have noticed that textbook publishers rarely give any thought to it and I cannot decide whether it bothers me or not. It would certainly make my life easier if I don't have to worry about floats jumping around in a LaTex document.
Any thoughts?

That's just logical order. Chronological would be in order of their creation, perhaps.

Yes, I updated the question.

There are many policies that publishers imply considering figures. The most common ones are:

All figures or tables (so-called floats) have to be numbered and get a caption.
All floats have to be placed at the top of the page, or at a page solely made of figures and tables.
All floats have to be referred in the text by their number.
Every float has to appear no sooner than on the page where it is first mentioned (i.e. if it's first mentioned on page 5, it shouldn't be placed on page 4, but it can be placed on page 6).
Numbering should be consecutive (i.e., no 1 then 3 then 2).
The first reference to the floats should be consecutive (with the exception where you basically only "confer it" (with "cf." or alike).

Some journals want you to provide figures and tables separately, some don't care, some have typesetters that do it themselves, some don't force captions, some allow in-text placement, etc. Just check what you have to do. If nothing is said, I recommend complying with the rules above.

If you are publishing your work as an article in a journal or a book with a publisher than it is often not your decision. It is even very common for the figures and tables to be all collected at the end, and within the text there is a text like --- insert figure 4 here ---. For that reason it most of the time hasn't bothered me. The only time I considered the exact placement of figures and tables was when I was publishing my own dissertation and I was responsible for the lay-out.

It may be that your journal's style guide will have something to say about this, so you should read it, but my preference is for figures and tables to appear in the order they are discussed in the text even if that makes them relatively far apart. You should do your best to get them $\pm 1$ page from their reference, but it's not the end of the world if they go further.
Sometimes you need a headline figure to appear somewhere prominent, but otherwise, it's usually worth relaxing a bit over figure placement.

I personally don't care. The default LaTeX algorithm does a decent job, and I don't consider it worth my time to tweak it manually (other than adding an occasional [!ht]).

In any case, the pagination of the document may change after the journal gets it, so any advance tweaking you did may be lost then anyway.


text:
Adviser wants to be joint first author, even though I did most of the research
In my research, my adviser only gives minimal advice that is limited to the direction of the research and defining the problems.
I can say I do most of the thinking, the actual solutions of the problems.
Even at one time I needed to explain to my adviser how my algorithms work.
The only "effort" my adviser does is writing the actual paper, since I'm still a master's student and lack experience of writing. Moreover, I'm not a native speaker so I'm still trying to improve my English writing.
Well, that's the intro of my background. FYI, I'm a CS student and I'm aiming to publish a paper in a conference in ACM.
The actual problem is my adviser demands to be joint first author.
I asked the reason and the reply was it was needed to progress to associate professor, with my help, and eventually gain tenure.
I suspect that the supervisor feels  under risk to be kicked from the university. With 3-4 years as an Assistant Professor but doesn't really have good research output (only 1-2 small papers every year).
I reluctantly agreed to assist under these considerations:
1. We can be joint first author but my name should be written first. Initially wanted their name to be written first because alphabetically the last name comes first compared to my last name.
Then I did a "bargaining" by saying that I want to be researcher in the future and I need my name to be put first.
The discussion ended and I was allowed my name to be written first.
2. I need to graduate
In my university, advisers have total control to let students graduate.
With this post I want to ask you for more suggestions.
Edit 1:
Right now I want to play "safely" rather than being kicked out, but I feel I'm being treated a bit toady. Usually the adviser likes to scold other students.
Edit 2:
The advisor does indeed write the most part of the paper, but it doesn't mean that I didn't take any part in the writing. I tried to write an initial paper, from the introduction to technical part, writing equations, making figures, producing results, etc.
The advisor helped me to polish the grammar and made the sentences neater.
I forget to say one thing, I have another adviser. Let's say A2. The one I'm having dispute with is A1. A1's most significant  contribution is writing the paper. A2 helps me with the "big picture". Because A2 is more junior than A1, A2 only becomes co-author.
Also thanks for everyone who wrote answers and comments. All of you gave me a lot of new perspectives.

I changed your tags around a bit. There are much more appropriate tags for your problem than the generic ones you provided.

Thanks, I'm new to this site although I'm an active user of stackoverflow

Your English writing is not too bad (based on the writing of this question). I would suggest you to write the paper yourself.

I'd love to write the paper by myself but the deadline is only 2 weeks (doh) and I still need to work on my program. Moreover, He can write a LOT faster and better than me.

What do you mean by "He can be the joint first author but my name should be written first" Is his name first or yours?

For example in writing the authorship:
Spongebob Squarepants* , Patrick TheStar*, Squidward TheSquid.
There is an "asterisk".
In the first page of the paper there will be a footnote that names with the asterisk "have equally the same contribution". Let's say I'm Patrick, but I want my name to be written first rather than second.

You do know that in DBLP, Google Scholar etc, no-one will actually read the asterisks.

Yes, the problem isn't about asterisk or ordering, but "Is it okay my adviser becomes joint first author?".

Because you said no one will notice the asterisks that's why I ask him to write my name first but He can be the joint first author.

