text:
Is it wrong to repeat yourself in the abstract, introduction and conclusions?
I find that when I writing a paper,
I use the same phrases and sometimes the same sentences
in the abstract, introduction, and conclusions.
When I compare this to non-fiction writing
(e.g. Malcolm Gladwell or Michael Pollan),
my impression is that they do not repeat themselves
in the prologue and epilogue.
However, I realize that they are writing non-fiction books/articles,
whereas we are writing scientific articles,
for a different audience and a different purpose.
My questions are:

Does using the same phrases and sentences
in the abstract, introduction and conclusions
make my paper boring to read?
Or is it easier to read and understand a paper if it repeats itself?

I'd rephrase the sentence for the sanity of the reader, but the content may be a repetition.

See also: What is the difference between Abstract, conclusion and summary?.

The three things are doing pretty different jobs, and so should be pretty different in content.
The abstract is an advert for your paper.  Someone might read a list of titles and abstracts (for example on arXiv) and decide on that basis whether it's worth their while downloading and reading the rest of the paper.  The abstract has to be attractive, but not fraudulent ('truth in advertising'!).  When you read an abstract, you're trying to find out: (i) is this paper in my area?, (ii) is it asking a question I care about? (iii) does the conclusion sound interesting?  You don't have to summarise the whole paper, but you do have to answer those questions.
The introduction gives your reader a map of the paper.  By the end of the introduction, your reader should have a pretty good idea of what they're in for, and where they're going to end up.  They should know what sections they're probably going to skip, and which ones they look forward to disagreeing with.  A paper is not a detective novel: you don't need cliffhangers or mysteries.
After that, the conclusion doesn't have a lot of work to do (at least in my experience).  It might be the last thing the reader reads of your paper (that is, unless they care enough about its contents that they'll re-read it), so this is an opportunity for you to frame their memory of it.  "We have shown that ..." is the sort of thing you'd find here.
Key points:

Remember the reader is a human being, just like you – talk to them, as you'd like to be talked to (far far too many people bizarrely forget this).
Make it easy for them to read the paper, and easy to agree with you (that's why the introduction has a map of the paper, to ease the reader's way through your golden prose).
Your reader is asking themself "why am I reading this paper?"  Make sure they have a good answer to that question by the end of the introduction. If you get a colleague to read your draft, get them to answer that question at that point.  If they don't give the answer you want them to, it's your fault; so edit.

There will probably be some overlap in text in the three parts.  That's OK, but it probably shouldn't be cut-and-paste.

There are many examples of papers where there is repetition in these part. While this is not wrong, it is not something one should adopt as a way of writing. It is important to write each part so that the text is adapted to be included seamlessly in that part.
The discussion should lead up to the conclusion(s) of the paper and from this perspective it is the origin of the content that will be repeated (in context) in the other parts. The conclusion should summarize the main findings of the discussion. Since the point is to provide the important points in a brief way, one should at least try to write it with the summarizing in mind. The abstract should summarize the entire paper and lead up to the main conclusion(s) of the paper. This is most often focussing on a subset of what is summarized in the conclusions.
Copy-pasting sentences from discussion to conclusions and to abstract means you build in sentence structures that may not be optimal for the different parts. I therefore suggest at least trying to rewrite the information for each part so that they become optimized in each case. If a sentence you have already written fits very well, then its use is fine but if you simply try to force sentences in the resulting text might not be as clear as it could be. So, in general, write everything as a new text based on the story you are trying to convey rather than inheriting structure from what you have written already stemming from a different context.

I'm not bothered by the repetition of sentences if they are isolated sentences, that serve as a link. However it is inelegant, you can always put a cross reference and reword what you say in some other place, for several reasons:

Style in writing, you should show some knowledge about the language and the capability of paraphrasing.
Fit better the contents to the context where they are.
Writing the same thing in several different ways helps people to understand what is written there. English, as most (probably all) other languages has an inherent level of ambiguity, some sentences can have several meanings. If you rewrite some sentence with some different words by doing so you can make clear that the meaning of both sentences is in the intersection of the potential meanings of both sentences.

I find the third reason is the most important and other answers were missing this aspect, so I had to drop another...
Having said this, the repetition of a paragraph is unacceptable for me. If there is some paragraph in some part of the paper and you want to refer to this same piece of information you should summarize the contents of the paragraph in a sentence (sometimes in a term, e.g. when the paragraph is a definition).
This answer isn't very constructive and I feel obliged to provide constructive answers so...
Take the abstract as a reference. It will summarize the paper, as the introduction does and also the conclusions.

In the abstract you provide the shortest summary and describe what have you done.
In the introduction you extend that summary and describe the context of your work (some people include the motivation). It is different from the abstract because you don't say what you have done, but why it was missing, why you have done it and where in the paper you explain into more detail these aspects.
In the conclusions you evaluate what you have done, how it serves to fill the gap that you identified in the introduction and the gaps that remain (future work).

All these are similar but not equal.
BTW: related question: https://tex.stackexchange.com/questions/181080/automate-the-description-of-the-paper I should get back to that...


text:
How to share computer code?
I am writing a paper with my adviser.
Some of the key contributions of our paper include:

A computer simulation model of an inventory system
A set of simulation experiments and results to validate the simulation model
An implementation of an inventory policy which we propose
Simulation results of our proposed inventory policy and inventory policies which are currently used in practice

We want to make our computer code freely available to others.
The simulation model was written in the Java programming language so other researchers should be able to run the code on their own computers fairly easily.
By sharing our computer code, we hope that other researchers will develop inventory policies which they can test using our simulation model.
(Of course, it would be beneficial for us if they would do so and cite us in their paper!)
Question: What is a good way to go about sharing our computer code?

Where do I host the code?
Which software license should we "publish" the code under?
How do I make it easy for other people to run the code?

And screenshots or (even better) working examples on web (without any installation) do miracles.

CC licenses should not be used for software. This is unfortunate, as there's no similarly clear pick-your-license-rules for software. http://choosealicense.com/ or http://tldrlegal.com should help you choose.

@TimS. There's one exception: The CC0 license can be used for software. It's a simple permissive license.

Not relevant to you, but IPOL is a journal in image processing that asks you to publish an implemented code along with the paper, in a way that enables anyone to test it live: check it out: http://www.ipol.im/ (go to any article to test its code in minutes).

You might be interested in the Software Heritage initiative: https://www.softwareheritage.org/

Answer to 1: Where should I host my code?
Depending on what your University offers you, you could choose to host it with the University, or perhaps with an open-source repository such as Github, Bitbucket, SourceForge, or similar.
Many of these services have a "paid" subscription option for private repositories if those are required.
Answer to 2: What open-source license should I choose?
This question is relevant because we're having this discussion right now within one of our own research projects. I happen to know a little about open source software, having researched it in the past and having taught a few courses on it.
Though there are a lot of open-source licenses out there, they really end up coming in two main families. They're either permissive open licenses (ex: MIT, BSD, Apache) or they are Free (GNU Public License v2 or GPLv3). Here's a brief lowdown by the Open Source Initiative
Permissive open licenses These licenses generally allow you to release your code and anyone can do anything with them that they want as long as they retain certain copyright information with the code. In reality, this has a number of implications.

Someone could take your entire code base, create a product with it, and sell it.
Someone could take parts of your code, put it in their own project (commercial or not).
Because the license is more permissive, you yourself could take the code, close it, and then keep under wraps any future releases so you can make money off of the code or hide it from the public.
Because the license is more permissive, you might generate more interest as a result. People may take code from other projects and use it to improve yours. On the flip-side, they could also make improvements for your source code and never share them back with you.

On the flip-side, the GNU GPL is a Free Software License that disallows you from doing certain things. In that sense, it's more restrictive, but does so for a number of ideological reasons.

If you release software under the GPL, you can't close-source it. Ever. It's going to remain in the open, and if someone asks you for the source code you are obligated by the terms of the license to provide it (if you host it on Github or another public repository, then you have already satisfied this requirement).
A company could take the code and make products with it and sell it (it's their right to do so), but they would have to do so under the condition that any source code that they write for the project is also released under the GPL. Because of this, a lot of companies who make a lot of money writing software don't like this because they have to continually release code to the public. On the flip-side, any cool stuff that they do gets put into the public under the GPL, so you could fold it back into your project and improve it. They can't take your code, improve it, and then never share it again.
If you happen to have used any GPL code in your project (let's say you took a few lines out of the Linux kernel or Git version control or whatever) then you'll have to release your code as GPL as well.

