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I'm very late to applying for postdocs because I was aiming for industry jobs and didn't think I needed one - how much trouble am I in?
I'm about a month away from my PhD defense, and my goal is to work in industry (I'm in medicinal chemistry and I've been doing high-throughput screen and in vitro inhibition assays of a particular enzyme). I started job searching in industry about a month ago, thinking that I shouldn't have problems finding suitable positions. However, as I've started searching and applying, I've noticed that a lot of the jobs in biopharma that are posted require things like mammalian cell culture work, transfection, genomics, immunology etc., which I don't have experience in. Therefore, I'm thinking that I may need to do a postdoc after all to gain experience in those areas - there's some very important skills that I'm apparently missing! Of course, if I get an industry offer, I'll go ahead and take it, but it seems like I may not be qualified for PhD-level positions (I'm open to taking a MS-level position but most employers would consider me "overqualified"). But it's a month before my defense and it's rather late in the game when it comes to postdoc apps. My advisor can only fund me for another 2.5 months (end of June). How much trouble am I in in terms of getting a postdoc that is rather significantly different from my PhD? How long of a gap is acceptable to potential postdoc PIs?

Why do you need to do a postdoc to learn those skills? Can't you learn them in an industry job for 3x the salary?

Job descriptions are often “wish lists” -apply anyway!

@astronat I’m planning on applying to both industry jobs and postdocs at this point. I would very happy if industry were to train me, but I’m not sure if they’d be willing to when they have many other candidates who already know those things. I’ve also heard that not all postdoc jobs pay the NIH minimum - some pay higher than that (usually ones not at academic institutions) and I’d be interested in those.

@8263xiao On some occasions, professors can redirect their funds from supporting a Research Assistant graduate student to supporting a postdoc. So if you see an announcement of graduate studentship in the area of your research -- give it a try: talk to the professor and enquire if (s)he can spend those dollars on a postdoc. This may work out.

I started job searching in industry about a month ago

I am not familiar with your individual situation, but for any job search I would recommend allowing a minimum of three months.  If you expected to find a job within one month then you would be in very bad trouble.  Keep in mind that a job application often waits a month to be read and a job offer often takes a month to be approved by an employer.
The content of a job ad is not an accurate predictor of the qualifications of the person who is hired.
Look up the profiles of people who have the job you want.  That will get you data, as opposed to opinions.

How much trouble are you in: that really depends on what country you are looking for postdocs in. Positions open up at different times in different regions. For me, the academic year starts in September, so there are lots of postdoc positions being posted now.
However, if you want to work an industry job, then you are far better off just applying for them. Your skills are transferable, and what you don't know you will learn on the job. Your ability to learn quickly is more important than what you have already learned, especially when you are going to be applying for more junior positions anyway.
Don't be intimidated. Just go for it and most importantly, be open to change.

Not my field, but I suspect that the big industrial players (e.g. the Pfizers) will have structured training schemes available to fill in any skills gaps, whereas startups (and indeed postdocs) tend to talk about "hitting the ground running" and be stricter about looking for people matching their exact requirements.

I'm in the US. I get tons of conflicting advice over what to do. I'm currently applying to industrial positions but will be sending out postdoc apps in the coming week. I'm especially interested in postdocs in which I work with potential therapeutics in cells and/or ex vivo, which will provide a good bridge towards more biology-oriented industry positions (who tend to prefer those with postdocs anyways, or so I hear). So yes, I'm trying apply to both since my end goal is industry; it's just what I can get with the current market and what skills I need training for.


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How best can I explain my three years of unemployment during my PhD applications?
I am from an Asian country, 29 years old. I did my bachelor's and did a year of internships in R&D. I then got accepted into a good master's program in an EU country and got a job as a research technician in another EU country soon after. I worked there for 5 months but got laid off and also had a terrible boss that mentally affected me a lot.
I returned home, trying to do PhD and job applications to go back to EU, nothing seems to be panning out. I have done nothing in the past 3 years (I also gave up and stopped applying in the middle because of mental health issues).
I did one year of freelancing in a completely unrelated area, but nothing else. I am very passionate about doing a PhD in biomedical research. I have the following questions :

what are my chances realisticallys to get accepted into a PhD program in Europe due to this 3 year gap?

How best can I explain the gap in my application or motivation letter?

Is it okay to say "I was talking care of older family member" rather than mentioning my mental health issues in my cover letter to explain the gap? (even though it wasn't really the case - it is my own chronic depression)

Can I also be vague in my resume and day that I did some freelancing during this time. Will universities in Europe check for the freelancing history for the application process?

Were you taking care of a older family member?

Not really, I was mostly dealing with mental health issues, but i am not keen on putting that on my application letter.

Well, certainly don't lie to anyone ...

I lightly edited your post, but I would suggest you reorient this into something actionable. We can't tell you that it will drop you from 50% chance to 20% chance of getting in somewhere. You can't change anything, so ask a question about what to do.

Hey, I think this question here is very similar: Should I just stop applying for admission to PhD with my research gap of 8 years?. There were many comments there that I think might help you understand what you might be facing in your submission processes.

I can't speak for Asia, but understanding of MH concerns, especially when diagnosed are becoming more accepted in the West. I'm sure you won't be the only applicant that briefly explains a gap due to MH issues.

You have a longer gap, but the responses to Should I mention about the time wasted (6 months) due to depression in my CV when I will apply to PHd programs may be informative.

Have you got your mental issues sorted? PhD is not a cakewalk. Your health is more important than you doing a PhD.

there is another question on the same topic that I think might be very similar to your case: Should I just stop applying for admission to PhD with my research gap of 8 years?
Now to your questions:

Is it going to be impossible for me to get accepted into a PhD program
in Europe due to this 3 year gap?

No, many programs accept people from different backgrounds, and many supervisors don't bother with that. Some do, and they are going to reject your submission. But you should look at those as a good sign that you dodged a bullet.

Is it okay to say "I was talking care of older family member" rather
than mentioning my mental health issues in my cover letter to explain
the gap?

As others have already said, don't lie in your cover letter. Lying to your potential supervisor will harm you more than a three-year gap. Just be honest and try to spin it into something that might make you a better candidate. PhD is an arduous and long journey, it might be good that you are more conscious about your mental health and you know how to deal with that.

Can I also be vague in my resume and day that I did some freelancing during this time. Will universities in Europe check for the freelancing history for the application process?

Did you do this freelancing? If they checked, would that be bad? Again, don't lie to your potential supervisor. It will be worse once they discover it. You don't need to be 100% honest if you are uncomfortable, but don't lie in any documents or conversations with them. If you did freelancing, you probably should talk about it. PhD is a big and long project. Having experience with project and time management is good for a PhD application.

Speaking from my experience now. In the UK, there are many types of candidates for a PhD: people with no research experience and fresh out of their master's, older candidates with industrial experience trying to change careers, people with gap years, and everything in between. There is no reason to be overly anxious about your situation. For me, the best thing you can do is find contacts that work on your research interests. They might know a supervisor looking for a student for a particular project. You should also try to do some research on your own (if possible in your field), which will show interest and show that you know how to do research. You don't even have to publish anything. Remember, the application process serves to find the students that best align with the supervisor's expectations. If you fit in those, the 3-year gap will make no difference.
Best of luck to you!

What you describe does not look good. The following stand out:

You worked as a research technician and got laid off after 5 months. Although it's not as serious as being fired, it still suggests that they don't think you're a very valuable employee.
You then apparently did nothing for two, arguably three, years. This is a long time. Since you've barely worked (i.e., earned a salary) up till now, it's improbable that you can fund such a long career break. In turn, it suggests that someone - presumably your parents - was subsidizing you, which looks bad on your ability to be independent.
You claim that you are very passionate about biomedical research. Considering that you apparently did nothing for 2-3 years, this is hard to believe. Someone who is very passionate about biomedical research would at least get some things done (like take some courses at the local university).
Your defense against all these is that you had mental health issues. However, three years is a long time. Are you actually recovered, or are you going to relapse after admission?

You'll need to explain all these things in your statement. Since it sounds like freelancing was the only constructive thing you did in the last three years, it's probably a good idea to elaborate on that, especially if it's related to biomedical research. You might also want to get your recommendation-writers / doctor to vouch for your mental health issues, since it could look like an excuse.

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Putting dataset in CV
In my field (linguistics) sometimes datasets are important and scholars tend to include them in their CV. I want to know how to include my dataset in my CV?
This is the approach I have in mind: Uploading dataset in Harvard Dataverse and include the DoI in CV with the following style:
XXX dataset, The most important dataset in linguistics, DOI:XXXXXXXXXX

How does it look? Please share your thoughts on it.