@Alexandros, okay, thanks for your feedback. I made this questions because it's not usual for me. In the country where I live right now, people don't speak English, some students did research but because they weren't good in English writing, their advisers wrote papers for them. They are still granted as first author. But If you said so, I respect your view. Maybe I'm wrong. But what makes me to question about this, my adviser admits that this practice is unusual and somehow told me "explicitly" that he needs to be joint first author so he can be an associate prof. It is really fishy

I am also sorry to become too sentimental. I put a lot of efforts in this research all year where my advisers only write the paper in one moth before the deadline.

If the deadline is only two weeks, I suggest you to spend time to write your paper, instead of spending time here.

Yes, but the tasks been assigned, I need to implement one remaining algorithm in c++ and he said I shouldn't modify the latex without his permission except some technical part.

In some areas of CS, alphabetical order is the standard... is your advisor asking to be the "primary" author, or just asking to follow the standards of your field?

Hi @Max, the standard in my field is based on contributions, first author has the most significant contributions than others.

That's why being first author is important. So he asked to be "joint first author" along with me. This means there are two first authors.

A very much related question http://academia.stackexchange.com/q/2467/546

Hi @scaaahu, thanks for the link.
"...the first author is generally the person who both had the "main idea" and led the effort to ensure that the efforts to carry out the research and write the paper occurred properly... " I have "the main Idea"+efforts but my adviser helps me with the writing.

Yeah, I guess, that's right. I can't argue more. I will discuss with him and get out from his research group as soon as possible since this is not my first dispute with him (I actually I have a lot issues with him). For the future I will polish my English writing skill. Thanks all, I will mark @EnergyNumbers's as the answer.

he is more senior than you, right? So, in my opinion, his name should be written first — The only sensible standard for joint first authorship is to list the first authors alphabetically.  Otherwise, there are (as here) fights over who gets to be the first first author, which is just stupid.

@JeffE I've always felt bad about suggesting alphabetic ordering for anything (my last name begins with an "A") and have wondered what my opinion on alphabetic ordering would be if my lastname were to begin with a "Z".

@scaaahu: " he is more senior than you, right? So, in my opinion, his name should be written first". Why? Seniority does not mean that he is better in research. With time and the reality of academia it usually means that the more senior person will be worse in research (as he takes on more teaching, management, logistics - vital activities, do not get me wrong, but which do not contribute to pure research which is later published)

@WoJ I decided to delete my previous comment because it's misleading. Yes, you're right that seniority does not determine the first authorship.

You write:

The only "effort" my adviser does is writing the actual paper

Well, in many fields, that would make them sole author. It certainly gives them a very strong claim to be first author, in fields where authorship is determined by contribution to the paper.
If you want to be first author, then write the paper yourself.
And if you can't, then don't expect first authorship, and be grateful for co-authorship (rather than an acknowledgement).
You've now added that you have done a bit of the writing, but your adviser has done most of it. So yes, they would, in many fields, still get first authorship, and you would get a co-authorship on that basis, assuming what you've written is a non-trivial proportion of the whole.

Yeah, you make a good argument. He does write the most part of it. But it doesn't mean that I don't take any part in writing paper. I tried to write the technical parts, writing equations, etc. But He helps me to polish the grammar.

I don't know fields other than CS, but I have an undergrad students who done a very good research. His writing was quite bad at that time but his adviser helped him in writing the paper, He's still the first author.

Ok, I changed the title too

+1 You are right that writing the paper in most cases grants first authorship. But this "...be grateful for co-authorship" is a bit too much. I know some professors only "acknowledge" their students without giving them co-authorship despite the fact that students have done all the coding, experiments but that does not make it right, nor the student should be grateful if he is given the co-authorship he rightfully deserves.

Another thing, I did most of the thinking by finding the algorithms/solutions while my advisers guide me in "the big picture". In other words, they told me about "the goals" without telling me the "how to reach" the goal.
Is this eligible for first author?

Any field where writing up novel results performed by others without authorship for others is intellectually bankrupt.  I do not know of any such fields, so I think this answer is just wrong (or reflects a particularly unscrupulous individual or department, not a whole field).  If I'm wrong, maybe a few words about which fields are like this and why it's even remotely justified are in order?

@RexKerr: There's a deeper issue here regarding the proper way to provide credit to collaborators who contributed to the research but not directly to writing the paper. It's compounded by the widespread tacit assumption in many parts of academia that "author" = "contributor", even though in many cases this can be demonstrably false.

@IlmariKaronen - If there were a widely-used method for determining credit other than authorship, that'd be wonderful.  But I'm not aware of any--are you?  As such, although the metric may be distorted by additions to the author list that are unwarranted, leaving off the people who provided most of the work and insight is not making things better!  But, again, I'm not aware of a case where it's considered fine for sole authorship to go to someone who is writing up others' results.  And journals do try to reign in honorary authorships, e.g. http://www.sciencemag.org/content/327/5961/12.full

@RexKerr: Alas, no, I'm not. And there's more to the problem than just "honorary authorship"; if I do some novel research, but have no control over how that research is presented (because someone else wrote the paper, possibly in a language I don't speak), should I really count as an "author"? What if I really dislike the presentation, to the point where I'd rather not put my name on it, but I'd still like to receive credit for the research itself? The standard answer is "ask for a mention in the acknowledgements", but that's little consolation if my funding committee only looks at authorship.