In the end, the choice of license affects more about how you want the software to be used (and the eventual community it might bring in). If you plan to commercialize the software, (and implicitly allow others to do the same), then you might want to lean BSD. If you don't want people to take your hard work and profit off of it without showing you the results, then you want to go GPL. If you don't care either way, then you could probably just choose one. I think BSD is popular in academia precisely because of the commercialization aspect (for example LLVM is gaining a lot of traction because of its permissive license).
Answer for 3: How do I make it easy for others to run the code?
You make it easy to run code by engineering it to be easy to run and by being extremely detailed with your documentation.
Packaging/distribution can actually be pretty hard and usually take more effort than most people would think. A good way to make the software easy to run is to test it on multiple machines. Make sure that you're not forgetting any of the libraries that you're using in your software project, for example, and when possible, try to use software libraries that are common and well-maintained. Use mainstream languages with easy-to-manage package repositories.
When appropriate, use installers, installer scripts, Makefiles (distutils, which uses automake/autoconf is better), etc. Even shell scripts are better than nothing. If you can provide binaries and/or an installer, that will make things even easier. The problem is that this is a LOT of work!
Accompany it with documentation. Ideally, the documentation will contain a description of how to set it up and run it, with descriptions of necessary packages/libraries, data that you might have to get, and what to type or click on. Usually, something called README or INSTALL will attract attention. Put the instructions on the web page as well, most of the hosting solutions also allow you to have web pages.
Hope this all helps. The hardest part of the process is by far Step #3 and most people don't get as far as to use good techniques like installers, automake/autoconf, and so forth because it's a LOT of work and development often moves faster than you can write documents. However, no one is grading you on your style so it's often easier to get it out than it is to clean it up and prettify it first.

Re your part about paid subscriptions: Bitbucket has a free plan for academics only that gives you unlimited free private repos.

Whatever license you choose, you can always use it yourself in any way you like, because you are the copyright holder. This means, you can use it in a closed source project, even if you have chosen GPL as the license.

Keep in mind that GPL is a non-exclusive license. So if you are the owner of the copyright (careful: if you're paid for your work, in many jurisdictions the employer owns the copyright!) you can in addition to the free & open GPLd version provide non-free, closed versions. I.e. GPLing your code still allows you to sell non-free/closed source licenses e.g. to a company who wants to use your code in their non-free/closed product. (Of course only if your doesn't include third party software with a license that prevents this)

If you release software under the GPL, you can't close-source it. Ever. It's going to remain in the open, and if someone asks you for the source code you are obligated by the terms of the license to provide it. This is false. If you release your own software under the GPL, you can relicense it at any time. Others are still allowed redistribute your GPL-published software and its source, but you have no obligations, and you can also decide that from a certain point onwards new versions are no longer GPL.

Under point 1, I would add a note about the importance of using a system that archives your code. For example, zenodo integrates with github to provide proper archiving of github releases. This is essential for academic work. https://guides.github.com/activities/citable-code/

"They're either permissive open licenses [...] or they are Free [...]." Nope. A free license can be permissive or copyleft. Any permissive license is a free license. A given license is free iff the user is granted the four essential freedoms as defined by the Free Software Foundation.

Actually, if you plan to commercialise your own software, GPL gives you considerably more commercial advantage than a BSD/MIT license. While the GPL prevents your competitors from adding features to the code without giving away the source (thus letting you distribute it with your GPL'd code), you, as the code owner, are under no such restriction for your own code and can sell features for which you do not give away the source.

Back in the day when Docker wasn't a thing, distributing "executable code" was really hard. However, I'd suggest the OP have a look at Docker as a potential way of distributing the runnable code as a docker image for folks to execute without installing anything other than the Docker Engine.

Careful! As long as the code is yours, you can do with it as you please, going forward. I.e. release version 1 as open source, modify it and close it as version 2. Version 1 is open source, and stays that way. Also make sure the code is yours. If part of a research project, whoever granted the monies probably has rights on the results. If you were hired by the project, the project is owner of what you wrote. At least here in Chile, by law whatever you develop as part of your education belongs to your school.

To some extent, the answer will depend on what you wish to accomplish with this release.  There was a fantastic blog post recently on that precise topic.
If the code is of great shape, and you hope others will build on it, then choosing the licence is going to reflect your philosophy. A BSD style license if you just want the algorithm and code out there, or perhaps a Copyleft (GPL) style licence if you want to make sure improvements return to the commons.
If the code isn't in such great shape, but for transparency's sake needs to be out there, consider something along the lines of the CRAPL, which acknowledges the messy nature of modern computational sciences. I think the preamble is worth quoting:
I. Preamble

Science thrives on openness.

In modern science, it is often infeasible to replicate claims without
access to the software underlying those claims.

Let's all be honest: when scientists write code, aesthetics and
software engineering principles take a back seat to having running,
working code before a deadline.

So, let's release the ugly.  And, let's be proud of that.

As far as the actual mechanics of putting the code up, use GitHub or Bitbucket. These services are going to give you code hosting, a home for the project, the ability to manage contribution, and the ability to track bugs and issues.

As an addendum, both Github and Bitbucket offer academic accounts if you register with an institutional e-mail address. That way, you don't even have to mix up with your regular account if you already have one.

Something to maybe use in conjunction with github and bitbucket is readthedocs (https://readthedocs.org/)  It would allow for you to generate a nice site with code documentation, installation instructions etc... Very useful site.

I would warn agains copyleft licenses (unless someone has a very good reason to go with it). It is de facto restrictive, as not every product can use it.

@PiotrMigdal: as long as it is a non-exclusive license (such as the GPL) and the original copyright is in one hand, copyleft is no problem: you (or probably rather: your employer/university) can license it in addition under different terms to anyone who needs special terms. It often becomes a problem once you have several owners of copyright for parts of the code. I'd put more emphasis on having a similar license to "surrounding" software (e.g. for an R package, copyleft is perfectly sensible even if that is not already required due to dependencies of copyleft packages)

@cbeleites It is non-exclusive, but as soon as other people start contributing (and it is one of goals of open licenses), to put another license on the new content, AFAIK, requires every contributor to agree.  If project is successful to any degree, it effectively becomes impossible. I don't claim that people should not use GPL (certainly, there are use cases); just that its consequences are less trivial than a newbie in open software can imagine (most importantly, that copyleft is not the most permissive).

Matthew G. and Irwin have given great answers, but I'd like to provide some additional
resources and references for those interested.
First, take a look at answers to this similar question on scicomp.SE:

What material should I include with a journal article (or post online) in order to make my computational research reproducible?

Reproducibility was the subject of a 2012 workshop at ICERM; you'll find a lot of useful material on the wiki and in the final report (see especially appendices D, E, and F).
Archival/hosting
Update:You can get a DOI and permanent hosting for a snapshot of your code via Figshare or Zenodo.
Licensing
See this section of the wiki for an extensive list of resources.
Making it easy to run the code
There are some sites and tools out there aimed specifically at this.  These also solve the hosting issue:

ActivePapers: An ActivePaper is a single file containing all the software and datasets related to a research project.
RunMyCode: This service is based on the innovative concept of a companion
website associated with a scientific publication.

A major hurdle is often re-creating the correct environment (including libraries and such) necessary to run the code.  To overcome this, you could

distribute a virtual machine or use Vagrant or CDE
ensure that your code runs on some cloud platform, like

Wakari
SageMathCloud
Amazon web services
Windows Azure

It can be useful to put your code in a worksheet format, where you can intersperse comments and even mathematical formulas (for instance, using the IPython notebook  or a Sage worksheet.  Here is an example.
Examples
Finally, here are some examples of my own efforts.  They're far from perfect, but may still be helpful.

+1 for mentioning virtual machines. I think that this is a big deal for a number of disciplines where reproduction has historically be difficult.

I recommend github.
The other answers given are well detailed and include it but given a bunch of other choices.  Choice is obviously good.  Without specific advantages listed though I am suggesting you just go with github.
My rationale is that I feel that github has become a clear leader in the field of code storing and sharing.  It's underlying technology of git as a modern dvcs system has largely replaced older technologies such as svn.  It now has over 2.8 million users which is quite impressive.
Github is also great for code collaboration, allowing for multiple people to edit and merge their changes in in a controlled but decentralized fashion.
Github allows you to have both public (anyone can view) as well as private repositories that you control view access to.  For updating, you add the requested users ssh keys to grant update access.

All the answers above are great. I would just like to add that, if you plan to publish it on your lab's website or any personal website, you should also copy it somewhere else.
In many fields, it appears that data (including original programs) is disappearing all the time. When a lab moves to another University, closes, or undergoes any kind of restructuration, its website is likely to change, and data stored there can be lost. So, unless your University has a centralised repository, you should put your code where it can stay for decades, for instance on Github.

In my opinion, It is related to the specific code you want to share.
I just want to give an example, for JavaScript code you can share it on http://jsfiddle.net/
We can test our JavaScript, CSS, HTML or CoffeeScript online in the web. There is also an option for inviting people to collaborate in developing our code.
Good luck.

Nice point; welcome to academia.SE!

For my graduation paper I shared my code by printing it all out as a companion volume to the main research paper.
Mind this was pre-internet, and the paper (and code) was classified so very few people would ever read it.
I did put it all on floppy and included copies of that with the printed paper as well.