If you're given a DOI for the dataset, definitely include it. I agree with Bill below that authors are advisable - treat it as you would a paper citation. Harvard appear to have a standard citation form for their datasets which looks reasonable.

So what is the most important data set in linguistics?

@FranckDernoncourt it is a comical name given to hypothetical dataset.

From the Harvard Dataset users guide:

Download Citation
You can find the citation for the dataset at the top of the dataset
  page in a blue box. Additionally, there is a Download Citation button
  that offers the option to download the citation as EndNote XML or RIS
  Format.

So if you go that route just upload your data and click that button.

It seems pretty presumptuous to call it the most important dataset in your field. If it's got a DOI, then you can leave off the editorial. Just give the title and the DOI. An author list might be appropriate if there is a consistent set of authors. If the dataset is continuously evolving or growing, you might leave the authors off. This may depend on the conventions of your field. Also, if there's a marker paper that describes the first use of that dataset, and you're an author on that paper, you should also put that on your CV.

Actually "the most important dataset in linguistics" was a comical description given to a hypothetical dataset. Actually I don't have a DOI for the dataset but the paper (which is submitted) has DOI; however the dataset can be used in different researches (and therefore cited) so I was thinking about mentioning Harvard Dataset's DOI in description. Having said that can the aforementioned style be any good?

Do you think it would have been better to provide a real example of what you were planning to put as the citation?

For example I am developing the first Kurdish Speech Corpus for training HMM Text-to-speech. this endeavour (training a software for TTS) solely can be considered as a Research output and published. The corpus on the other hand can be used in other areas for different purposes so I'm thinking about uploading the corpus in the Harvard dataverse so that others can easily Download, Cite, and Reuse my data. and also I can easily put the DOI in my CV so that the admission committee of the universities I'm applying to can easily find my work.

@adelrahimi, finding a way to get permanent hosting and a DOI would be ideal. No matter what, cite it in your CV, but not in the "Peer-Reviewed Publications" section. Make a new section for it, like "Research Procucts".

@BillBarth I cite them under the heading:CODES AND PROJECTS
thanks for your help.

@adelrahimi, that sounds like a fine heading.

We don't generally subdivide CV entries according to the usual P&T requirements, though if you're in a sub-area that's more remote within linguistics, like computational, then there might be different standards. The standard format of the entry in an academic CV would be:
2015a. Kurdish speech corpus. http://hdl.handle.net/1234.5/678910, Harvard Dataverse, V1
or if co-authored, with the added tag ("w. Y. Matras & G. Haig", or whatever is appropriate). (You can also deposit it at TROLLING).

Thanks for your great reply I actually got the idea after receiving the announcement for TROLLING.

If the job you are applying for requires dataset creation, then list one of your skills as "dataset creation" and in the text next to it explain that you created the Harvard Linguistic Dataset. If the dataset is important in the field you are applying to, you need only name it. If the reader of your CV doesn't know the dataset is important, it's perhaps not worth even mentioning.

I'm applying to grad schools and the people reading my CV are scholars from my field.
Of course the dataset is important in our field and mentioning it alone is enough; however by mentioning DOI I want to 1. give a clear address where they can thoroughly and easily (I can upload it in my personal website for example but giving a URL can never be as short as a DOI) see my research data  and 2. they can cite, see and download my data.

If the dataset is important in the field you are applying to, you need only name it. — Strongly disagree.  This is like saying "If the paper is important in the field you're applying to, the title is enough." Like any other artifact, if you cite a dataset (either in your CV or in a paper), you must give proper credit to all co-creators, and you must provide enough information for a novice user to find it (DOI and/or persistent URL).

In my experience, academic CVs, unlike those for industry, don't usually have a "skills" section. And in a field that uses data, listing "dataset creation" as a  skill would be about as silly as listing "writing papers" - every applicant must have this skill, so what's the point of writing it? You might as well list "breathing".

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Separating your publications into journals vs. conference/workshop
It seems typical in some fields (e.g. engineering) for researchers to classify their publications on their websites and CVs into two groups: journal vs. conference/workshop. This appears to be because journal papers are considered more significant, in some sense.
This doesn't appear to be the case in other fields, such as computer science, where conferences are seen as more significant. With more people in engineering publishing in top CS venues, and the lines between the two fields becoming a bit blurry, the reasoning for separating papers into journal vs. not journal isn't clear.
Question: What is a good strategy for organizing publications in on a website/CV?

Could you phrase the question so that it does not look like a poll? The Stack Exchange model works better for questions that have a definite answer.

@FedericoPoloni Thanks, I've edited the question

It is still just a poll. How about: What is a good strategy for organizing publications in a CV?

Even in Computer Science fields where conferences reign, it can still be worthwhile to categorize publications. For instance, I currently divide them into journals, book chapters, major conferences, specialized conferences, abstracts, and non-peer reviewed. (These are automatically put into my web page as well, but there I only distinguish between long and short papers.) Each paper is also marked with the acceptance rate, where appropriate. What is the value in doing this:

Journals show a depth of work. Having some work in each category means that you aren't only publishing in conferences -- that when research needs a deeper treatment you are working to provide it. (In CS I have far fewer journal publications than would be expected in Engineering.)
Specialized venues can illustrate involvement in smaller communities, and it is often easier to take leadership in such communities. These communities might also know a specialized area better, meaning that there is better vetting of ideas.
Separating non-peer reviewed papers seems necessary from an ethical perspective - they are a different category. I put this in the last section where it sometimes indicates invited papers that go along with a keynote.
Breaking things up allows someone to quickly see the breakdown of where you are publishing to notice points like the above. I often distrust one monolithic list because it's hard to see where work is actually going.

Overall, I suggest that breaking things up facilitates the fast read and avoid any ethical issues about artificially inflating your CV.

I happen to prefer a chronological listing. But it is really up to you. For example, if you work regularly in two different research areas you could even list publications and such separately for the two areas.
The chronological listing makes it easier, IMO, to follow a thread or trend in research where other divisions don't.
But, if you have access to examples of how others do it in your field it would probably be best to follow along.
You are asking here for what amounts to opinion and those opinions may not be valid in your field. Do what is expected, I think.

I don't mean to sound negative but I agree with the others, this question looks awfully like a poll. So a reframing might be a good idea.
Speaking about the CV, the only thing that matters is the perspective of the reader. On average a CV is glanced at for 30-45 secs, if interesting then read for an additional minute or two. In that light, the only sensible thing to do is to put what matters to the reader first and easily distinguishable.
So if you are applying for an academic position or a position where academic merits are important, and work in a field where journal papers are valued highly, you put (possibly a selection of) your papers in reverse chronological order, so that the most recent/relevant one comes first.
If you are applying to industry where conferences might have higher value, then you highlight them. Or if you have given talks at big international conference you might want to focus on them instead.
There is no one-size fits all here.
As for your own personal homepage, where you have your bio without any intent of application and/or particular audience in mind, then do whatever you feel like. It's your own page! :)

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Does tenure generally account for extended research in a different field?
I am a working professional in India looking towards a career in research and thus interested in academia. However, apart from having a definite field of interest that motivates my direction in academia, I intend to spend time pursuing major research (that requires minimal to no funding, as it is mostly theoretical) in another field in the future which might not particularly ally with the primary field of interest.
If I do finally graduate to a tenured position in the future, does the promised "freedom" of tenured positions account for freedom to pursue extended research in a divergent field ? Alternatively, for those willing to answer, a more general question might be: what are the terms and conditions or obligatory research output specifications of tenured roles generally ? (Specifically India, but I'm also interested in how it is abroad)

@Buffy Yes, I'll edit the question to add that. Thanks.

US based answer: if you are, say, a math professor, then your research output in math (or a very closely related area) is what is going to count when your research productivity is being evaluated. If you spent your time composing a symphony, or publishing essays about medieval Japanese weapon-making techniques, that’s not going to count, even if those things are valid scholarship from the point of view of other disciplines. I hope these examples make the general principle clear…

@DanRomik Thanks for the reply ! Are there any specific benchmarks for this productivity or is it evaluated by committee ?

This is not a question that can be answered in a short comment. In any case I have no knowledge of how these processes work in India.

@DanRomik Understandable, thanks nonetheless !