I still have control how the paper are written. The main issue here My adviser thinks that he should rewrite the paper by his own words since he's better in English. He's correct. I can discuss with him about several paragraph, how they should be written, what are the main ideas, etc. I also contribute to the entire figure and producing the results by myself.

I mostly agree with @RexKerr, I own the entire research, but the paper is contributed by my adviser. After I think about others feedback and also considering about the risks I have, I decide to accept this answer although it's really correct. I guess I just need to accept what my adviser wants and get out from his research lab.

My adviser thinks that he should rewrite the paper by his own words since he's better in English. He's correct. — No, he isn't.  You should write the paper, because he's better at English.  How else are you going to improve your English?

Hi @JeffE, I am not allowed to do that, He wants to write the paper by himself. I just assist him in writing the preliminary manuscript.

I think this is due the problem I'm still working on my  program and I need to produce some more results. In this case, the submission deadline is approaching And I can't do both coding and writing.

Azer89,
Sorry this is stressful for you, most of us have had some sort of grad drama. I suggest you relax a bit about it. If your adviser demands "co-first authorship" I'd let him have it, for a number of reasons:
1) He is your primary job reference and entree into the academic world, keeping him happy is important. Your career will be better served with a good reference than any one paper.
2) It sounds like he has in fact met the standard for co-authorship, I wish my MS adviser would have anything to do with the manuscript!
3) Finally, and most important, is what kind of collaborator you want to be. Academia (and industry) is full of territorial, jealous types who are concerned only with their own academic "reputation". Don't be one of them. In the long run nobody cares if you are sole or joint first author on some paper. They care if you are a good collaborator they can work with. Take the moral high ground and get the paper out. If he's a real jerk you'll never work with him again, but you'll be the guy people can get along with.
Good luck!

Yes, I after thinking a bit this morning, I'll just let what He wants. I'm still a master student and I am offered a PhD at another uni. After I graduate, I plan to cut my collaboration with him. To be honest, when I started this question, I'm little bit temperament and What you said is right, Academia is full of ambitious people, I hope that I can be a humble researcher in the future.

Remote doctoring issues between students and advisors is always difficult, but I'll have a stab at it anyway.

In my research, My adviser only gives minimal advice that limited to the direction of the research and defining the problems. I can say I do most of the thinking, the actual solutions of the problems. Even at one time I needed to explain to my adviser how my algorithms work. The only "effort" my adviser does is writing the actual paper, since I'm still a master student with lack experience of writing. Moreover, I'm not a native speaker so I'm still trying to improve my English writing.

While your advisor may not be the most contributing person to this research, calling this "no significant contribution" may be too much. It sounds like he is doing standard advising plus helping you write the paper, which is certainly in line with what you expect from an advisor.

The actual problem is my adviser demands him as joint first author.

Yes, that is a problem. It's good that you push back here.

He told me that He wants tenure position and He needs my help so he can be an associate professor.

I don't quite understand that. For all universities I know, advising students is what is expected from assistant professors. So from a tenure point of view, advising a student to write an excellent paper is not much different than writing one yourself. Maybe he is overestimating the additional value he would get from being first author.

(Oh man, did he beg to me or what?)

Try to stay focused on the facts, and don't let it get personal. Nothing to gain from this.

He can be the joint first author but my name should be written first.

I am still confused about the notion of joint first authors (I always assumed there can really be only one, but apparently I was wrong). Anyway, I would say it sounds like an ok compromise.

I need to graduate In my uni, professors have total control to let students graduate.

That is indeed a practical problem in many universities.
A few concluding statements:

Authorship really isn't something that should be negotiated after the project is almost done. As many members here never get tired of saying, details of authorship are best discussed at the beginning of the project, so that everybody knows where everybody else stands.
From your short description, it seems to me like you are somewhat underselling the contributions of your advisor, even delivering some underhand blows in a few places. You are likely a rational individual - try to not be emotional about it, and then re-check what your advisor actually does for your project. Further, keep in mind that students tend to over-value the technical "doing" of the project and undervalue the "big picture" (deciding on a research project, defining research issues so that the outcome is both achievable and novel, etc.).
Somewhat related: your advisor is not supposed to be an all-knowning, all-understanding supreme being. It is completely ok that you occasionally need to explain the details of an algorithm to him. That does not make him incompetent. You will for sure have to do the same thing with your new advisor.

Thanks thanks thanks :D
I'm quite emotional right now but you made my head clearer.
(1) In the country where my university is located, there is a rule that assistant professors aren't tenure and have obligation to publish. If not they can be fired.
(2) In computer science, joint authors means the authors have equal contribution.
(3) I forget to say one thing, I have another adviser. Let's say he's A2. The one I'm having dispute is A1. A1 contributions is writing the paper. A2 helps me with the "big picture". Because A2 is more junior than A1, A2 only becomes co-author.

@azer89 Your comment does not make much sense. I have never heard of "joint authors means the authors have equal contribution". In a ACM CS conference, there are (let's say) 3 names on top of the paper. All 3 names are considered co-authors. What is this "joint" authors you are talking about. Can you post an example paper at a ACM CS conference where this happens?

(1) yes, I understand, but for professors the expectation is that they publish with students usually, (2) I am also from CS, and that is incorrect, (3) maybe you want to edit your question, as this may be relevant.