These days, you'd likely put it on a server somewhere where all those who have access to the paper can access the code, and nobody else.
Of course you will need to figure out who that will be. Most research papers are considered company secrets (or department secrets) and not for public distribution. Your code would fall under the same restrictions.
Just throwing it out there on github, google code, or source forge without prior permission from your employers/coordinators isn't going to make you many friends, in fact you could end up with a rather hefty claim for damages and/or prison time for doing so.

Perhaps.  Please be aware that with github you can have a public repository that is effectively 'throwing your code' out there.  Github does, however, also have private repositories that you control access to via people ssh keys.

I strongly disagree with your view on access to the code. If it is a scientific research paper, you would by definition want as many as possible to be able to read it. As scientists and researchers I believe we have an obligation to ensure that our published research results are reproducible. If software that we develop is responsible for those results, we should publish that software along with the paper. Otherwise, the results are not worth much.

@ThomasArildsen that's nice in theory. In practice much scientific research falls under NDAs and security regimes that make public disclosure impossible for a long time after completion of the project, and/or without prior permission from the organisation funding it.

@jwenting It is very unfortunate when funders' requirements restrict research in this way and I think we should try to avoid it as much as we can. In the last two research projects I have been involved in, our receiving the grants has been positively influenced by the fact that we promised to publish all of the code.

@ThomasArildsen yes and no. As there are often major commercial incentives involved in the results of your research (and/or major political consequences) security if often needed for the sake of those funding the program. Yes, you not being able to talk about it to just anyone without getting that person to sign an NDA as well can delay or prevent ideas from entering the team, but without that process there'd often be no team at all.

There's lots of good advice in the various answers; I'm going to address only point 3, "How do I make it easy for other people to run the code?"
The answer here is to automate as much as possible. This will have the added benefit of making your life easier, too, as you'll spend less time typing (and retyping) magic incantations and checking output.
Start, as early as possible, with a top-level script (I usually call it Test) that builds and tests all your code. (This is always the first thing I write.) In your case it sounds like it's too late to start with it, but add it now and grow it in the same way.
Every time you do a new checkout or clone of your repository, start by running the Test script. When it reaches the first error of any kind, consider how you could tweak the script to get rid of that error (if that's easy to do) or detect the error condition and give some informative message to the user. For example, if you depend on libfrozzit and its header files being present for you to compile, you may not be able to install it, but you can at least try to check for its presence and, if absent, fail with, "libfrozzit not found. Install with apt-get frozzit-dev or yum install frozzit-devel?"
Write tests of any kind, whether basic unit tests or functional tests, for your code. Even picking the simplest function and sending one value through it, or running myprogram --help and ensuring it prints any message whatsoever, means you've started a test framework and makes it much, much easier for someone else to come along and add a test. If you can get up to, say, 5% test coverage of your code that's a significant benefit because even that much will be a great help to someone who's wondering if the code was built properly.
Making code easy for others to build and run isn't magic, and can't be done by waving a wand or running a special tool. It's a matter of saying, every time you find yourself doing a manual tweak to get things to work, no matter how simple, asking yourself "how would I automate away the need for that manual tweak"?

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How large may included parts from other people's work be in an academic paper?
Of course, it is absolutely important to quote all thoughts that did not originate from the author. This makes one think that it would be OK to include works of others when referencing them correctly.
For example, consider that one had that really great list of problems that also apply to your own paper. Is it legal and/or legitimate to write about that list, include the key points in your work and reference the original author?
I am facing that situation where I want to include some key aspects but quoting all of them and describing them individually feels like copying too much, even though I explicitly state that the aspects originate from another paper with referencing to it.

You can include any material that is published as long as you appropriately cite the material (source). If you think any phrasing made by the author(s) is key, then you can do it as a quote where the text is reproduced in verbatim. If you do not use quotes you need to rephrase the text in your own words since it would otherwise be considered as a form of plagiarism. So, just be careful with referencing and quotes if necessary. It is better to have cited one time too many than the opposite.

Thank you! Does "published" mean that it simply is available? Saying it the other way round: Is there a distinction between works that are for sale and those that are freely available?

Isn't there a copyright issue if large parts of a work are reproduced, though?

In general, I cannot see any distinction as long as the material is cited and quoted appropriately. What you are alluding to is something that would be covered by a copyright law that prohibits any reproduction of even a formulation. There is clearly a limit to how much can be included although the limits is not easily determined.

Idea-wise it's hard to tell. It'd depend on how different your interpretations of the problems are compared to the original author's. It'd be prudent to consult a couple other researchers/peers for some objective inputs.
Format-wise, of course you can cite anything up to any amount. One way to do that is through block quotation. I have seen pages and pages of run-on quotes. Just double check, again, with some people in the same field to make sure your quoting style is not too outlandish, just because it's legal to do does not mean it's culturally appropriate to do.
Since it's just a list of questions, another way I can see working around this is to tabulate them in your work, attributing the list to the original author in the caption or footnote of the table. Then, in your text, refer to the questions through the table.

It would be prudent to look up the journal's policy on such matters, as the exact answer depends on the publisher. Example: Oxford Journals let you copy a maximum of two figures (post-1998) from a journal article, and five per issue. Above these limits, specific permission is needed.
If in doubt, ask the publisher of the material you're citing if it's OK.

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Can I be admitted into graduate school in the US without undergrad degree (if I have master degree)
I am considering getting a PhD or an MBA in the United States. I do not have a bachelor's degree, but I'm working on finishing a MSc in Computer Science from a UK university. By the time I'll be done with the degree, I will have more than ten years of experience in the IT sector in various positions and in various corporate environments (startups, corporate, government).
Do most universities in the US waive the undergraduate degree requirement if applicants have a UK master degree (without any undergraduate degree) from an accredited UK university?

could you clarify your past education? I find the Msc degree(how many years 1?2?) part a bit confusing. Also, do you have any other (CS-related or not) degree?

The MSc is two years and includes a thesis. I finished high-school (got distinction award for being in the top 5% in the country for that year). I have been in senior positions as an engineer/researcher and junior positions as manager. I do not have any undergraduate degree.

I've tried to reword the question to be clearer and seeking answers more fact-based and less opinion-based.

I do not know the answer for my own (US CS) department, but I'll ask.

The simply fact of the matter is that you have to ask each program you are interested in directly. Some schools have a specific bachelor degree requirement, some don't. Like all bureaucracies the costs of bending this rule can be quite large. Being an international student might actually make it easier since the offices that deal with international students have to do a lot of personalized evaluations anyway.  What all schools do have is a contact address for exactly these kinds of questions usually it can be done by e-mail now. So my best advice is to ask directly the people who make these decisions and not the "internet."
Once you learn whether or not there is a possibility of this plan working then you can worry about funding. The resident versus non-resident price difference only applies to public run universities but can be very significant. It does vary by which state the school is in does really matter. For example in North Carolina I know of a person who work for three years as a sheriff deputy (county-wide police officer) who was not granted in-state status at their universities.

Note that most PhD students shouldn't have to pay tuition charges; this should be taken care of by the advisor or department. This is almost an iron-clad rule in science and engineering. It may or may not be true in humanities departments, but I can't ever recall a PhD student who actually had to pay tuition for her studies.

@aeismail outside of science and engineering it is common for PhD students to not be funded the whole time. In pre-professional masters programs like MBA, actuary, law,  anything health related funding is rare.

I know professional programs are rarely paid for (the one exception I know of is an MD-PhD program). However, I also believe that the tuition charges in many humanities programs can decrease significantly once the candidate stops taking classes and starts doing research (and teaching) more or less full time.


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What exactly does one do in a PhD?
I am a first year undergraduate student pursuing a B.S. in Chemistry (I'm very much interested in Biology too), and I am new to this world of Academia. It would be very helpful if someone could answer my questions.
What exactly does one do in a PhD? I know that in the first year, you take a lot of advanced courses on your specific field of study, and then you decide on a topic and start researching. But when do you stop? I see that there is no definite time limit for completing a PhD. It can be anywhere from two years to... is there an upper limit? Do you complete a PhD when you have discovered something new and published a paper on it?
I realise a lot of what I'm saying might be my own ideas of what happens. Please feel free to correct me.

The Ph.D. Grind, a 122-page e-book, is the first known detailed account of an entire Ph.D. experience.http://www.pgbovine.net/PhD-memoir.htm

But when do you stop? - About a year after you're completely sick of your thesis.

@J.A.F that was a good read, thank you for posting the link!