This is not an India specific answer, but more based on general principles. First, tenure is understood differently in different places and is related to, but not the same as academic freedom. Tenure is a surprisingly recent practice, actually.
Generally speaking, if you hold tenure, then you can be fired only for cause, such as misconduct or institutional financial reasons. It is intended to protect the work of academics from governmental interference and censure. Basically, it says you can explore unpopular ideas.
But tenure doesn't mean that you need to be rewarded in any way for what you study or what you write. If you are tenured in a mathematics department, then rewards will come from your contributions to that field and to that department, and not much else, though external service is often rewarded somewhat.
So, if you want to be successful in a math department, you have to "do" math and teach it effectively. Other things may not be rewarded at all. And, if they reduce your effectiveness in the math department, nothing about tenure says that the head can't give you some unpleasant duties that you have to carry out to avoid a charge of misconduct; a heavy teaching load, perhaps.
Some people, however, are able to hold dual appointments. A mathematician might also work in the philosophy department, for example and hold dual appointments. At tenure, the person would probably be given some special assurance that this will work for them. It might even be possible, though I can't name a case, in which you hold tenure in more than one department.
So, tenure is about what you can and can't be fired for and having outside interests or unpopular ideas isn't one of the bad things. But your employment contract also specifies expectations that you must meet. Life might be unpleasant if you don't meet them because of other interests.
I've known people (tenured, actually) who couldn't advance beyond associate professor because they had those outside interests that got in the way of their main tasks. Over time they got larger teaching loads of lower level courses.

Thanks, this answered my question !


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Should I provide experimental results for a paper presenting an algorithm?
In a paper I proposed an algorithm for something (extracting data from a webpage), I described the steps and the result of the algorithm using a sample webpage. Do I need provide experimental results on various websites?
Here I think my purpose is not to compare something with another thing, the precision of the algorithm depends on its input provided by the user, I just want to say the application based on this algorithm is easier to use by providing how the application works, and extendable to similar websites by justification its approach.
I am confused!, if I always for any algorithm I should provide experimental results, then please let me know by Yes always, if there are exception then please let me know what are those?

Are you asking "Do I only need one data set to test my algorithm?" ?

@scaaahu yes, just to say how it works, if it was proved then I expect it works for similar purposes.

"it was proved" How did you prove it?

@scaaahu "proved" or "shown", I think  an algorithm can be proved by examining its steps and its execution. using "input" it gives "output"

If your intention is to publish a paper in good journals and conferences then you have to show that your algorithm works in more than one case, just one page is not enough, except if that is the specific intention, lets say, collect data from Google Finance pages about each company.
First prove correctness, which could be done formally, running a good number of different cases or just obtaining results that are similar to other established algorithm.
Also you have to prove the value of the algorithm, which could be done demonstrating his complexity using the big O notation; or benchmarking against other algorithms that solve the same problem. Eventually you will discover that the algorithm is better in some metrics (false positives/negatives, response time, memory usage, power, network traffic, ...) and not so good in others.
I suggest that you verify how other algorithms are presented in the same area, specially in the journals or conferences that are good fit for it, and try to use the same methods and data sets. That will make easier for readers to evaluate how good is the algorithm when compared with others that solve the same problem.

First prove correctness, which could be done formally, running a good number of different cases or just obtaining results that are similar to other established algorithm. — You cannot prove the correctness of an algorithm experimentally.  On the other hand, you cannot demonstrate the practical utility of an algorithm theoretically.

It is always a good achievement to develop an existing algorithm or write a new algorithm. But your paper will be highly evaluated if the algorithm works for various dataset. The strength of the paper will again increase if you can make a comparison with various available dataset and concluded the performance of the algorithm. You can also give the algorithm as a supplement.

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Which to cite: Review and Survey papers or Research papers?
Review papers are long papers gathering the results of various researches and have many conclusions. When I want to address an issue or a conclusion about something should I repeatedly cite a Review paper and use points in that paper or I'd better find important papers on that topic and cite them?

What field are you in? The practice varies greatly from one field to another.

@CarlMummert Computer Science

I want to add to the other answers that, it happens sometimes that researchers read the review papers and not the original papers that are referred to in the review papers; but when they want to cite the content in their papers, they cite the original papers which they have never read.
The point is that, you should cite exactly the source you read. If you are reading that content from a review paper, you should cite that review paper. If you are reading the original paper, cite that original paper. Look at this example:

In case you only have read the review paper, not the original one:

In the review paper  we read that the method x is perfectly applied to examine that [...][1]

In case that you read the review paper and then read the original paper:

In the review paper  we read that the method x is perfectly applied to examine that [...][1]. It is clearly indicated in the original paper [2] that the method x only discusses parts of the instances of the experience including; instance a, instance b and instance c [2].

In my opinion, review papers are not always so precise and it happens that some content is misunderstood or wrongly copied in quotation and rephrasing in the review papers; so, if you find some content interesting, go to the references of the review paper and try to find and read the original papers as well.

Then again, there are fields like mathematics, where it is research papers that are imprecise and full of errors, and review papers (at least) try to improve on that.

@darijgrinberg Yes, Exceptions always exist. Even in engineering field publications, one may find review papers in which errors are tried to be discussed and improved.

Both. You cite a) the overview papers when referring to the suggested area and the comparison between the different methods and then you b) cite the original paper (when a method was introduced) when you refer to that individual method.

To add to Alexandros' answer. Refer to the review paper for the over-arching conclusions drawn in that paper. If you need to refer to results emanating from an individual paper, you should refer to that particular paper. Remember that you should cite the source and you should avoid citing work through others. The purpose of a review paper varies but usually involve summarizing, synthesizing and finding new structure or gaps in knowledge from a large body of literature. These are the "conclusions" from such a paper which you should cite. It is also common to cite reviews as good sources for literature on a particular topic.
As with any research there is no guarantee all material used in a review paper is well represented, mistakes or misrepresentations occur. It is therefore necessary to go back to original works if you cite material that is key to your own paper.


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How many points should a journal paper have?
Suppose I have done a work that has many features or aspects A, B, C, D,... when I want to present it as a journal or conference paper, should I cover all of them? or just to focus on one or two aspect? because I feel some of these features are irrelevant and not close to the topic or aim of the paper.
It seems, to explain each of them I need distinct introduction, review and experiments and mixing all of them could make the reader confused...
Is it better for my paper be focused on one or two arguments? Can we say journal papers are usually about one point?

Sorry, I'm not quite sure what you are asking. My knee-jerk reaction to your question is: if a referee thinks additional points are necessary, then you should comply with their request, or state why that is not a good idea in your response to the referees.

In addition to @MadJack question. What kind of paper? Is it for a conference, a research paper, thesis or dissertation, or something else? The type of paper can determine length and level of detail which help to determine the number of arguments which should be or can be covered.

@JGreenwell as I edited the question, its a journal paper... In my language when we say paper we usually don't mean thesis or dissertation, I didn't know in English it covers them too.

I'm going to take a fairly strong opinion here and say that every paper, no matter how large or how small, should have precisely one core point.
That one core point may have as many or as few lines of evidence in support of it as are needed given the research context: that will be very dependent on the particulars of the paper and the community to which it is addressed.  Everything, however, should support the one core point, whatever that may be.  If you organize a paper otherwise, then in my experience both as writer, reviewer, and editor, it will tend to result in a paper that is poorly focused and scientifically weak.
So if you find yourself wanting to make multiple points with a paper, I would recommend considering the following two questions:

Are these different points really different aspects of the same core point?
Should this really be more than one paper, with different papers focusing on different core points that require different lines of evidence?

In the case of a new language, for example, there must be some key motivator for building the language, which is what you want to highlight.  At the same time, a new language will be much less mature and well-developed than many existing languages, and so there are certain to be aspects of comparison where it will show up poorly---but which may not matter.  The question then is this: what is the important thing to be learned, relative to existing pieces of work, and how do you provide evidence supporting the notion that you've done this better than existing languages and yet not introduced fatal flaws in other aspects.

Thank you, it almost answers the question. I myself favor one core point for a paper, as it has been the aim of the researcher! there are few times that we target many things by a work...


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Reference management software to get the link of references
I use Mendeley to organize and view articles (pdf files). It is almost good, however I wish something similar with one additional feature. A software to make a link for every reference in the Reference section of any article I read (not my own articles) and when I click on the link it searches the web for it, or if it has a downloadable version, directly points to that file and if it is already exists in my articles opens it.

When using LaTeX to write the article, you can do this with biblatex and hyperref, see https://tex.stackexchange.com/questions/23832/biblatex-make-title-hyperlink-to-doi-url-if-available

@JaapEldering thanks, that is possible for my own articles, but I want to extract all links to references of any article (pdf files)

Digital Object Indentifier (DOI) names might be a possible solution. Sometimes article citations in major databases come with them - if so, you can use them to directly access the paper (in a web browser, at least).
For example, for Claude Shannon's seminal work A Mathematical Theory of Communication, the DOI name is 10.1109/9780470544242.ch1. This can be resolved either by using this website, which also describes DOI names in detail; or by using a direct link, such as http://dx.doi.org/10.1109/9780470544242.ch1.
You can find these DOI numbers either by checking reference databases (which often include them) or by checking a website such as crossref.org.
IIRC, Mendeley actually includes a field for the DOI name, if known. I've seen it automatically populated when I use the browser clipping tool (sometimes, not always).