@Alexandros, perhaps is like this:
http://graphics.cs.kuleuven.be/publications/GLLD12GNBE/

(2) In computer science, joint authors means the authors have equal contribution. — This is incorrect.

Hi @JeffE, could you help me to describe joint first author? I'm still new as a research student. I hope your info can help me in the future :)

Oh, you meant joint first authors. Yes, that means equal contribution.

Azer89, I don't know what advice to give you in this situation. But I'm very surprised by the number of people thinking your adviser can be the first author or even the sole author.
Check this site http://www.stanford.edu/~engler/

According to ACM this is their most downloaded paper ever. I wrote it, but everyone else did all (I mean: ALL) of the technical
  work.

He wrote the paper alone, and he put himself as the last author since other people did all the technical work. This is what great professors do.

I had a meeting with him yesterday. I could say his policy regarding authorship is too weird for me.
I don't really expect if the paper gets published I can still be the first author, perhaps I should be thankful if I can be co-author. I even don't care. Well life goes on, I'm going to graduate in 2 months. I get a phd position at another uni. I hope I can do other research with my new research group :)

Emotions aside, I believe that the intent of a paper is to present results. There are people who are better than others in English but a technical writer is not the one who does the research. Should he/she be the first author because he did the logistics work (writing the paper)? I do not think so.
The CEO of a company will not have drawn her/himself the fantastic ad you see on the street. But (s)he is still the one who is the face of the company. Not the graphics professional who did the work.
So writing the paper, even if this requires experience, is logistics. Which grants you, at best, co-authoring.

"I do no think so.". The "no" should be a "not". Also, the last sentence, "Which grant you, at best, co-authoring." reads a little strangely. I'm not sure what it means.

Typos corrected. What I meant by the last sentence is that writing the paper (as opposed to doing the research) should give you, at best, the possibility to be listed as a distant second author. This is a work for a technical writer, a very important work, agreed, but still a logistic one.

Ok, the extra `s' makes it clear. And for what it is worth, I agree.

I agree, your answer reflects my personal view

First, writing the paper is not mere "logistics". The difference between a well-written paper and a badly written version of the same paper is huge. Second, according to the question, the advisor directed the research and defined the problems: again, two very significant contributions. You see it as the adviser-CEO seeking credit for the student-artist's work; maybe it's actually the student-bricklayer seeking credit for the advisor-architect's building? (Probably, it's neither of these things.)

@DavidRicherby: The OP claims "In my research, My adviser only gives minimal advice that limited to the direction of the research and defining the problems." + some explanations. Together with the change of the title of the question which gives the supervisor more credit, he (the supervisor) is a good candidate for second author. Again I assume that the description of the OP is true and not biased. Finally, the reason given by the supervisor is not that he is the "architect" you mention but needs to be prominently published to be tenured.

@WoJ Bear in mind that students tend to underestimate the contribution made by their advisor. I'm not claiming that the advisor definitely ought to be first author; I'm just saying that I think the situation is more complex than you do and that we don't have enough information to make any call about who should be first author.

@DavidRicherby: absolutely agree with the estimate, thus my comment about bias. Now: as much as it may be difficult for a student to estimate their supervisor's contributions, I have seen many (way too many) cases where a student was forced to get invisible by his n+whatever supervisor. This was particularly true for interesting results.

(followup from previous comment) I had the great chance to never have been subjected to that - it was actually the other way round twice (the first time my supervisor asked to be second author, while I fairly rated his contribution as first author; in the second case he asked me to be removed from the paper "because this is really interesting work, not worth diluting with a second author").

No, sounds like you've been stiffed. It is not unusual for an academic to write-up the results of research for a masters or UG student, but they should be using the opportunity as a chance for you to develop your writing skills (to complement your research skills) not hog the credit (as in this case). What you supervisor is doing verges on academic misconduct in Computer Science. Ignore the many ill-informed comments on this site, your supervisor has failed in his duty to help you develop as a researcher and is exploiting you for his own selfish ends.


text:
What to do when a referee wants to criticize someone else through me
A couple of months ago I submitted a paper for which a referee review came back recently, recommending minor corrections. There are two methods to calculate some quantities in the literature which do not agree between each other. My paper agrees with one of them and not with the other, which I know is incorrect. However, in my paper I did not point this out (that it is incorrect, I do mention the other method), but simply focused instead on the method I use.
Now, the referee seems to be eager for me to profusely comment on the incorrect method and specifically refer to several papers written by people from the same group using this particular method. I get the impression that this referee is trying to use me to criticize them. I would prefer to be as diplomatic as possible, and remain in good terms with the others who use the incorrect method, who I have met in person several times. However, openly stating their method to be wrong, even if choosing the wording to be as nice as possible, would make that difficult.
What should I do in this case?

However, in my paper I did not point this out — Uh-oh.  Don't do that.  You don't necessarily need to criticise the other method, but you do need to admit that it exists and differs from yours.

I mentioned it exists, and that it's a different approach. I left it at that, because if I say it's incorrect then I obviously need to argue why.

By saying the two methods do not agree, do you mean that they give different outcomes, or only that they arrive at the outcome by different routes?