First, it may be important to remember the purpose of graduate school and a research education. When you receive a PhD, it signifies that you have reached the pinnacle of the education system (some compare this to a pyramid where the Phd education is at the top; there is no higher way of organized education). You have reached a level where you should be able to learn on your own without supervision or advise. More specifically, you should also have reached a level of critical and creative thinking where you can successfully function as a researcher, coming up with new ideas, applying and receiving research grants, be considered an expert in your field, able to teach and advise PhD students. These are all overarching goals with a PhD education. As you can see it is partly a deep understanding of your field but also deep understanding of general academic skills.
Phd programs are different in terms of length and content. Some will have up to two years of courses (such as math programs in my country) and some may not have any course requirements (sometimes defined by an individual study plan defined by the student and his/her advisor). The course work is there to provide necessary background for the project done within a PhD. In most cases, I would argue that the exact courses taken during a PhD are of little formal value, the PhD thesis is what counts in the end. In general, the course work should provide you with whatever basic skills you need. My own experience in graduate school was, however, that I found that I did not need all the courses I planned for when I started. I simply felt that courses became inefficient ways of learning, that I could do it on my own faster. This, for me was a revelation, but, I believe, a natural development. So the amount of course work is individual and depends on the field/topic you are studying.
The length of a PhD project will vary from, for example, 3 year as is the case in the UK to maybe 6-7 years in other academic cultures. Around four years seems to be a fairly normal period. What is achieved within this period is defined by the results but not in terms of excellence of the results. There is of course nothing wrong if you come up with ground-breaking results, but that is not something that can be ordered. Instead the importance lies in the skills you display in terms of the scientific investigations (techniques, analysis) through the conclusions you draw from your work and to how well you write up your findings in a thesis (be it a monograph or a collection of papers). Your advisor should be there to coach you to take the necessary steps towards reaching these goals.


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Reviewing demo papers, poster papers or extended abstracts
I have a fairly straightforward approach to reviewing papers: I start by figuring out the main claims the paper makes, and figure out how those claims are proved. From there I start "zooming in to the details". But the primary question is always: does the paper make a claim, and if so, is it proved?
However, some tracks of conferences do not require a full paper. Instead, they require short form papers or extended abstracts describing what the authors will do at the conference. For instance, describing a poster or a demo they will present.
What are some general criteria/strategies for reviewing such papers? How can I come to a well-reasoned decision to reject, if there are no "mortal sins" (like a flawed evaluation) for such papers?

Not an exhaustive list, but the standard questions of novelty, relevance and so on may be a good starting point. But I suppose you are asking for things specific to demo / poster papers.

IMO, the following guidelines might help:

Extent of novelty
Quality of the figures and tables
Dedication

Although the third point may seem a little fuzzy, it can be easily observed on sight, especially in the case of poster presentations.


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Advisor accused of personal misconduct -- what should I do?
My advisor was recently accused of personal misconduct. He says he is innocent.
I am posting here to ask what I should do. I am heavily reliant on his letter of recommendation. I will always be grateful for his support. However my fellow colleagues said that I should distance myself, as continuing to be associated with him will harm me professionally.
The university has already found him responsible for the misconduct.

There are a few considerations, at least.
First, is that if you feel personally at risk from the alleged behavior, keep your distance just for your own safety. That is distinct from academic considerations.
Next, the behavior is alleged, not proved. While it is appropriate to be wary, don't try to judge it yourself unless you have additional information.
Next, in many cases, I would say most, it is appropriate to distinguish between personal behavior (possibly very bad) and scientific/academic quality of the work. Let me focus on this aspect.
In the history of academic discourse and advancement, many fine results have been obtained by terrible people. This is true in many fields and over a long period of time. The work done by these people doesn't disappear just because they wound up chastised by their peers, or even arrested and jailed. They get referenced. Historically, you won't find all of the cases as they are often covered up, but some you will and they can be pretty bad.
My advice, even if the person is guilty, is to separate the person from the work. If the work has merit, then cite it as usual. Focus on the work.
The question of continuing to work closely with the person is a different one, however, as is the question of the value of letters of recommendation. Some separation of the person from the work is possible here also, but perhaps not as completely. For example, it is probably a mistake to become a defender of the person if it can be interpreted as a defense of the alleged actions.
Letters of recommendation may be necessary and may be fine as long as the letter focuses on your work and doesn't imply anything more. But you may have to explain, in interviews and such, that you distance yourself from any bad behavior, even if not proved. Here the distinction is between the bad behavior (distance) and the person (neutrality - more or less). However, don't depend solely on letters from someone who has been severely sanctioned either legally or academically.

Perhaps you answered before J. Doe edited, but they've now stated the university has found him responsible. I'm not sure whether you're still considering that "alleged."

Well, @AzorAhai, I'll guess I'll leave it on the theory that answers should be somewhat timeless and useful for the future. I think my answer would be the same though one paragraph is a bit obsolete.

Fair enough, just giving you a heads up since it tells me they were posted around the same itme.

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


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For undergraduates, is publishing "weak" research better than not publishing?
As an undergraduate student, I have worked on some projects for my own interest, and recently a professor said that one of these works can be published (in a Elsevier journal with impact factor of about 2). I personally think that this work is not strong enough to be published and included in my resume. (I don't have any prior experience in publishing and related stuff.)
Can a weak research article published in a journal affect my application for graduate school in a negative way?

I don't think it'll have a negative effect for graduate school as this is not expected from undergraduates. In my case I had one article in preparation when I was applying, but I don't think that was a decisive factor for my admission. The rest of the people I know didn't have one and yet got admitted.

I asked a related question, but from the other (hiring) side: http://academia.stackexchange.com/q/7908/929

Unfortunately, weak published work is usually considered positively, while personally, if I see something which I find to be a waste of paper, it degrades my appreciation of the author (... unless they're an undergraduate, in which case I'll chalk it up to the follies of youth or something).

There are very few circumstances under which I think it's a bad idea for undergraduates to write research papers. These primarily have to do with the quality of the journal: so long as it is a reputable, peer-reviewed journal, I wouldn't be too concerned with the "strength" of the work.
The reason is that publishing while an undergraduate—particularly as a primary author—demonstrates that you have already started to learn the basics of how to do research in your field. This means that you're less of an "unknown" quantity, and therefore less of a risk for a department reviewing your application. If you don't publish the research, then there's no tangible proof, and then you need to rely on your research supervisor to make that point in a letter of recommendation. (But then the question becomes: "if she could have written a paper, why didn't she?")
As for the exceptions above, so long as you don't publish in "vanity" journals (those which will publish basically anything, so long as people pay the appropriate publication "fees"), you should be fine.

do you include arxiv.org in "vanity" publication sites?

No. There's no publication fee associated with arXiv, and it's not a publisher. It's a repository, and unless it's the primary source for your field, it's not really "published" if it's in arXiv.

I fully concur with the reply from aeismail but will add the following:
Publishing means your paper will go through peer-review. With a journal with impact=2 (reasonably respectable) you are likely to get a good set of revieweers. This will either lead to rejection or to suggestions for improvements. If publsihed the paper will likely be better than when it arrived at the journal. So remember that publishing includes more work than just sending something to be printed.

By way, JMMV on impact factors.  There are a grand total of 9 math journals with impact factors >2 (since mathematicians write fewer longer papers than in most sciences).

That and they don't tend to cite very many papers when they write a new one.

I think your supervisor may want to extend the research with more experiments, data, etc. This will lead to an much stronger paper.
Good journals often reject weak papers, or ask authors to make major changes to their manuscript. So it is hard to publish a weak paper in a good journal. But always remember that Many weak papers are improved to strong papers in the review process.

1-"It is a fact that good journals almost always reject weak papers". No it is not a fact 2-"All Strong papers are amended versions of weak papers". No they are not. Not All of them. This is an academic SE please keep it that way.

@blackace but statistically, will those statements stand?

It is of course always much better to have publications in high impact journals, but this also depends on who is publishing. For a professor or post doc, the impact factor of the journal is  very important.
However PhD student or undergraduate is usually understood as somebody who still cannot deserve a very high significance of they research work just by they competence and hard work. It is often looked just like a success and matters less. As a result, publications in low impact ( > 0 ! ) journals in this stage are also good enough.


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Prolonging undergraduate school to do research
I am an electrical engineering (communications) undergraduate student. But my main interest is physics ( and/or CS, esp. it's common fields with physics - but it doesn't affect my question here ), and I want to pursue my graduate studies in physics or computer science. However for application, as an engineering student  I'm at a disadvantage as

I think my major is not considered rigorous enough by people in those fields
I don't have much (official) coursework in those fields, although I have studied (and am studying) even more than is expected from physics majors
because of the time I've put in studying ( and more importantly, exploring different areas of) physics and computer science,  my GPA so far is not good in electrical engineering.

So with these circumstances, I think the best or maybe the only way is to continue my studies in physics (and/or related areas) more seriously to do more rather good quality research projects and this way, show my ability and qualification for graduate studies in physics (and/or CS).
But, doing so I'll need more time for these additional studies and projects, and  I think I have to stay one year more at undergraduate school (5 years). Is this considered a negative point in application for graduate school?

No.
Nobody cares how long you took to graduate.  There is no advantage to graduating early, and there is no disadvantage to graduating late.  It is extremely common for students to take more than four years to get an undergraduate degree, especially if they change majors, as you are effectively doing.