I know JabRef automatically turns DOI into links like this, idk about Mendeley

@Oxinabox: The desktop version at least has a "lookup" feature that tries to convert the DOI name into a link to a database. So, assuming the DOI name is imported and the lookup succeeds...I guess this is a 2-click solution :-)

It might be worth including a screenshot with a red circle around the button.

I just started using JabRef and you can in fact, given just the DOI, let JabRef grab the complete citation including a link. You can also try to grab the full text automatically, if possible (don't know how exactly that works). A click on the File-icon next to the bibliography entry in the main window will open the web link.

A link for every reference? In the paper or the database?
In the paper  this isn't really desirable to have urls, the doi will do. Use the hyperref package in latex to create clickable links in latex.
In the Mendeley database this already exists. Copy the doi of the paper into the doi textbox of the citation and click the search icon to the right. It fills all the reference info, including a link to the pdf on sciencedirect or where ever it is hosted.

Thank you, however I mean to retrive the reference section of an article

Oh sorry, i didn't understand that, but that makes more sense. Sciencedirect has a reference section for each article there where all the articles with doi are clickable links. You could use flashgot or similar to download more than one at a time if needed. Not really a solution but perhaps it'll work enough for you.


text:
What does "indicative" mean for the literature review
One reviewer of my paper commented the following:

The authors should clearly state that the literature they have
  included in the introduction is indicative (both in the case of
  experimental measurements and molecular simulation of ILs) and
  redirect to some recent review articles.

I don't know what does he mean. I don't know If he expected that I add some introductory sentences before reviewing literature like (bold part):

Several experiments have recently been performed in order to understand the underlying dynamics of ILS, including XXX. ZZZ et al. [8] obtained the viscosities of the ILs XXX and YYY in a wide temperature range. Moreover, ZZZ and KKK [9] recently published atmospheric pressure self-diffusion coefficients of MMM tetrafluoroborates and NNN in the temperature range of 40-90 ℃.

However, in a previous paragraph I mentioned an introductory about ILs in General and not XXX in particular:

In the literature, experimental and theoretical methods have been employed to obtain the properties of ILs. Experimental analyses such as IR, H and F NMR spectra, polarizing optical microscopy, differential scanning calorimetry, and UV-vis spectra have been used to determine the properties of ILs [5-7].

That does seem an odd word choice. You'd expect it to say "is indicative of XYZ". Possibly they mean that the papers you're citing are just a small part of the existing literature, and you need to make that clear in the introduction.

Your reviewer might be Italian! In Italian, you can say that something is just "indicative" (or indicativo) if it is only there to give you a rough idea.
You can probably just state that your literature review is not exhaustive.
Some examples of a titolo indicativo

It is what I first thought. Italy here.

It isn't only an Italian expression. I've heard that usage of "indicative" in the French-speaking world, also.


text:
How to find ISSN number of IEEE Sponsored (or IEEE related) Events?
My University of Technology requires me to limit my research paper publications to certain venues, which have an associated ISSN number.  How do I find out the ISSN numbers for IEEE Sponsored events, such as in Croatia (Europe), when I can't find an ISSN number on their Web pages?  Here is the IEEE related conference URL: http://iwcmc.org/2015/?  Thanks so much!!!

You can look at this list https://www.ieee.org/documents/2005_present_list_of_titles.xls from IEEE of upcoming events, and events from 2005 to present with all corresponding publication numbers.
As a comment points out, many of the listings do not have ISSN numbers. However, you can look at line 10935 of the excel sheet and see your conference.
IWCMC.  The IEEE conference number is 34432 and ISBN 978-1-4799-5345-5

Note that most of these IEEE conference proceedings don't have an ISSN.  In my experience, journals are assigned ISSN's, but conference proceedings volumes typically have an ISBN and no ISSN.  As conference proceedings volumes go the IEEE proceedings are generally considered to be pretty good, but not nearly at the same level as the IEEE Transactions On  journals.

@BrianBorchers Your right that the document does not have many ISSN numbers, but not sure that it is true for all conferences.  As of prestige, that would depend on which conference and journal, and what your criteria is.  H-Index by googles shows many fields where conferences are ranked higher than journals.

@BrianBorchers for example ICCAS http://2014.iccas.org/ posts their ISSN number, and the conference appears in IEEE, but the list does not include an ISSN number.


text:
How should I cite something learned second-hand (eg, from Wikipedia) when I haven't seen the primary source?
I want to cite something that I have learned from a Wikipedia page. However, I'm loathe to cite Wikipedia because of the perception of it by my tutors, so I try to cite the original source.
What should be the correct thing to do when I'm unable to have sight of the primary source myself, or find it in a collection (for clarity, I should add that I have the details of the source - I just can't find it in collections available to me)? Should I just cite as much original information as I can, or should I defer to citing Wikipedia? I'm hesitant to do that, because a glance at the citation would suggest that I was 'too lazy' to source original material or just dig deeper.
For additional clarity - I know that citing Wikipedia is 'bad' etc.  The emphasis is on how to cite something that has been learned via Wikipedia (as an example) but for which the original material cannot be seen or retrieved from available collections or searches.

Why can't you look up the original source?

@James The FAQ assumes graduate-level research, so questions will be approached from a graduate-level perspective. Certainly some questions apply to both undergraduate and graduate work (as this question seems to do), but my understanding is that some level of applicability to graduate-level work is a requirement for academia.SE.

Some information on Wikipedia is highly specialised, but some information is quite "commonly known". If the information is sufficiently commonly known, you can get away with citing nothing at all. For example, you don't need a citation for "The Earth revolves around the Sun.".

Except for the Wikipedia-specific component, this is a duplicate of http://academia.stackexchange.com/questions/1922/whats-the-correct-way-to-cite-a-paper-cited-by-another-paper

This isn't a postgrad research question - it's way too junior. And thus off-topic for this site. Voting to close.

@EnergyNumbers there is nothing in there specific to undergrad studies, so I think it's on topic. Just because the answer is not very complicated doesn't mean it's not a valid question people might ask… And I think this one is a valid question, and on-topic.

@James, what is your purpose of a citation? Do you want to use their result directly, or only show alternative approaches?

What you're referring to is an indirect source. In general, you should always work as hard as you can to find the original source. If that is not possible, all of the major style guides include a way to cite indirect sources. Note that you should not cite Wikipedia (see the "do not cite Wikipeida" note at the end of this answer). If an indirect citation is absolutely necessary, it should come from a reputable, peer-reviewed journal or other academically respected source.

According to Purdue University, the MLA rule is to name the author of the indirect source in the text and cite the work you have in-hand:

For such indirect quotations, use "qtd. in" to indicate the source you actually consulted. For example:

Ravitch argues that high schools are pressured to act as "social service centers, and they don't do that well" (qtd. in Weisman 259).

Note that, in most cases, a responsible researcher will attempt to find the original source...

Williams College further clarifies that the indirect work should be included in your Works Cited list:

...include the indirect source in the Works Cited.

The APA rule (also from Purdue University) is to exclude the indirect source (called the "original source", below) from your reference list and only include the work you have in-hand (called the "secondary source"):

...name the original source in your signal phrase. List the secondary source in your reference list and include the secondary source in the parentheses.

Johnson argued that...(as cited in Smith, 2003, p. 102).

[...] Also, try to locate the original material and cite the original source.

The Chicago rule (once again, from Purdue) is to cite the indirect source, followed by the in-hand resource:

...Chicago discourages the use of [indirect sources]. In the case that an original source is utterly unavailable, however, Chicago recommends the use of "quoted in" for the note:

Ian Hacking, The Social Construction of What? (Cambridge, MA: Harvard University Press, 1999), 103, quoted in Manuel DeLanda, A New Philosophy of Society (New York: Continuum, 2006), 2.