@JessicaB They give different outcomes

Well, since I see from your profile that you're in Physics and doing numerical simulations, I have ask if the formula other guys are using/proposing is provably wrong in the mathematical sense of the notion of proof or just a worse approximation in practice. It kinda hinges on that how you present your case. N.B. I said formula for simplicity, but it's probably something more complex like an algorithm etc.

@Respawned_Fluff It's a formula that is used outside its range of applicability, based on the approximations it hangs onto.

In my opinion, having a proof that a method is incorrect and keeping it to yourself due to diplomatic/social concerns is neither the scientific nor the friendly thing to do.
If I was working in a group which uses a method frequently I'd expect a friend knowing that it was flawed to share his/her concerns with me in a constructive and friendly manner, knowing that the next researcher who discovers such flaws might not be friendly about it. I'd also hate to be putting time and effort based on something flawed.
Once that was done by that friend, we could find out between us whether the method is really flawed. If it is, I won't be offended if it's published in a paper he wrote.

If the two calculations give different results, then writing one in a paper gives a proof that the other is incorrect. As I understand it, the OP simply doesn't want to write the corollary 'so the other method is incorrect' explicitly. The reader will have to decide for themselves which they believe either way.

How about talking to them about the different results, instead naming various people using as using an inferior formula in a published paper?

First, remember that the review is not "the word of (your) god", it is a professional view of a peer. Now, it is customary to report on aspects that support and do not support your findings. Whether it is reasonable to mention the second, apparently flawed way to do a calculation, cannot be judged here but you should see if it can and indeed should be at least mentioned. In the end, you also have the right to have a different opinion than that given by your peer reviewer. Hence, you should provide your view to the editor on why you think following this particular point is superfluous. It does not appear to change anything in your conclusions and of that is correct it seems as a no-brainer.
So first consider if you can work in a comment to the fact that there are other ways to do a calculation, if need be with an argument why you have chosen as you have done. Second, make your point clear to the editor stating that you do not see a major point in dwelling on the reviewers point since it does not affect the result you have arrived at. How and what you express will of course only be possible for you to judge.

In your paper, you do need to acknowledge the existence of the other method, especially if it is a frequently used alternative.  This is because you need to explain why you chose the method that you chose.
You do not, however, need to criticize the other method as wrong.  Instead, you can simply explain what are the advantageous properties of the method that you are using.
A good way to think about this is to remember that you are not actually choosing between Method A and Method B.  Rather, you are choosing Method A as sufficient for your purposes, regardless of the existence of Method B or the opportunity to try to create a new Method C.

This is what I did more or less. My question is more about how to deal with the reviewer. The approach I use would be the "mainstream" one.

@Miguel You can still likely say that the approach you choose has certain advantageous properties that the other does now.  As for the reviewer... honestly, you just need to be seen to make a good faith effort to take their comments into account.  And since it's only a "minor revisions" the reviewer might not even see it again.

It sounds from the question like the results from the two methods directly contradict each other, and the OP thinks one of them is actually incorrect. In that case, I think the OP should explain their objections to the result they are not using.

We're all in the same pursuit in science - we want to understand what's happening on a fundamental level. If there are disagreements in calculated or measured/observed quantities, I should think that the natural response to reported discrepancies in those quantities should be "Why do we disagree? What is happening here that we obviously don't understand fully?" or similarly. These disagreements can be turned to something constructive and really ought not be seen negatively by anyone worth their salt in academia. Or so I would think.
There was a similar instance in my own work previously. If you're particularly concerned with a personal outcry from these other researchers, what you could do is reach out to them personally to tell them your findings and try to discuss the answers to the questions I stated above. This way, you're free to publish your results and you might even have a "stimulating discussion" that would allow for future work or collaborations on similar measurements. After all - these might lend themselves to better comprehension of your field of study, and isn't that your end goal?

You can contact the editor directly. Explain your position calmly, as you have done here - you feel you have addressed the issue, and that you think the reviewer's approach is too strong, or why it is not a good fit for your paper. In my experience, editors try to be fair, and if the editor will require you to make the change, they will be able to tell you so directly.

Reach out to the group that has published the "wrong" method and discuss it with them. There may be more to their method that you realize. If at the end of that conversation you agree that there is a problem, they ought not to mind if you publish. If you get to see their point of view you can include it in your response to the editor.
Nobody likes to be surprised by a negative publication (so give them fair warning/try to sort it out) and in scientific publishing you should state the truth as you see it, with appropriate language to convey what is fact and what is speculation. Deliberately leaving things out is inappropriate: there is an old saying in Dutch that "gentle doctors make stinking wounds".

Seems like there are three possible cases here.
1) Do you get comparable results with your data, using both methods? Then that's a useful thing to say: "I chose to use this method, but similar results are obtained with the other method". You can leave it at that.
2) If you get DIFFERENT results, then that's rather more important: you need to describe the difference in outcome, and to explain why your cherry-picked method represents a true interpretation of the data, and why you feel that the differing result from the other method should not be heeded.
3) If the method affects data-gathering, so that you can use only one or the other, then you can't compare them without running the experiment again... which is someone else's job! You have already mentioned the other method, and explained which method you have used. Your method is the mainstream one. Papers exist on the topic of which method is better, and about discovered flaws, but your paper is not about this, so you don't even need to cite those papers: it is an irrelevance.
If it is a bugbear for your reviewer, that's nice for them, but it is not relevant to your paper, and you do not need to go into depth about your selection of the most mainstream method. If you were choosing a minority method, an explanation is relevant, but otherwise it's sufficient to say which method you used, so that people can reproduce your experiment.