I think there are a lot of students who spend an extra year as an undergraduate, and I know of a number of very good students who have done so, and will almost certainly get into very good graduate programs.
However, that said, I think the value of the extra year as an undergraduate depends largely on what you spend that year doing:

Will you be taking classes that will help your application to a physics program?
How much research will you be doing, and how will it help your application? (Is it physics-related, or EE-related?)
How strong is your GPA in your physics classes? (This won't make up for a weak GPA in EE classes, but it can at least partially mitigate it.)
How much will it cost you to spend an extra year before starting graduate school?

As for rigor, I don't think there's as much stigma as you might think. There's far more overlap between fields now than there used to be, and engineers do things that used to be primarily in the province of physics, chemistry, and even mathematics.


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Can I submit published articles to arXiv as well?
I have several math research articles on my site.
Some of my articles are published in open access journals.
Some of my articles are currently available only from my site.
I may probably publish something in a closed access journal.
The question: Should I put these kinds of articles at arXiv (and possibly replace articles on my site with redirect to arXiv)? I think yes, because it would increase visibility of my articles, as many people search on arXiv and/or receive arXiv mailing lists.
Is it ethical to put an already published article also at arXiv?

Well you can put your published articles on arxiv just for visibility purposes, but you will be having problems with the copyright of the journals and conferences in which your work is published. Essentially, the editors will not get too busy to track you down, but it is not ethical.
There is one way to go around this problem, publish in arxiv the draft versions of your articles, the ones that are a little bit different from the published ones. In that case you would not have any kind of ethical issues (you can also put them on your webpage, but always look to the copyright forms)
Good luck!

It is not always (nor in all legislations) true that you'll automatically be violating copyright or doing something unethical!

It is also not true that posting a draft vesion to the arxiv is compatible with the copyright policies of the journal. That being said, most journals I know of in mathematics allow you to put an "Author version" on the arXiv, that is, as long as you don't use the version that is typeset by the journal, it is usually fine. But you will have to check the individual journal's policies.

In the field of CS, I know uncountable cases of Professors that put draft versions on arxiv. If they can put the author version, well good for them.

Usually math journals allow arxiving, but if they don't its the journal who is behaving unethically.  Allegedly the reason the ask for copyright transfer is to help and protect the author not to attack the author.

I suggest you first of all check

the copyright transfers you signed
the publisher's FAQ on rights you retain as author
Many publishers nowadays allow you to self-archive the version of the manuscript that passed the review. Some do not allow self-archiving on public repositories (but e.g. Elsevier makes an exception explicitly for arXiv). For a quick overview have a look at the SHERPA/RoMEO site.
and your local copyright legislation.
E.g. the German UrhG now allows secondary publication (e.g. to arXiv) of your manuscript (including the version with exactly the content of the published paper) for journal contributions that were financed mainly by public grants.

These agreements also sometimes distinguish between the final author copy which you can usually post as a preprint and the final journal copy (after copyediting and typesetting) which you often can't post.

Albeit not a mathematician, I like to add this: if your work was supported by a public agency and got accepted for a peer-reviewed journal, public agencies may have a policy to make these manuscripts available for everybody.
See (as example) the public access policy by the U.S. National Institute of Health:

The NIH Public Access Policy ensures that the public has access to the published results of NIH funded research. It requires scientists to submit final peer-reviewed journal manuscripts that arise from NIH funds to the digital archive PubMed Central immediately upon acceptance for publication.  To help advance science and improve human health, the Policy requires that these papers are accessible to the public on PubMed Central no later than 12 months after publication.

Depending on the journals listed in PMC, some articles are "Free Access" immediately (if published in journals like like European Journal of Histochemistry), delay of six months (like Organogenesis) or twelve (like Optics Express), for example.
While not a mathematician, I'm glad to see NIH does fund work in mathematics, too (according to their publication database).  Of course, NIH's public access policy is in regard to the single articles published, not the entire journals listed.


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Can a psychology article be published without verifiable results?
I wrote this article with a radically new idea what is the function of the sense of humor.
I sent my article to one journal. They said they won't publish because they publish only experimentally verifiable results.
In my article I propose several brain experiments, but they may provide only circumstantial evidence for my theory.
Also my cites list may be outdated.
I am not a psychology professional. Can this article nevertheless be published in a reputable psychology journal?

I notice your experiments are firmly rooted in the unproven (but widespread) assumption that brain activities are the best indicator of mental functions.  You go even further out on a limb by assuming that laughing gas must be related to a sense of humor.  By the same logic, we could study grief using tear gas.  Do you see the absurdity of that?  Consider this comment as a peer review by a fellow non-psychology-professional.

You should take a look at psych.se. this question is probably not a great fit there, but some of your related questions might be.

I am not a psychology professional. Can this article nevertheless be published in a reputable psychology journal?

In principle yes, anyone with scientifically valid results may publish them. Many reviews are "double-blind" for exactly this reason.
In practice, the learning curve is steep, and it is rare that someone outside the community can even judge the merit of scientific work, let alone produce publishable work.

They said they won't publish because they publish only experimentally verifiable results.

Though some very well-reasoned ideas may be accepted by simply being verifiable, for a radical new idea, you really need some proof. I doubt anyone will publish your work unless you run one of those experiments and get proof for your theory.

BTW, I tried to give a neutral answer to your direct questions rather than commenting on the "content of research." But lest I be misunderstood, let me be clear that I am not recommending you put more time into this. I do not think your article is close to publishable, and you would do better to pursue other activities. Just my 2c, psychology is not my field. Peace!

Relativity theory (at least general relativity) was a radically new idea, but it was published before experimentally proved.

"I doubt anyone will publish your work unless you run one of those experiments and get proof for your theory".
(...or run one of those experiments, falsify your theory, and then report the results anyway.)

@porton there were strong theoretical reasons for believing relativity. Theoretical reasons still must give way to experimental evidence of course, but they provide justification for conducting the experiment in the first place.

There is one piece of "meta-advice" I have for everyone whose goal is to publish in some journal: read it, a lot. You will learn for yourself what they will publish. For example, what the readers and reviewers of that journal expect in terms of result validation, what kind of jargon they use, and everything else that will help you understand where your work fits in. Then you can answer your own question about whether your manuscript is appropriate and developed enough to be published there (and know how to build from there to make it publishable).
This is really the main impediment in my view for "outsiders" who want to publish in a journal. Read and know the field as covered in that journal, and you cease to be an outsider. There will always be (unfair and wrong) biases of course, because this is a system of humans, but they are limited as the journal quality suffers from them.
I realize this seems like a lot of work, but look at it from their perspective. Publishing (and even reading) your manuscript will take precious time that might have been devoted to some other manuscript. You may perform this research and reading/writing as a fun past-time, but they do it as a job in which they probably never have enough time to do everything they want to.


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Would you submit your paper that got rejected in a top-tier venue to a lower rank conference?
My question is simple: If you have a paper that got rejected two or three times (border-line* rejects every time) from top-tier conferences, would you polish it and resubmit it again to similar or another high rank conference or would you try some lower rank venues ?
* Border-line reject: every time got 2 good reviews and 1 bad review.
P.S. Every time the paper got vague suggestions like: compare with this or that. And the first and second time we DID in fact address all concerns, but another concern showed up next time.
P.P.S. I am concerned with CS conferences.
Thank you.

It depends on the reviewers and the research problem.  If they note that the problem or findings are not significant, then go to another venue, assuming they are correct.  If not, then revise your arguments.  However, if there is an issue with your execution/validation/presentation, then I would continue to re-submit the paper after revision.

I would not continue submitting the same paper to top-tier conferences after three rejections.  The Universe Has Spoken.  Move On.
Many of my colleagues do submit such papers to lower-tier conferences, but I usually just send my papers directly to journals after two conference rejections.

I think my plan is to go for a second-tier conference and later try to extend the paper for a journal submission.

I usually send my papers that I do not consider top directly to journals. Otherwise I waste everybody's time. But many times we tend to highly overestimate our work and think it deserves to be accepted to STOC etc. If a paper has been rejected more than 2 times that's a good signal to either go for journal or lower tier conference (I do not see direct purpose for that latter tho)

There is only so long any paper, whether it be for a conference or for a journal, should be held up in the review process. While it is stuck in review, other people may be able to publish similar (or stronger) results, at which your work loses the "novelty" factor, which will make it less competitive in the future.
At a certain point, you have to cut your losses and move on. Where that point of diminishing returns for presenting in a top-tier conference is depends upon your risk tolerance. But I'd much rather get my paper presented or published somewhere within a year in a second-tier conference than wait for two years to present at a top conference.

I guess I should do the same and perhaps submit to a second-tier conference.
Unfortunately the conference publication game is becoming more like a random game of luck these days...