That said, do not cite Wikipedia in a formal document (unless, perhaps, you are actually writing about Wikipedia or collaborative editing techniques). I love Wikipedia, and I believe it is reasonably well-maintained and has a lot of good information. However, you have no way to verify if the information in an article is true -- or, if you do have a source to verify it, you would just cite that source. Aside from the tired, "Anyone can edit it!" complaint, two severe issues with Wikipedia as a citation source are:

You get whatever version of an article stands at the exact moment your web browser fetches the page. No matter how hard Wikipedia's editors work, they can't stop a bad edit from reaching your web browser if it was made seconds before you fetched the page. Wikipedia doesn't undergo any kind of pre-publication review; all review is post-publication, which means you may see totally unreviewed information. (You can mitigate this by citing a specific past revision, but it still stands that a post-publication review process means that any given revision of an article could have claims that have been reviewed by absolutely no one except the author.)
In order for a reader or reviewer to ascertain the usefulness of a source, it must have an identifiable set of authors (or, for anonymous works, at least a consistent, reasonably small set of authors). Wikipedia makes that requirement incredibly difficult to satisfy. (Again, it's possible to satisfy this requirement if you cite a specific revision of a page and find out what contributors wrote each part of a page, but it is still difficult since a potentially huge number of contributors have helped build that revision.) It's hard for a Wikipedia article to be reputable where there are no clearly identifiable authors to which a reader could attach a reputation.

First, I would try harder to get the primary source. Really. But, if that isn't possible (price, availability, etc.), you may have to do without. In that case, a few solutions:

Find another secondary source, possibly one that is more “academically acceptable” than Wikipedia. For example, try to find a textbook on the topic that make mention of the fact you want to source, or a review article, a book, etc.

If not possible, what I have usually seen people do is cite the primary source anyway. That's bad, but people do it. If you write for a journal, where the reviewers might not allow a reference to Wikipedia, you might not have any other choice.

What I would recommend, if the format and/or editor allow it, is to cite both the primary source and the secondary source, possibly indicating the relationship:

J. Doe, Journal of Failed Experiments 10, 1024-1028 (1971); as cited by secondary source

Note: This is written from the perspective of a postgraduate student in applied mathematics.
1) Do not cite Wikipedia.
This is not about perception or laziness but rather, your thought process as a researcher. Suppose I read about a mathematical fact that might be useful to my research. I need to verify that the fact is true and have some ideas about why this is true.
By stating that the mathematical fact has been published in a reputable peer-reviewed journal or in a reputable textbook, I demonstrate that I have at least verify its authenticity, and perhaps even read technical details about it.
However, if I cite Wikipedia, it demonstrates that I accept facts off the internet without verifying or having technical understanding about it (Wikipedia usually don't go into deep technical details). This does not bode well for my reputation as a researcher.
2) Try to find an academically acceptable source to cite the same information from.
Suppose I want to use an equation. Random example: Kullback-Leibler Divergence. But lets pretend there is no source or citations on Wikipedia.
What I will do is to search directly for "Kullback-Leibler Divergence" using search engines like Google, Google Scholar or Google Books. I will also try to search for the term in my university or local library's search tool.
Assuming this fails. Then, I would look at topics that the Kullback-Leibler Divergence is in or is related to. For this specific example, I would look for textbooks or materials on "Information Theory" and look up their index or table of contents for "Kullback-Leibler Divergence". If this fails, I will dig deeper: think about what this equation does and search for similar topics. For this example, it compares two probability distributions. I will then look for ways to compare two distributions in Information Theory.
Once I find a paper or textbook talking about it, it shouldn't be too difficult to locate the source or pick a suitable paper/textbook to cite the equation from. If after all these searching and perhaps asking my supervisor/professor, I cannot find anything acceptable to cite from, I would ask myself these questions: Is this equation valid? Why should I believe in the authenticity of this equation?

#1 says it all, never cite wikipedia

I don't think you can cite something to which you have no (original) source. I mean anyone can edit Wikipedia (or any other similar webpage) so that would practically be citing a random person, without any way for a third party to check up.
Luckily Wikipedia articles usually have references you can check (to see whether or not they are actually accurate and relevant) and cite accordingly. If there is no reference then you should probably not be citing (or trusting) that piece of information.

Wikipedia is not really citing a random person, but rather citing a collective opinion by a random group of people (although there is probably a big bias caused by the fact that you probably only edit an article you feel you have knowledge about). But I agree that external references, preferably peer reviewed, are needed. But in general, the level of Wikipedia is ok.

perhaps I didn't make myself clear enough. Without a valid source, anything on wikipedia could be a random person claiming a particular piece of information. That kind of info will eventually get cleared out by the community but it might just be so that you retrieve the "misleading" info before someone with more insight on the matter corrects the article.

Note that if the Wikipedia article doesn't have the original source for a claim, then that section of the article is a work in progress that is below the Wikipedia standard. It requires a {{citation-needed}}, otherwise it could be "original research" which properly doesn't belong there.
It's probably a bad idea, in your academic paper, to quote Wikipedia material which the Wikipedia itself disavows!
There should never be a need to cite the Wikipedia, since anything credible is supposed to have references to the outside. In serious work, you always borrow the citations from the Wikipedia, not the text. Citing from the Wikipedia itself is good for cafeteria arguments.
When you make any kind of citation, you are basically expressing trust in the author. This is because you are not reproducing all of the research, such as experiments. You trust that the data haven't been falsified and so forth. There is some safeguard in that the paper appears in some trustworthy publication, and that it has been peer reviewed.
Suppose that the Wikipedia is actually the only source for some paper. Firstly, that situation is wrong and blatantly violates the Wikipedia's rules about original research, so the page will probably be deleted. Secondly, the Wikipedia isn't a journal that reviews and publishes material, so you would have to take that paper completely at face value. The Wikipedia cannot lend any credibility to anything, according to its defined mission and scope.

+1 for "there should never be a need to cite Wikipedia." If it's not supported with valid evidence, then there is no reason to believe it is true.

In addition to many good points made in other answers: while I agree that Wiki is not an acceptable final "authority/source" for nearly anything, the better articles do give external references that can put one onto the right track for more primary sources, as well as giving internal links via other keywords... As to how-to-cite, I have gotten more and more into the habit of at least footnoting that I found a reference (to a primary source) via Wiki.
Yes, of course, in one's primary "specialty", one should have better pointers to the "official" literature than Wiki, but with regard to necessary but peripheral topics for one's work, often Wiki can provide hints, which can then be verified afterward, after one has become aware of them.
So I use Wiki to begin to get a grip on keywords and vague ideas in things unfamiliar to me, to get started. Also, sometimes historical pointers are more readily accessible there, and then subsequently verifiable on MathSciNet, after one knows what to look for.
I note that "peer-reviewed" stuff should also be viewed skeptically/critically, especially with regard to recognition of prior art, and also simple correctness, since except for significant results, often referees are encouraged to not worry about certifying correctness, but more "novelty" and "interest". And history and prior art are often either omitted due to disinterest or ignorance, or pushed out by editing-down considerations, so that papers often do not give an effect look "backward".
Finally, in the spirit of giving credit where credit is due: when I find Wiki useful, I don't pretend that I didn't! Not that I view it as authoritative, either. A new category of information, perhaps.

If you consider citing Wikipedia, don't, as others have explained, but IMHO you should at least acknowledge it as being helpful, either with just a mention like that or a list of "non-cites" that could be used as starting points for others wanting to review Wikipedia's (latest) views on your topics.


text:
What's the name of Wikipedia's default referencing style?
What's the name of the Default Referencing Style that Wikipedia Uses? Specifically, I'm looking for the name of the style that is used when you use the referencing styles use by default when you click one of these four options:

Did you mean "English Wikipedia"? Or are you really asking of the whole wikipedia.org (280 languages)?

As you can see above, references to journal articles from the English Wikipedia are styled in the following manner:

Author, First A.; Author, Second B.  (year). "Title goes here". Journal of failed experiments volume (issue): pages-pages.

This is documented here. It corresponds to the APA citation style, with additional quotation marks around the paper title (which are not present in the standard APA style). Also, the references are styled as footnotes rather than “(author year)”.
In addition, note that it is not a strict Wikipedia requirement: the documentation I quoted above says:

There is currently no consensus on a preferred citation style or system for Wikipedia. If you cannot decide on which style to use, or if you do not know what information to include, an example partially based on the APA style is given below.

There's one other difference: APA's version of intext referencing is the parenthesis version, Wikipedia uses footnote referencing.

The other difference between wiki and APA is that there's also a PubMed Identifier if there is one available. So there are a few differences between APA and the format Wikipedia uses by default

APA style has a huge manual that cover "all" possible cases. Wikipedia is certainly inspired by APA, but it's not the same for all details.


text:
Should I include a reference for an image that is released into the public domain?
I am writing my thesis and came across an image on Wikipedia that I would like to use. The licensing on this image is:

I, the copyright holder of this work, release this work into the public domain. This applies worldwide.
  In some countries this may not be legally possible; if so:
  I grant anyone the right to use this work for any purpose, without any conditions, unless such conditions are required by law.