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PhD Advisor is Inexperienced Junior Faculty, Possible Bully, Who do I Tell?
I was accepted into a PhD program 3.5 years ago. They hired a new faculty member 2 years ago and I was reassigned to this 'new' person since she didn't have any students of her own. She is interpersonally aggressive and hard to 'read.'
Over the last two years she has produced 1 publishable paper, which was rejected by the journal. I've published 2 in that same time. She was assigned 3 classes to teach by the department, and assigned me to TA for all 3, essentially leaving me in charge of all 150 students. The more work I do for her, the angrier she seems to be. The problem, however, started when she gave me inaccurate information about my requirements for graduation. She told me I had to prepare my dissertation prospectus before doing the department's 3rd core exam, which turned out to be incorrect. I wasted months writing, was then told by another faculty I had to rush my (mandatory) exam, which I failed (6 weeks ago). This is the first thing I've ever failed here.
My advisor told me all students fail the 3rd exam in order to build 'character' in them. However university rules state I am now on probation and another failure would mean I am terminated from the department. She also shared that she was a grader on my 3rd exam and had chosen to vote 'fail' rather than 'conditional pass' because "she wanted to see me do it again." There was no constructive feedback, it just seems like bullying. There was zero information on how to re-do the exam or improve. This is high-stakes.
If the department does fail all students as ritual hazing, I believe the department is doing something unethical. If that statement was false, I consider my advisor to be doing something unethical.
I would like to voice my concerns to the university. What person should I approach? Department Chair? Dean of Students? Dean of College? Office of Graduate Studies? A lawyer? I fear retaliation.

What you describe is extremely bizarre. Why were you “assigned” to this advisor? Normally students have some choice in the matter. Have you talked with other students to compare experiences? Is there a “director of graduate studies” that you can ask about requirements and expectations?

perhaps see https://academia.stackexchange.com/q/78220/72855

+Thomas My department is bizarre; we only have 3 faculty after our PhD program 'split' in half (11 faculty in the other program). My former advisor retired. It is normal for us to be assigned advisors. Most of our students graduate in 4-8 years. I am currently the most junior student here because we have not been accepting new applicants.

Yes, this sounds very unpleasant, but, unfortunately, not entirely unrealistic. Which country? This will inform your procedure. In many Anglo-Saxon countries there are ombudspeople to support students, so this would be the first go-to-point there. Prepare to switch programs/unis if you at all can, the department sounds not in a good shape as described (3 faculty, split, retired advisor, graduation times, no new applicants).

This does indeed sound like bullying, or at least rather odd., and the other comments offer good advice. As a word of warning, though, do not try to judge somebody's worth as an academic by how many papers they put out in a short period - opening with this, or indeed trying to show that she's bad in some other way, probably isn't going to do you any favours. Concentrate on the behavior towards you and the effects of that.

Thank you all for the help. I am a PhD student at a US school. I mentioned the advisor's low publications not as an attack, but as It is part of our revolving conflict. She demands this semester I try to finish/submit two publications with her. In other words, while I study to retake my exam, she has asked I be as productive as I have been in the two previous years combined. I find it overwhelming and lowering my chance of a pass. I have quit one of my two jobs and am speaking with the advocacy center (ombudsman-esque) to get clear requirements. I hope to graduate; I love research.

"She demands this semester I try to finish/submit two publications with her." -- This is an unreasonable, parasitic request. To me that settles it: just run.

I believe properly answering your question depends on providing more specific detail, e.g. which is the country. Institutional structure and the corporate culture can be very different between, say, Mexico and China.
I believe you have a broken relationship with your current advisor. I will not attempt to judge a reason for why she did what you describe, or whether your account is precise and complete.
This means you should primarily focus on getting away from this person while trying to find yourself another PhD advisor. Accomplishing this will do most of the "official communication" for you. The department will know there is a problem, and you both will be moving towards a healthier relationship.
So my answer to you is: the person you should talk to is whoever is responsible for shifting advisors in your institution. If you cannot change advisors for whatever reason, then it is the person responsible for smoothly terminating your contract locally so you can get better training elsewhere. The conflict itself becomes self-evident as you move to a better stand.
Good luck!

Thank you for the advice. Should anyone else find themselves in this situation, please know I also am taking the following steps: 1. contacted the college's staff advisor. 2. Officially resigned (signed/submitted) my student employment; 3. Notified the "advocacy outreach," an ombudsman like place to request clarification of my responsibility/rights during the exam and time-line to graduation.

@Quixotic It is very nice of you to keep others here updated of your experience. Too many colleagues value the PhD degree and duration over the actual experience and skills gained. If it is not working out nor advancing you, moving elsewhere asap is usually the best option. Good luck!