Not only luck but politics. I look these days at lots of researcher's profiles and participate in number of talks about publications. What I learnt is that publication has 3 legs; quality, chance, and politics. However, sometimes politics is more effective than two others, especially when you see that a publisher who has couple of papers published in top-tier X conference (in the same year), was accidentally organizing member of that event!!! I don't extend such attitude to all CS researchers, but that minimal politics happens and cause you and other unconnected researchers to miss the slot.

Do you make any fundamental improvements after being rejected? If no, resubmitting it too many times can only reduce your chance of being accepted.
This happens to me as a reviewer. I reviewed a paper in 18 and rejected it. Then I was invited to review the same paper in 19 at a different conference. The authors changed the title but not the content. I compared it against the old manuscript in my mailbox. When I noticed the authors did not make anything new out of it, I simply gave it another rejection.
The group of people working on your topic can be surprisingly small and you are very likely to encounter the same reviewer when you submit to top-tier conferences again and again. I believe they will do the same thing as I did.
But if you follow the reviewers' suggestions to improve it and/or add new content to the paper after being rejected it will be a different story. I would think of it as a new paper, and will definitely resubmit it to top-tiers if I think the paper deserves it.

It is a very common practice to start from submitting the paper to the high end journals but then submit to lower level journals if rejected for not being "flashy" enough. If the paper is further rejected, it may be converted into poster and presented in some conference. If it does not make into top tier conference, then still might be good enough for a small local conference.
A good professor can tell at glance where in this scale the work stands and is it possible to improve it and get higher. However professors mostly gain this experience from the known accepted and rejected submissions.

This question is about computer science conferences which (unlike in other fields) are both more visible and more selective than CS journals.

@JeffE Will in general I agree (esp. about visibility), do you think that TOP conferences in CS are more selective than TOP journals in CS? For whatever reason, I like to publish most of my work directly to journals.

I have spend lots of time in academic environment, just this is the way things are. Also, if the paper is really bad, I expect all reviewers to be in consensus.

@PsySp Yes, absolutely. Top CS conferences are more selective than top CS journals.


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how to find whether this paper is already available or not, if authors just changed the Paper title & author name?
I am the editor. I received a paper from some author. I need to check whether that same paper is already published in some other journal or not. For example some authors downloaded a paper from some other journal, they just change the paper title, and author name and they send that paper to us. So in this case how can I find whether this paper is already available or not?

There are several software available for checking plagiarism, which would also fit the problem you are investigating. The journal (actually the publisher) for which I am editor use iThenticate. I am not in a position to compare the numerous software and services around, some free, some commercial. However, a simple check that can easily be made is to to a Google search on bits of text. I have personally used this to check on similarities between manuscripts and earlier published articles to check on the degree of overlap and it works fine. It will give you a first indication at which stage you can decide on continuing with a more advanced analysis.
See also answers in What is the easiest way to check for plagiarism in student essay papers?

And, of course, a slightly-clever plagiarist will continue tweaking a paper until Google ceases to produce too-good hits.

Then it seems the effort is more to plagiarize than to actually get another publication. This, on the other hand indicates it only the not so clever ones that can get caught. Do yo have any support that supports your statement? It would be very interesting to check it out in order to get a strategy for catching the more clever ones.

Some evidence: in the late 1990s and early 2000s I taught courses on crypto and on coding, in which I required a written project. Some plagiarism was hinted at from use of language that I suspected was beyond the ken of the given writer, and follow-ups confirmed. More subtly, some cases came to my attention only later when some phrase in a published paper resonated with a student project. Some discreet inquiries on my part strongly suggested that "clever" people plagiarized considerably more subtly than just cutting-and-pasting...

... namely, by making substantial "cosmetic" changes so that a superficial appraisal would be less likely to detect plagiarism. Beginning in the early 2000s, just as search engines could easily find resonating phrases, the "clever" plagiarists would just as easily spend a little time running tests on the match-ability of their plagiarized documents... as I was told. Eventually, I decided to not corrupt my general approach to students... Perfect enforcement is too expensive. General deterrence is feasible, but will be imperfect. I don't know any really strong solution...


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Which elsarticle documentclass parameters in LaTeX should I use for different Elsevier journals?
So here is the thing, I recently submitted a paper to an Elsevier Journal (EJOR) and prepared it using LaTeX. I used the elsarticle documentclass that Elsevier provides.
When doing this I tried to figure out how the layout of the resulting PDF should be. Specifically, I could not find any information on the parameters of the LaTeX documentclass.
In the template from Elsevier there are these example snippets (commented out):
%% Use the options 1p,twocolumn; 3p; 3p,twocolumn; 5p; or 5p,twocolumn
%% for a journal layout:
%% \documentclass[final,1p,times]{elsarticle}
%% \documentclass[final,1p,times,twocolumn]{elsarticle}
%% \documentclass[final,3p,times]{elsarticle}
%% \documentclass[final,3p,times,twocolumn]{elsarticle}
%% \documentclass[final,5p,times]{elsarticle}

So depending on the journal, I have to choose different parameters. For EJOR I used this
\documentclass[authoryear,final,5p,times,twocolumn]{elsarticle}

although I am not entirely sure this is correct. I was not able to find any information on this: which journal requires which parameters? EJOR looked like 5p, but isn't there an official source for this? Next, I want to publish to Computers & Security and, again, I can't find a hint on this. Am I looking in the wrong place?Does anyone know more about this? A site where they publish this?
Thanks a lot!

I vaguely remember some obscure and hard-to-find table that contained this information, but I fail to find it now.

Did the instructions to authors say you must prepare the initial submission in the journal style?  Most people in pure math don't do this, but I don't know about OR.

@Kimball A number of people in pure maths don't submit to Elsevier either.

The options not only allow you to chose between three different two-column layouts but also one column modes. The role of the two-column mode is to allow the journal to type-set the article once it should be published. You can therefore use the settings to to see the length of your final article (in terms of journal pages. In other words, you as an author have access to the type-setting mode of the journal paper, this is a side-effect of the versatility of LaTeX class construction in the manuscript handling phase.
The fact that there are no instructions for which to use means you can chose whichever suits the format best. I am, however, sure the journal can take the final manuscript in any of the modes since the only thing they need to do is to switch a comment between two lines if your choice is not optimal. I would send in the manuscript in single-column format and let the journal worry about which of the formats they use in the end.

Commenting out the appropriate lines isn't the only thing the journal needs to do.  If you prepared your paper in a one-column layout and they switch it to two-column, there might now be lines that are too long or too short, equations that don't fit, images that are too big, etc, etc.  The copy editor will probably try to fix these, but may not do so in the best possible way.  (For example, it's often hard to know how to properly break an equation into two lines, unless you fully understand the equation itself.)

It seems like there is no rule for the format when submitting a paper. I personally like to have the paper in its final form so I can fine tune the things Nate mentioned.


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PhD thesis layouts from around the world
About to do this PhD thesis here - but am not really satisfied with my layout. Could somebody point me to some interesting layouts, templates or whatever?

Check the regulations before going too wild/creative. Some universities are strict about the formatting.

Absolutely follow David Clarke's advice. I had to write my thesis inside a template file that I was given by my institution.

Try the Latex template we've applied in our Research Group. As it is a sourceforge project, you can modify, and suggest further improvements. http://sourceforge.net/projects/risetemplate/

Sharelatex seems to provide a variety of different thesis formats from different universities.
Many formats are available here.

Use the one that is provided by your institution.  The formatting guidelines are not "guidelines", but are instead "requirements" that are checked by someone who deeply cares about them.  So you should use a template that has successfully been used in the past at your institution.  If you do otherwise, you are setting yourself up for a lot of formatting work.  All of that said, University of Oregon's style file, which I used for my degree there, may be found here: http://www.ctan.org/pkg/uothesis

I agree with the recommendation that using an existing package/style file is the best way forward because this will save lots of time fiddling with style. However, I don't agree with the sentiment expressed that one should follow the ``house'' style because somebody in the home institution deeply cares for it. Usually the house style is enforced by people who don't care about/haven't got a clue about typography. I'd aslo be surprised if they care to check. I suggest you contact your thesis adviser if you want to use a non-standard style and use it if they're happy.

At least in some institutions margins, double-spacing, font, headers, ... are indeed requirements, and are checked by people who don't know anything about typography, but who will require compliance and send it back...

Incidentally, who is it inside a university that really cares about the thesis format? Obsessive-compulsive librarians?

@FedericoPoloni +1 for that.

I don't know who cares or why, I just know I had to re-TeX and re-print (on the special paper) many pages of my dissertation due to margin and layout issues before I could actually have my dissertation accepted by the graduate school. I have heard rumor that my experience is not unique.  I have also heard rumor that the absurd nitpicking is due to microfiche(!?) requirements, but do not know if that rumor is true.

I wish my university had guidelines, would save me a lot of time on deciding how to make things look.

@Peter: What makes you think the university has detailed guidelines, let alone requirements? My university has only one requirement, and that is Margin size (which is for purposes of ensuring the binding works). There is in many universities plenty of freedom. (Higher-ups at my uni says this is completely intentional.)