Should I still include a reference to indicate this image is not my own work, if so, who should be given credit (the author is not known in this case)?

I don't know if you have to (IANAL), but I would still state where you found it (Source: Wikimedia Commons) to avoid claims of plagiarism.

Should I still include a reference to indicate this image is not my
  own work

YES If the idea is not yours, you need to reference it.

Who should be given credit

That is a harder question. Ideally, you should find the original author/source. Given a reasonable attempt to find the original author/source fails then reference the secondary/reproduction (i.e., wikipedia/wikimedia).

+1 I don't know how many students have submitted papers to me including images in the public domain thinking they do not need to be cited. No citation means you are claiming you are the author.

There is a huge difference between (not) having to cite due to laws and having to cite because of the idea that you seperate your own ideas from someone else's.

Here are the recommendations from Wikimedia Commons:

Content in the public domain may not have a strict legal requirement
of attribution (depending on the jurisdiction of content reuse), but
attribution is recommended to give correct provenance.
Other restrictions may apply. These may include trademarks, patents,
personality rights, moral rights, privacy rights, or any of the many
other legal causes which are independent of copyright and vary greatly
by jurisdiction.

The rest of the page is very informative as well.


text:
How to find someone online to collaborate on a joint paper?
I would like to know where (a website) I can find anyone to publish some joint papers?
I thought such cooperation can be shaped as the following:

We could share some ideas for papers through email or a web tool and ask the opinions about them (in fact if the person is an expert on a field who could transfer his knowledge and experience to me and direct me in the right way would be a plus :) )
I would try to prepare a draft of the paper

Somethings that I wish the other one can guide or help me on are:

I don't know much journals to publish a paper in, in this regard one could send the article to the journal
My English is not perfect and the other one could modify the paper or guide me for some modification

Update:
it seems the way I wrote it, the relation could be like two keen researchers with common field of interest or like an expert who guide a PhD student.

Are you an independent researcher, or are you in some sort of institution, like a university?

I am in a university and must mention the university affiliation

I don't think there is a 'dating site' for scientific collaboration. Maybe you could explain why you are looking for someone outside your university, is it because no one has the necessary expertise? That might increase the chances of getting meaningful answers here.

Related: http://academia.stackexchange.com/questions/6035/how-do-researchers-from-different-institutions-collaborate/6037#6037.

If this is all you need, you should probably be looking for a Professional Editing Service, not a co-author....

Yes I need an expert on the fields of my interest, I modified the question

Are you studying a PhD? If you are, your supervisor should be your main collaborator in the first papers. If you are not yet, then you should search for a supervisor for your future master or PhD and (s)he should be your collaborator. If you have already finished the PhD, then there are many things that I don't understand and I cannot help you.

@Trylks No I have a master degree, but I teach in university, before to apply for PhD I must publish some papers, even I had a PhD, still some experts could guide and help me like a supervisor

Your update does not do what I assume you wanted: You recognise the ambiguity but you do not solve it.

The things you seek from a coauthor (advice on journal selection and English usage) are not in themselves a sufficient basis for coauthorship, but rather just being thanked in the acknowledgments.  A coauthor on a scholarly publication needs to make a substantial intellectual contribution by being seriously involved in the research.
I do not know of any website designed for academics seeking coauthors, and I wouldn't recommend approaching it from the perspective of "I'd like to publish a paper and am looking for someone to help clean it up and submit it."  That's not likely to find you the sort of intellectual connection that would lead to genuine coauthors.  Instead, you may get no responses, or you may get unscrupulous coauthors who just want an easy way to get their names on papers.  (And even if that doesn't bother you, think about it this way: if someone's willing to put their name on your ideas, could you really trust them not to add some plagiarized text to the paper?)
Instead, research collaboration should come before coauthorship, so the question becomes how to find collaborators.  That can come in all sorts of ways: you can talk with people at conferences about common interests, you can write to people whose papers are on similar topics, etc.  Sometimes collaborators meet through participation in websites where they discover a common interest.  (They aren't necessarily collaborating on the website, but they may start to correspond after interacting through the website, and the correspondence may turn into a collaboration.)  Once you are actively working on research with someone, writing a paper together will come naturally.

'unscrupulous coauthors who just want an easy way to get their names on papers' That was a pretty accurate prediction judging by the recent comment posted on the question...

Thank you much for your complete advice, yes you are right I must add that I need an expert on the field of my interest, but my other problem is that I am forced to publish some papers within one or two years, I thought such a person could fasten my efforts to publish some papers


text:
publishing a conference paper in a journal
some years ago (2007) I have published a  paper in a conference as a poster paper. Now I want to send it to a journal and change the affiliation, or maybe some minor changes. I didn't see any policy about a previous published paper in a conference, however there is a policy as the following:

The submission has not been previously published, nor is it before
  another journal for consideration (or an explanation has been provided
  in Comments to the Editor).

Could I send my paper to this journal?
Is it a normal thing to first publish a paper in  a conference and then trying to send it to a journal?

In any case you should mention the conference publication when you submit your manuscript, so that the editor can make sure this is acceptable.

In my field this would be not only acceptable, but expected, as the review process for conferences is less stringent and the submitted abstracts are substantially less detailed than a full manuscript. A conference presentation is viewed almost as a necessary step to publication: present the first interpretation of the results, get feedback from colleagues, and incorporate changes into the full-length manuscript.
My only concern would be if the conference paper was closer to a full manuscript, both in length and in the rigorousness of the review process.


text:
Can Design & Implementation sections be combined in a project report?
I'm writing a postrgraduate project report on a system I've built. It is not designed with the user in mind, it is a backend system to a simple web application.
I'm struggling to separate the Design chapter from the Implementation chapter in my report, as I didn't so much design the system as build it as I went, changing how it was built depending on issues I encountered during implementation.
Is it possible to add all design and implementation information under one chapter, as they are fairly intertwined, or is it necessary to separate them?

Edit
I have solved my problem; the Design chapter is the idea and outline you had in the beginning of what you would like to create, with the various components you think you'll use, and the Implementation chapter includes all the issues that cropped up along the way, creating the need to change the original design.
Thanks for all your input!

I am not sure, but I am feeling like Academia.SE is not the correct place to ask this question. May be English Language & Usage Stack Exchange helps you more.

I didn't so much design the system as build it as I went — Don't do that.

This question appears to be off-topic because it is about software documentation.

@JeffE but isn't that an important part of writing about software design research?

This seems like the type of question that only your advisor can answer.

If you've solved your own question, you should add the solution as an answer (note that you can accept your own answer if it's the most helpful to you), not as an edit to the question. This way, other users can vote separately on the question and answer, and people who come across this post in the future (because they have the same problem!) can more clearly identify your answer as a solution.

The answer is:
The Design chapter is the idea and outline you had in the beginning of what you would like to create, with the various components you think you'll use, and the Implementation chapter includes all the issues that cropped up along the way, creating the need to change the original design.

It seems you were given an assignment to design and build a system and then write a report to document your work. However, you decided not to do that assignment and instead you decided to build a system skipping the design step.
I would expect the person marking your report would see it as you did not complete the task as assigned. As JeffE's comment implies, there is a reason why you were given a task that included designing first then building.
I think you should ask your lecturer if what you have done is acceptable or if you must restart your assignment.


text:
Why are some research papers scanned with OCR instead of actual PDF?
I have some research papers in PDF format that are actually scanned (and then OCRed) instead of being the original PDF. Some are so badly created that text cannot be properly searched inside.
For example this paper published in 1994 is all about advanced computer technology and there is no proper digital copy. This extended report related to the above paper is even more horribly digitized.
edit: I am unable to access the actual horribly scanned paper. That extended report also had issues in copying.
Why is that? Why are some computer-science publications, which are not even so old, not available in a proper digital format?

I fail to see any hints that the second document has been scanned or OCRed. The only thing I see that impedes searchability is due to standard LaTeX’s encoding of ligatures, which is unfortunately somewhat backwards.

Yeah, it looks like the second document has been converted from a postscript file that used bitmapped fonts (which would explain why it looks bad but shows no signs of being scanned).

@Wrzlprmft I am unable to access the actual [horribly scanned paper] (http://dl.acm.org/citation.cfm?id=239773&preflayout=tabs). That extended report also had issues in copying.

The second link appears to be converted to PDF from an old PS file. Perfectly digital, just technologically outdated. pdflatex hasn't always been around, and people had to go through PS to create PDF files.