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


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What can a student do if a professor makes special allowances for one student in a course?
In one of my software engineering courses, the syllabus includes two exams (midterm + final), daily quizzes + participation mark, spot quizzes and a group project.
A lot of us asked the professor to drop the midterm and add more weight to the project because we all wanted to build a beautiful project, so eventually we can also add it to our resume. The response was that it would not be possible to drop the midterm but the weight might be reduced, but would have to think about it. (Fair enough).
However, a week later we found out that one of the students in class got exemption from writing midterms, daily quizzes and spot quizzes. That student only has to worry about the project. We asked how this is possible and we learned of a special deal with the professor. So basically when the group projects begin that student will in charge of holding group meetings with different groups and providing feedback to the professor on their progress. So since they have a lot of "workload" they won't be writing quizzes and exams. This option was never mentioned by the professor when the class as a whole asked her to drop the midterm.
So I am wondering, is this legal or even possible? There are a lot of international students in the class too that are simply scared to speak up. I feel it is not fair that one student is exempt from doing all the work.
What should I do? Just keep quiet and mind my own business?
This is a Graduate Computer Science Program.
Additional Details
In the first two weeks the other student wrote quizzes like everyone else and the professor was not happy with the grades of quizzes of some people (everyone except this one person had good marks), so it will be worth a little less. Eventually a week later the student stopped writing quizzes after making this special deal.
I have great relation with the Department Chair and I am also working on a project with them, I am not sure if I should bring this up in our conversation.

@dgraziotin done, thanks for suggestion i changed it to group meeting i think that should be more clear

@gnometorule He is neither of the 2 cases. infact there are other students in class with higher gpa , more industry experience than him. That's why we are all confused how this is possible.

Have you considered that the student may have some health problems or personal circumstances that they don't want to share with the whole class, and this is why the professor made special arrangements for them?

@Johanna Did consider it. Infact he is only taking 1 course this semester others are taking 3 or 4.

Added additional Details.

@Corvus "faculty are often asked to make accommodations for students" Accommodations that make other students suspicious don't seem very accommodating I think?

@Corvus Why does the alternative have to be during the semester subject to the observation of the other students? They don't know about Disability Services. It could be that the teacher is being unfair. Does democracy not request transparency? It could just be after the semester or something so as to not arouse suspicion, be so conspicuous, etc.

@Corvus Please make your comment as an answer, so that I can upvote it. The links to these sources you provide are invaluable.

Is he or will he be hindering towards your success? If not, then solve your problems first and then those of others.

I had a physics class where on the last day, the professor excused one student from having to take the final exam, based on her performance elsewhere in the class. It had exactly zero effect on my grade, so good for her. And good for your fellow student. May you one day be so talented and fortunate as to make a similar impression on a future professor.

This "special treatment" happened to me.  I had a course conflict, and instead of wasting time giving me a special exam, the professor gave me a short take home exam that I finished in 30 minutes and gave me an A+ on the grade.  Why was this done?  The school did not recognize my prior college education, gave me only elective credits, and am forcing me to take introductory CS courses after being in the industry for 8 years.  My midterm was 100%, and showed coding complexity way beyond his course, so he just didn't feel the need to make me take the final.

@JackBauer Does democracy not request transparency? -- With extremely rare exceptions, the classroom is not a democracy.

The arrangements that the professor makes with any other student are absolutely none of your business. I don't see any indication that your grade is threatened. If you are learning what the course aims to teach, it is not your place to second-guess the way that your professor chooses to run her class.
Faculty are often asked to make accommodations for individual students for any number of reasons, and these reasons are not to be made public. In fact, I'm required by law both to offer alternative forms of evaluation where appropriate, and not to explain why I am offering the student an alternative form of evaluation.
For a US perspective, read up on the ADA and FERPA and you'll see an interesting intersection of required accommodations and required privacy on behalf of students with special needs.
[Comments converted to answer by request.]

"what can you do?"...the best answer is that you can...and should...educate yourself on exactly how this other's individual's position and arrangement has anything whatsoever to do with YOUR learning experience and grade in the course.  Is the answer "absolutely nothing?"
There is exactly one way to get ahead in this world, and that's by embodying excellence, and doing good works.  There are, however, a lot of people out there that think there's a second way, which is to diminish the work of others, push them to the side so that your mediocre accomplishments seem adequate in comparison.  This doesn't actually work in practice, at least not for very long.
So the answer is to ask yourself why 1) you think you have all the information about why this particular arrangement has been made, and why an ostensibly smart and experienced professor would make "such a mistake," and 2) why it has anything to do with you?

A harsh answer, but I can't disagree with this. And I'd add that reflecting on this answer can be, imho, very beneficial for the OP.

Having been is a somewhat similar situation myself, I must ask, doesn't this open up new ways of cutting corners for the "right students" without any form of recourse? From the question, the student the op is referring to does not seem to be disadvantaged (having a disability and/or poor economic status); he has taken quizzes for two weeks and then was assigned a task taking less effort by the professor without notifying the remainder of the students of the possibility to do so. While not impacting the op directly, this may have adverse effects on motivation.

There are two possibilities, either the student has some kind of favouritism, or he is being accommodated for health problems. You cannot know which one is it, nor it is your place; but if you suspect the first, you should bring this to the Chair's knowledge. He is the one that can ask your professor for the full story, and he can  make a judgement and has the power to enforce it.
When talking to him, do not make accusations or hint that this may be illegal: just explain the facts as they happened from your point of view. The most you could do is to let him know that you are concerned this may not be fair.
As this arrangement does indeed sound suspicious, he may already have been informed by the lecturer of the situation; and if you start bashing someone because he has a health problem, will make you look bad.
Lastly, be prepared for the answer to be "we have looked into this, and we deemed it appropriate, and that is as much as I can tell you".