@Oxinabox Most universities I have encountered have them. I also recall commiserating with graduate students in other places about the (different!) ridiculous formatting requirements that we all had to suffer under. I'm glad to hear that this is not universal. Ask your higher-ups about their experiences at other places. I suspect getting burned by this elsewhere caused them to ensure that it didn't happen where you are.

The following are all LaTeX related.
I really like Uggedal's thesis design. You may download the sources from https://github.com/jrk/uggedal-thesis.
Other starting points are Andre Miede's classicthesis and Lorenzo Pantieri's classicthesis packages.
@Manual{classicthesis,
    author    = {Miede, Andr{\'e}},
    title     = {The Classic Thesis Style},
    keywords  = {latex},
    date      = {2010-01-24},
}

@Manual{arsclassica,
    author    = {Pantieri, Lorenzo},
    title     = {Customizing \texttt{classicthesis}
                  with the \texttt{arsclassica} Package},
    keywords  = {latex},
    date     = {2010},
}

I love classic thesis. I am forking a version of that code for my own dissertation.

Look at these options, I personally prefer the third option as Latex is always the best.

http://www2.imm.dtu.dk/teaching/phd/
http://www0.cs.ucl.ac.uk/staff/c.clack/phd.html
http://theoval.cmp.uea.ac.uk/~nlct/latex/thesis/thesis_a4.pdf


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MD-Phd (MSTP): What are the benefits?
I have BS in Biotech, an MS in Neuroscience and applying MD-Phd next June. I have always wanted to go into academia and eventually establish my own lab. However, I have been receiving a lot of critical feedback about MD-Phd programs. Suggesting that to be a good Physician, you don't need a PhD, and good PhDs don't need the MD. That most MSTP graduates end up utilizing only one degree. I was under the impression to do good translation research--an MD-PhD would be the best option. What are the befits/disadvantages of applying MD-PhD?
I know the faculty I would like to work with, already. Would contacting them improve my chances during the application process?

As the question asks about the benefits, I'm only going to post this as a comment: I completely agree with the feedback you've been hearing, an MD-PhD is almost always completely unnecessary.

For what its worth, my brother in-law is a notable researcher in his field. He has complained about not having an MD. He reports that an MD-PhD is one of the important evaluation criteria used by some grant-awarding organizations.

Doing good translational research is hard because it requires a good understanding of clinical issues (both from the patient and carer sides) and a strong research background. In order to obtain those skills you need to spend time in the clinic and time in the lab. An MD-PhD program guarantees that you will have the opportunity to spend time in both environments. It is worth noting that having that opportunity doesn't mean you will capitalize on it. Further, you don't need to do an MD-PhD to have that opportunity.
Another advantage of some MD-PhD programs is that you can get funding for the MD side. If it is what you want to do, saving 100k USD isn't a bad thing. If it isn't what you want, trading a few years of an MD salary for 100k is a bad investment.

It depends a lot on the kind of research you envisage doing. Since you say that you want to go into academia, I'll look at it as "what added value does an MD provide". My understanding of these things is that if you want to do almost anything patient facing, having an MD makes it a lot easier. Others have mentioned access to certain kinds of grants as well. But for example if you plan to work with flies or mouse models, then getting an MD in addition might not be a good time/money trade off.


text:
Submit to arXiv with a different order of authors
Recently I have published a paper with my adviser and, although I was the main contributor, for some issues with our university my adviser became the first author (Seemingly, he couldn't get any credit from the paper if he was named as second author). I mean, there was no doubt or conflict between us about me being the first author.
Now, I want to submit a preprint of the paper to arXiv. I was wondering if I can name myself as the first author in the arXiv submission. My adviser is OK with this, but I wanted to know that:

Is it acceptable according to arXiv's rules?
Can I somehow show my real first authorship by doing this?

Instead, you should mention These authors contributed equally to this work immediately under the address list (for example, see this instruction from Nature). Do this on BOTH arXiv and journal version. Swapping order between versions will result in confusion, not - extra credit.

@PiotrMigdal The paper is published now. I wanted to do this just after it got accepted, but I though it was a bad idea for me (to write both authors contributed equally), because I contributed way more than my advisor!

If you contributed more but are second author, it means: you will receive much less credit for your work than 50% AND that your advisor did it against academic ethics (unless he genuinely considered him being as the main or equal contributor; or perhaps unless you voluntarily waived your first authorship).

It could be that he is circumventing some restriction, which was imposed by the university to see if staff members have also other papers than just those mainly done by their students. In that case the reordering wold be dishonest.

@PiotrMigdal Actually, I don't see the OP waiving his first-authorship as something that would make this ethical. One cannot ethically change the order of authors when it is supposed to be ordered by contribution, even if the authors agree.

I don't think there are any rules against having a different author ordering on the arXiv version, but I'd recommend against trying this.  The author ordering on the published paper would be regarded as "official", and doing things differently on the arXiv would certainly not be considered to demonstrate the real first authorship.  Instead, it could easily be misinterpreted:

People may assume you were careless about author ordering in submitting to the arXiv, which wouldn't be good for your reputation.
Worse yet, they may assume you were dishonestly changing the author ordering, which would be a disaster for your reputation.
The best case scenario is that they would assume the author order changed between the preprint and the published paper, because the authors changed their minds about who should be listed first.

The only way to avoid these dangers would be to add an explicit note explaining the change, but I assume that's out of the question.  After all, if you deserve to be first author on the arXiv paper, then you should have been first author on the published paper as well, so such a note would just raise ethical questions about the published authorship.
It sounds like you should have been first author all along, since author ordering should not be determined based on how much credit the university gives.  If it is still possible to fix the author ordering before publication, that could be the best approach, but the arXiv is not a good way to fix it after the fact.

+1 for "author ordering should not be determined based on how much credit the university gives"

Thanks. How about this: in my resume where I have mentioned this paper, I have written the following sentence in a footnote (referring to my name): main contributor (contact the corresponding author if needed)

@Mostafa: I'd be careful about adding such a note.  I think it will attract attention, which will be negative for either you or your advisor.  When people read it, they will think "Wait, if the student and advisor both agree that the student was the main contributor to this paper, then why was the advisor listed as the first author?"  If anyone asks your advisor, then either he admits to misconduct regarding author ordering, or he throws you under the bus by saying "Sure, Mostafa contributed a lot, but not quite as much as I did, which is why I was first author."

It's possible your advisor doesn't think the misconduct is so bad and actually will admit "Yes, Mostafa was the main contributor, but I really needed the first authorship, so I decided to list myself first."  That will look bad for him.  But I'd guess that if it reaches the point where he has to explain, he'll realize that the explanation isn't looking good, and he'll instead decide to defend the published author ordering.

authors: Vladimir F Героям слава


text:
We want to start working in a new research direction. How to proceed as the first student in the group?
I'm a graduate (Master's) student in Engineering/Applied Physics (EE, specifically). A few months ago when I wanted to choose my specific research topic, my advisor got especially interested in one of my suggestions and, even though no one in our department had worked on that topic before, she insisted that I pick this as my dissertation topic (I think because of the novelty and hotness of the topic, besides my own interest). She told me that, starting the next year, she will ask the new students to work on this same topic. I accepted and started my studies.
Now since it's my first experience doing research as a member of a research group, I'm a little confused about how we (the group) should proceed about starting a whole new research direction. There are some new basic materials (like unfamiliar/unconventional math and physics for EE students) that are actually needed to be learned, besides the leading-edge research papers.
From my own perspective, this is my dream topic to work on as I'm going to get back into serious Physics after some unpleasant engineering years, and I think in long-term this is going to be great for me as a researcher, as I'm getting familiar with a field while still being in its dawn. For PhD, I'm planning to move to one of the leading research groups in the field. What are some advice for me, as the first student working on this new topic in the group with no one having any prior experience in it, to make the best outcome in short-term (publications, PhD admissions) and therefore being able to prove my competence in research?
(Also as a side-question, from the group's perspective: How do research groups, especially small ones, embark on a new research direction? Does it start with an enthusiastic student convincing the advisor to start working on the topic, or with an interested professor finding a enthusiastic student? What are the student's and the advisor's responsibilities in each case, as both have near zero experience in the field?)

Could you clarify: do you want to continue on as a PhD student in this university, or use this as a starting point to go to a different school? If you leave, would you want to stay in the same research area, or just the same overall (EE/Applied Physics) field?