In many cases, even through the early 2000's, publishers produced print journals using older type setting systems and did not produce PDFs of the papers for online publication.  Once the papers were type set for printing, the publisher might have discarded all of the files associated with the papers or they might have just kept a file containing a print-ready image of the paper.
Many journals had old material of this sort dating back decades.  Since it would take a huge effort to type-set all of those older papers again, journal publishers have settled for simply scanning the earlier papers (or retrieving saved images of the papers) and then publishing the images of the papers online.
Using optical character recognition (OCR) is one way to extract the text from these images.  However, OCR isn't 100% accurate, and in any case it can't preserve all of the formatting of the paper.  Thus OCR text from a scanned image of a published paper may be somewhat useful for indexing, but it really isn't equivalent to having the original document as a text PDF.
A different issue is that you may have received a copy of a paper from someone other than the publisher.  For example, if you made an inter library loan request to get a copy of a paper, it's possible that someone at another university library scanned a printed copy of the paper and sent that scan to you.

PDF is a younger format than you think it is, having only been invented in 1993. Before that, documents would have been in PostScript at best. Many things you might think are OCR are actually bad PS conversions: it is very hard to unscramble the PS egg in some cases. The first linked paper appears to be of that type.
For others where is no version even that good, it is simply that the cost of a better conversion is higher than the value per old paper. Maybe this will change someday, but right now the high quality OCR systems have higher priorities.


text:
Developing meta-cognitive and emotional skills during PhD?
I am convinced that I possess sufficient "cognitive skills" to succeed doing my PhD. Reflection on myself, however, confronts me with the fact that my "meta-cognitive" (time management, mental discipline, focus) and "emotional" skills (motivation, patience, work-life balance, monitoring own health) are underdeveloped.

I feel that I am always making the same mistakes. I am often working hard for days. Stress and coffee distort my sleep pattern, making my mind empty for days. I recognize clear patterns. I also have trouble maintaining a healthy life-style. Instead of taking a little bit more time to eat healthy or sport, I am captivated in "the illusion that there is always more work to do." As a consequence, I am (on average) physically sick two days in the week -- eventually, losing more time. Finally, though I was happy living my introvert life before, the long days of no social interaction and just staring at my computer screen are becoming more dreadful.
My meta-cognitive skills also seem to be weak. I have trouble focusing on one subject for a very long time. I often get bored after some weeks, wanting to jump immediately to something else. As a result, it appears that the first phase of my research (almost 9 months) is very fragmented. I don't see any linear progress. I often doubt that the time I am investing in some subject will be useful later. I feel that I am not really spending my time the best I can. I keep track of my work hours in Excel files to be sure that I accomplish my weekly goal of 45 hours. In order to accomplish this goal I mostly have to push many hours to the weekend. I am aware that this bad time-organization will affect the quality of my relationships in the long term; and damages my work-life balance in general. I feel that I am working 24/7 at half capacity, whereas I would prefer to work 5 or 6 days in the week at full capacity.

I am starting to have less and less satisfaction from my work. The butterfly feeling of wonder and passion for science are disappearing. I am feeling more like an input-output machine which needs to be managed. The work I am doing also seems to be driven and conditioned by external factors (deadlines, presentations, publications, expectations promoter) instead of internal factors (pleasure, interest).
More concrete questions:
(1) Is it possible to improve one's meta-cognitive and emotional skills? How would one do this in practice? Can a person really change?
(2) How can one restore those feelings of wonder and true passion, and step out of the "routine" where one feels like an input-output machine which needs to be managed?

Instead of tracking your working hours, set reasonable weekly goals and track a progress towards goals. These can be things like: read a paper, go to gym, run experiment 1, run experiment 2, etc.. At the end of the week, you'll have something concrete to look back, and over few weeks you will start seeing a progress.

Question (2) is separate and should be moved to another post (on Stack Exchange it is important to ask one question per one question). But for a quick link: http://amasci.com/~billb/cgi-bin/instr/instr.html

I empathize, as this is something that I (and many others here, I am sure) have also struggled with.
My first piece of advice is simple but difficult: you need to start valuing yourself. Eat well. Sleep well (or at least defend an eight hour block of time where you lie in bed and rest). Get outside and move around. Your mind lives inside your body, and you cannot build on a broken foundation.
My second piece of advice is to help yourself do this by getting help from a therapist. I particularly recommend looking into cognitive behavioral therapy, given your description of self-regulation: it is very good at helping people get out of dead ends that are more intellectual than organic.

Note that the average adult needs only seven hours' sleep, though younger people often need more (ISTR reading that teenagers average more like nine hours). So you don't necessarily need eight hours but definitely make sure you're getting enough time resting, relaxing and sleeping.

@DavidRicherby It's actually 7-9, depending on how you value error bars it might be 6-10: http://sleepfoundation.org/how-sleep-works/how-much-sleep-do-we-really-need

@DavidRicherby Don't worry about the exact number too much: if you're too messed up to sleep, use 8.  If you're able to sleep OK, don't set an alarm.

I'll start by trying to answer your specific questions.
(1) Yes, it is quite possible to improve your meta-cognitive skills (I think some people call this executive function) and emotional skills. I considered developing a part of my Ph.D. education. Actively seek to develop it now and for the rest of your career. You can make a positive change for yourself.
(2) Now, this is where long-term thinking will really benefit you. You need to rest. Taking time to rest each day and weekend will help you the most, because then you are refreshed. I had a revelation earlier this week: Just because a behavior feels productive, doesn't mean it is productive! That includes arbitrarily set long hours. Treat your research as a job if it helps. Set hours for yourself each day, and then go home and let your mind rest when the day is over. That being said, I don't think you should count hours on a spreadsheet as you have been. You haven't accounted for the quality of your work, which will suffer without rest. Even if you work fewer total hours, your net productivity will increase if you make the time to rest.
I sometimes had difficulty feeling passion and wonder, and I had a couple of slower years before I figured it out. It is perfectly normal for you have a slower, difficult period during your research. Don't beat yourself up over it, because research is inherently difficult and you will thank yourself for persevering.
I actually became most productive towards the end of my Ph.D. program when I was able to relate how everything I was doing worked towards completion of the degree, which is something I really wanted. What I am trying to say is that I really wanted to understand the research field I was working in and because I made sure I was rested and had the right support system for myself I could focus on the research when it was time to work.

I agree with @jakebeal and @James Palmer, as well as the comments.

I used cognitive behavioral therapy (CBT) to get through my Ph.D., and it helped.
I also used mindfulness practices. I recommend yoga and meditation. There are different types/approaches to meditation, and mindfulness is not exactly the same as meditation, but it includes a form of meditation. Jon Kabat-Zinn has a number of books on mindfulness, and his approach appealed to the analytic part of me. In particular, I recommend The Mindful Way Through Depression: Freeing Yourself from Chronic Unhappiness which combines mindfulness practice with CBT. Kabat-Zinn is not the primary author, but the book includes a CD with guided meditations by Kabat-Zinn, and the authors' approach to mindfulness is in line with Kabat-Zinn's approach. (Kabat-Zinn is not a therapist.)
You can develop the meta-cognitive and emotional skills to finish your Ph.D., but I wouldn't not depend on your colleagues and mentors to help with that. Many people in academia don't have those skills themselves, and it is possible to succeed in academia without adequate skills in those areas. It may eventually catch up with people, and success without such skills may cause a lot of collateral damage to health and family and friends along the way, but it is possible.
Whether it's for the sake of succeeding or for the sake of valuing yourself, you have to take care of yourself. Nutrition, adequate sleep, relaxation and recreation, and meaningful, nourishing social interactions are crucial for success and happiness. It was hard for me to prioritize those needs, so I understand. If it helps to think of fulfilling those needs in order to achiieve academic success, that's fine. I think that along the way, you'll find that fulfilling them is an end in itself for your own happiness. You are worth it.
So hang in there. We've been there. Academia has a lot of dysfunction (like any achievement-based endeavor), but if you get to do what you want, you may find that it is worth it nonetheless. Remember academia is not the same as the subject area you are passionate about. Academia is the predominiant context that your subject area is pursued. Let your passion for the subject drive you to make sacrifices and get through the grind of it. In the short term (which may include the whole time of completing the Ph.D.), you may not feel much of the passion. It's the longer term passion that is the motivation. If that is gone, then you need to consider if you are on the right path. (You may or may not be. I can't answer that.) In other words, don't give up if you don't feel the passion in the short term, but if you don't feel it in the longer term, think about it.

Good luck!