I must say that this seems like a somewhat conflicted situation. The professor doesn't consider the syllabus of the course weighted enough, so he emphasizes the project and charges a student with a administrative duty, but relieves them of the written exams and quizzes. You, on the other hand, consider the written part more or equally weighted (although you feel the project needs more weight), so you find it unjust that one student has been relieved of it in exchange for other obligations. Are you really sure the student misses a lot by completing only the project and not the written assignments? Further, are you really sure it is "easier" to lead and prepare group meetings than to learn the materials for exams and quizzes, although you would presumably need the same knowledge to complete the project?
I can understand that you might be agitated that the professor didn't mention such an opportunity in class. Perhaps the student was approached by the professor with some special reason (could be that the professor considers them to be good enough so they can skip the written assignments and/or someone to be a good group manager, or just someone the professor has a working relationship with).
Is this fair? I find this difficult to judge.
What can you do about it? Probably nothing effective. You could talk to some students' delagate or some other institutional body. You could also talk to the professor. In any case, you should be sure what exactly you find unfair (and be able to argument it) and suggest what exactly could be done to mitigate the situation (appoint you you to lead the groups, relieve you of the exams, enforce the exams back on the chosen student, etc.)

It is definitely easy to hold group meetings as he is only reporting on the group progresses nothing more. All the other students feel it is unfair and are not happy. he has only 8 months of industry experience while other students in class have 3 years or 2 years of experience and also they have higher gpa.

Added additional Details.

@user2733436 Being happy is not the purpose of graduate courses.  Also, GPA is irrelevant, once admitted to graduate school. Which student the teacher chooses to cooperate with, depends on soft skills (e.g., not whining, better attitude, less arrogant) that are hard to quantify. However, this student actually did better on exams than you. Perhaps you should strive to catch up with him?

+1 for Being happy is not the purpose of graduate courses. Another +1 for GPA is irrelevant, once admitted to graduate school.

authors: الحياه شبه انعافت


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Research Topic Suggestions
I am applying for Postgraduate degree research but for that I need to submit a Research Proposal with the application and it is very confusing for me because I never did any kind of research before.
I have been a small business owner for the last 7-8 years and I want to do research in the same field (Entrepreneurship or small- or family-business related), but I just don't know how to narrow down and select a specific topic.
Can you suggest some guidelines to select a topic?

I've edited the question because asking for advice about specific research topics is out of scope for this community.

I strongly suggest discussing this issue with the faculty who are writing your recommendation letters; those letters are supposed to address your potential for research.

I have been a small business owner for the last 7-8 years

Have you run into issues/problems in those 7-8 years? Are those problems specific to your own business? Could other business owners have the same or similar problems?
Can you generalize those problems so that you can conduct research on possible solutions to those problems in academic approach?
Can you find the causes of those problems from academic perspective? How would you propose to do so? Should the government play a role or not? How could the society as a whole participate? Etc. Etc. There are hundreds of topics out there. Take your pick. Good luck!

Why do you want to work as a Postdoc in this field? The answer to this question (as long as it's a scientific answer and not reputation etc.) can lead you to a good research topic.
Nonetheless, thechniques like creative writing, brainstorming etc. can be helpful, but this is a bit out of scope for this platform.


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Publishing a work; not sure what should I do
I did a research project for a class. It was a simple idea but I checked literature and no one had applied that method  to that problem before. My method uses a bit of heuristic type stuff. If no one thought of it before is it because it is a bad method or should I publish? Having the name of my instructor is a problem; must it always be on a paper? What if I am instructed not to publish? My instructor is quite busy  and has no intention to deal with the issue and does not read projects so I can't really rely on him to judge.
I want to send it to a conference as the quality of it would not be very high. Should I wait until I have improved my skills for publishing in a respected conference or try to make it published at some other place, like 1st, 2nd 3rd IEEE on foobar of foos type conferences as a starter?

First, you should ask someone famliliar with the field whether it is

really unpublished
a good idea.

Sometimes ideas are very old and might be published in books which are not available online, and therefor harder to find. Or you might have used the wrong terms for your search.
If after that you still think it is a unique and useful idea, you should try to publish it. The "useful" is important here, sometimes people are publishing new stuff which noone applied to the problem before just because it makes little sense with regards to the big picture of the discipline.
If your instructor did contribute to the paper and the research, then it should be on the paper unless he declares it is not necessary. I would ask my student to come with a paper outline first (so you could approach your instructor with a clear plan of the publication), we improve the sketch and then the studet writes the first draft which I as a supervisor try to bring it in a form which suits the standards of the respective conference or journal. Usually, this involves some feedback rounds and includes additional scientific discussion etc. .
From your OP I got the impression your instructor might not be willing to put much effort in it, but sometimes people when they see someone is willing to go an extra mile.
If you are on your own, try to read some books about scientific writing, there are lots of formal errors which can be easily avoided.
I definitely encourage you to try to publish, it is a good experience and, if successful, is great for your CV.

to add to this, sometimes the results are published in a completely different field of study from yours