For your question from the research groups perspective there is no definitive answer. Many things are possible and it depends on the group, the students, the field and whatnot. However, if you plan to enter such endeavor, you should discuss plans and responsibilities.
For a personal perspective: It is a lot of work to go into a new field. Read basics, but stay up to date. Talk a lot to people who work in the field to get a better sense, what the pressing questions, the important goals are and learn the jargon. Listen to talks on the topic, prepare well ad ask questions to get in discussion.
The bad news is, that nobody can guarantee any short-term outcome (unless you can somehow figure out some low-hanging fruits in the new field)…


text:
During applications, how can I prove I was the first author of the papers that I couldn't become first author for various reasons?
One year ago, I started working on a subject with one of the professors of our department. The idea was mine, and all of the subsequent steps including modellings, simulations, generation of figures, writing the paper and even responding to the reviewers were done by myself completely, and the professor just reviewed the paper and reminded some typos and minor mistakes of this kind, and also added a short paragraph (completely unnecessary in my opinion) to the Introduction section.
But at the end he wrote his name as the first author and submitted the paper. He told me that being second author for him means getting no credit from the department.
Anyway, I'm going to apply for grad school, and he told me he will compensate in the recommendation he will write for me.
As this is my only published paper as an undergrad, and being first author means everything for me in my application, is there any way for me to prove to the admission committees (or the professors; whoever will review my application) that I was the main contributor of the paper?

Don't underestimate the importance of the letters of recommendation when you apply to graduate school. They are just as important as your vita - and for things like research, they are perhaps more important. You will also describe your own work in your research statement. In comparison to those things, the author ordering on a publication is not going to be very significant.

Even being "first author" is not always significant.  My name is first on a couple of papers to which I contributed very little because the authors' names are listed in alphabetical order.

I am under the impression that, unless a paper is of unique author, it would not get the committees attention. And I am personally adopting this principle in my applications to doctoral programs.

@Kurt That depends entirely on the field. In my field, theoretical computer science, one-author papers are not uncommon but two to four authors (almost always ordered alphabetically) is very much the norm. You certainly wouldn't hold it against somebody that they had "only" worked in collaboration with others.

@DavidRicherby: Yep, thanks. Indeed, I just want to share the OP with what I know, without any intention to arbitrarily generalize my opinion to a universal one. The decision right, of course, belongs and only belongs to the OP :)

@Kurt Of course, yes. When commenting and answering, it's good to bear in mind that many things differ substantially between different fields and be careful to state whether you're talking your own field (and state what that is!) or academia in general.

@Kurt Honestly speaking, I doubt whether your statement is true in any field, and I am curious what field you have in mind. Single-author papers by undergrads are very uncommon, unless they appear at undergraduate research venues (and then they are usually not full papers). So I'd think a paper authored by an undergraduate and a professor (no graduate student collaborator), that appears as a regular scholarly publication in a reputable journal or conference, would get any committee's attention.

His goodwill is worth more to you than a first author paper, at this stage in your career.

"He told me that being second author for him means getting no credit from the department." I am stunned to see how common this kind of argument is! Authorship and order of authors are not decided according to needs or benefits of the people involved, but according to their contribution and merit. Unfortunately, your best move right now is plausibly to let it be, and move on (while putting that professor in your personal black-list for the future).

Let's not forget that what the professor did was unprofessional and (imho) unethical. Think twice (or thrice) about if you want to work with them in the future.

Not that this really matters, but the title doesn't quite reflect the actual question. I came in half-expecting to answer "the only way you can prove you are the first author is to look at the list of names on the paper and see whether yours appears first :-P"

Without the professors input would you have got it published, e.g. would you have know how to get it published?

@Ian Yes, of course. Actually, the professor requested me to prepare the paper in a format that was obsolete according the the guide for authors (in the journals website), and I wrote the paper in the new, preferred format.

@Mostafa To be fair - whether the prof. was up-to-date in terms of which formatting they currently expect is hardly the important question.

@BenoîtKloeckner Re "Authorship and order of authors are not decided according to needs or benefits of the people involved, but according to their contribution and merit." Although an earlier comment mentions a field where authors are usually listed alphabetically.  Of course, if that's the case here, then the department would be quite unfair to only credit first authors.  (Why does Aho get so many more departmental awards than Zadeh?)

@JoshuaTaylor: my field is one of these, where author are listed alphabetically. It means that all authors of a publication are co-first authors, with equal merit assumed. In evaluation, the order of the authors is never considered, so the only issue in this case is authorship, not the order.

@BenoîtKloeckner OP said "[the professor] wrote his name as the first author ... . He told me that being second author for him means getting no credit from the department."  In an alphabetically-ordered field, no primary author in that department would want to work with any "alphabetic inferior".  My comment was more to point out the ill-informed nature of such departmental policies, not the practice of the venue.  Such a department would tend to recognize Aho much more frequently than Zadeh, since Zadeh would so rarely be a first author (or first-listed among first coauthors).

@JoshuaTaylor: this is no place for such an extended discussion, but departmental policies taking author rank into account hopefully only happen in fields where author rank is relevant, and not alphabetical.

@BenoîtKloeckner Of course.  I was just pointing out that in addition to the probably unethical behavior here, the department's policy is sort of strange, too.

Don't forget that in many institutions the 'boss' of a department gets first authorship (or last authorship depending on the institution) of all papers by default. That can be a fairly common thing, and if you write a note explaining all the work you actually did (but don't be defensive or bitter about the authorship order) that would be fine for an undergrad.

Unfortunately, your boss's behavior is rater unethical. If you want fix this you should do it in your school, most probably you have mixed chances to come out without injuries. I would strongly advise again bringing up this issue in a interview to another school if you didn't prove your right in your own department. That would sound really bad, and just make your position worse. Note, i do not say that what your prof did was right or anything like that - but focus on what doesn't hurt your career.

As this is my only published paper as an undergrad, and being first author means everything for me in my application, is there anyway for me to prove to the admission committees (or the professors; whoever will review my application) that I was the main contributor of the paper?

Short answer: no. Aside from the professor writing in his letter that he did indeed not do the work and just put his name front to brush up his CV, I see no way how you can prove that you were indeed the "actual" first author. And, given that this would essentially mean that the professor confesses unethical behavior, I see very little chance of this happening.
Anyway, I am not so sure whether being first author means "everything" for you. Undergrads are often not the first authors of publications (for many reasons, not just the unethical reason that you were denied first authorship). Further, if I see a paper with a senior author and an undergrad, I am not assuming that the professor did most of the hard work and undergrad just advised - independently of how the authors are ordered. I would assume your average admission committee to be similarly realistic.

This. It's implied; most will assume you did most of the work and know that having the professor as first author is really a (bad) formality at some places. I also agree that being first author doesn't mean everything; even being a co-author on a paper as an undergrad is a feat that fewer-than-average students accomplish!

Your question breaks down into distinct subquestions and assumptions, we need to call out each of them separately, especially because you have the importance wrong:

How important is being first named author [as long as you're second, obviously], in your field. You claimed "being first author means everything for me in my application"
Is fighting this fight worth it? Is it strategically worth picking this one or letting it go? 2b) Also: is it important going forward to preserve your relationship with professor (especially if it sounds like you'll stay in the same dept?)
How do you actually prove you originated the work/ideas? (This is pretty self-evident and is the least important question)

Answers from experience (almost all of us know people who've been in this situation):

You seem to be making a huge wrong assumption here, seems like you extrapolated the application's artificial format to believe in general you will not get any credit unless you're first-named. Generally everyone knows the deal with academia and tenure-track, it's an imperfect little world, people will understand he is under pressure from his own tenure-track metrics. Yes it's somewhat bad ethics, but this is utterly different to omitting your name entirely, stealing your idea for a startup or patent, esp. when rejecting the associated thesis, stealing your funding and redirecting it to other purposes etc. Outside in the real world noone gives a ****  if you were first named author; at interviews or in applications you will be given adequate chance to demonstrate whether you were/were not the prime mover; in fact people may respect the team-member vibe if you diplomatically say "we" and "our idea" while making it blatantly obvious you did the work and wrote the professor's promotion ticket.
To quote Def Leppard's fine song, "Let It Go..."
You have to answer this question: on a scale of 1-10, how was prof's behavior overall, and factor in "he told me he will compensate in my recommendation". Sounds like an 8/10 to me. Believe me, there are scumbags out there, and it ain't him.
Pretty self-evident, and irrelevant. Notebooks, notes, SCM checkins, emails, drafts. If in future you get a really clever idea [while in academia], send a dated email to yourself (/burn a CD and certified-mail it yourself, unopened). Read also about the concept Reduction to practice in US patent law, for the future when you're working for a company.

If you kept a stack of drafts, produce them. While not definite proof, it would be very hard to overcome even if the professor were to try. Likely, he won't and you win by default.

Seems like a perfect way to start one's career.

Even if this is probably a fight you can't (or don't want to) win -- *sigh* -- note that versioning repository timestamps or similar may work as proof, as long as you don't control the server (and hence the timestamps/commit messages are believable).


text:
Should I include impact factors / number of citations in publication list?
I am writing a grant application for a post-doctoral fellowship, and I need to provide a publication list. In the list of papers published in peer-reviewed journals, I wonder if I should include the following information:

Impact factors of the journal?
Number of citations the paper actually raised?

One of the papers raised a pretty large number of citations (several hundreds) despite being published in a low IF, so I wonder how to carry this information...