I can relate completely. My PhD has been dragging on for a long time, and I feel like years of life have evaporated. I don't have all the answers, but these are some of the things that helped me:

The pomodoro technique. From Wikipedia:

Decide on the task to be done
Set the pomodoro timer to n minutes (traditionally 25)
Work on the task until the timer rings; record with an x
Take a short break (3–5 minutes)
After four pomodori, take a longer break (15–30 minutes)

There are apps for this. The 3-5 minute break is important to refresh the brain.

Use exercise as a break. Makes body healthier, regen's brain.
Stop drinking coffee, or any caffeine, it's like baby meth. I read a psychology study where the participants who drank lots of coffee dropped a whole point for their GPA for the semester.

Answer to 2) You can never have the wonder and passion all the time. People who are constantly 'following their passion' are rare and perhaps mentally disturbed. Playing with ideas is 90% of the fun but 10% of the work. I try to find some pleasure in the tedious stuff by doing it 'right'. LaTeX helps cause it makes pretty things.

I agree that following your passion all the time is an ideal. I think in terms of deciding what matters to you. For most of us, that's not just one thing. So while you may have a passion of science, you also value time with family and friends, or whatever it is that matters to you. Then it's a matter of managing how your time to be able spend time on what matters to you. Also, LaTeX is a nice way to do necessary work that is satisfying and yet different so your brain gets a break.

TomatoTimer is an online version to apply the Pomodore Technique.

Unless your PhD is externally managed, completing a PhD is often dependent on learning soft skills.

I feel that I am working 24/7 at half capacity, whereas I would prefer to work 5 or 6 days in the week at full capacity.

Yep: at least in CS, people's productivity correlates more with efficient working and less with working a lot. (I believe math or theoretical physics wouldn't be different).
Cognitive behavioral therapy (CBT) might be helpful. In my case, similar problems were the result of perfectionism: imposing on myself standards that are so high to be harmful. According to rumors, perfectionism helps to enter a PhD, but it gets in the way of completing it. Don't trust me, a stranger on the Internet, but consider looking at this professional self-help material and seeking counseling.

I have trouble focusing on one subject for a very long time. I often get bored after some weeks, wanting to jump immediately to something else.

In the end, you should find a PhD topic that you care about enough to focus on it. How to get there, and which topics to study/work on, is something your supervisor should help you with—you might need to seek him explicitly.


text:
Set targets for PhD
I am currently starting my PhD in physics. I like the work and the working environment, thus I chose the project. The onliest thing I am a bit worried about is that my supervisor is known for changing tasks during the project, regardless of deadlines. I already saw that during my master thesis in the same group, where he told me to start and finish another (rather large) lab task two weeks before my final dead line. I managed to do it, but I would prefer not to have such events again.
Thus I proposed the usage of milestones or project tasks for the project. He responded that he would prefer not to use them, due to possible (yet unknown) new discoveries during the research phase, which then could change the topic completely. That argument makes sense for me, too. But is there still a way to set up at least some borders in order to prevent surprises?
Edit:
The lab task was basically designing, building, testing and running measurements with a new measurement setup for optical properties. It was discussed when I began, but never mentioned later, thus I may have forgot it (I am not without fault here, I have to admit). That lead to achieving the first real measurements ~30 minutes before submission deadline.
Some professors I knew and have seen the thesis afterwards made the remarks that that definitely increased the total scope of the thesis way out of the range of a common thesis.
Furthermore, I discussed the topic with him, and he agreed to make at least a rough draft of expectations, after he understood (as far as I could see) my concerns. So, I'll see...

It's not entirely clear to me what the source of the surprises is. If it's that you, e.g., run an experiment and get an unexpected result then there's not much you can do about that besides not running any experiments. You could refuse to follow up on unexpected results, but that could be detrimental to your thesis. If the surprises are coming from somewhere else, then where?

By adding new project goals/tasks which are not discussed before regardless of deadlines.

Could you perhaps give a (if necessary, hypothetical) example? What you've said could span anything from following up an unexpected result, or moving away from a dead end in your research, to your supervisor saying "I've been at a conference and everyone is talking about X. You will now do X"

PhD is full of such surprises, you are not certain what comes next. Sometime a good journal appear and you have to shutdown completely all your work and start writing paper.

@Ian_Fin: Added, is that sufficient?

Learn to say no. Part of your PhD is to learn how to become an independent researcher, and that includes learning to prioritise tasks.
If he proposes you a new task that you don't think fits into your schedule, either tell him that you are busy with something else and cannot do it, or that you are working on something, but you can look into that once you are finished (include an estimated date).
You may find helpful to make a short term schedule with future tasks. If your supervisor insists on you doing something, present him with the schedule and ask what should you remove or postpone to fit this task. My girlfriend (way more organised than I am) usually has one detailed plan for the next 1-2 months to avoid this exact problem. This still gives enough wiggle room to accommodate new findings, while keeping the project moving forward, without getting too sidetracked by small findings. And of course, it is not set in stone if something big pops out.
Another think that you should consider is that often, your supervisor has no idea how long the tasks he is proposing will take. This is very common in computational fields, where adding a new feature may be immediate, if you already have computed everything you need for it, or it may take weeks if you have to do it from scratch. So, if you are presented with a task that you think is too big, give your supervisor a time estimate and ask him if he still thinks it is worth it, and if he is still up for it, what to remove from the schedule.

I can understand that your professor expects unexpected things to come up, but that doesn't mean you can't make plans or targets. I would recommend being firm with your supervisor (their way of working is possibly less important than your ways of working, given that as a PhD student you will be conducting much more independent research) and getting them to help you make reasonable targets.
However, you do have to be open to scrapping those plans, and it might make your supervisor more comfortable if you stress this point. You can plan for what you will do if everything goes well, but know how to change your plan if you discover something else interesting and want to change your focus. It's worth noting that many people don't know what their thesis will actually be about for their first year or so.
At my university, we have certain monitored deadlines, so you have to have decided on a vague research topic within 9 months of starting, and have a sensible plan for what will be included in your thesis about 9 months before your end of funding. (I'm in the UK, so funded for 3 or 3.5 years.)
If your professor is resistant to the idea, you could talk to other students and academics about how they plan or make targets for PhD projects. If your supervisor throws you a curve ball that you don't want to take on, you don't have to do what they say if you can demonstrate that it is not useful work for you, if it is off-topic or you have enough material for your thesis without it and don't have the time.

The real issue is that your supervisor is known for changing tasks during the project, regardless of the effect it might have on your deadlines. did you explain to your supervisor why you proposed the schedule? If not, I think you need to explain your concerns clearly to him.
You proposed having a schedule with milestones, which is a very sensible approach. Frankly I think it would be insane not to have some sort of schedule planned out with milestones, even if it is very high-level and subject to change. Make sure your supervisor understands that this schedule is a communication tool as well as a planning tool; it would help you both see how task will affect your schedule.
If your supervisor still doesn't want to deal with schedules, ask him what alternative approach he proposes to ensure that you finish your PhD within a reasonable amount of time. Whatever he suggests, make sure that you are satisfied with it before agreeing. It's important to sort these things out early in your PhD.

during my masters thesis in the same group, he told me to start and finish another (rather large) lab task two weeks before my final dead line. I managed to do it, but I would prefer not to have such events again.

That's the starting point for this difficult conversation.  You'll have to present it as an "I-message".  An "I-message" is where you explain how what happened affected you, and how the prospect that something similar might happen in the future affects you.
Once you get across how the incident affected you, and continues to affect you, then you may be able to start talking about possible solutions.
When you get to that stage (and I don't know how long it will take for your advisor to be ready to enter that stage), try to take a brainstorming approach, where you allow your advisor to contribute ideas as well.
If your advisor has trouble taking your "I-message" on board, be patient.  Try again a little later on.  Give lots of positive feedback whenever your advisor treats you with the respect you want (and deserve).

You can set multiple plans for milestones, such as the main plan A, second alternative B, and the third one C.
If you fail in A, just move quickly to alternative B.
This is an standard way for doing PhD work, because it is an unknown world for us before doing exactly what should we do to reach the results.
My proposition is to have a overall milestone including details for each step of your project and also have multiple plans(aims) for doing the same project.

The OP's issue doesn't seem to be the possibility of failure, it's that their supervisor may make unexpected changes to the project which aren't necessarily easily reconcilable with the various timescales of a PhD. As a general rule, I think it's good to map out milestones for a PhD, but I'm not sure how doing this solves the problem that the OP is alluding to potentially facing.

authors: انگلیسی خطیر Eng_Khatir


text:
When should I ask questions about a paper?
Short intro: I am a masters student, and doing my master thesis in physics.
Currently I am working on a numerical physics project, and for calculating a formula I want to use an algorithm proposed in a recent paper. Unfortunately I am not able to fully understand and reproduce the algorithm, either because I am lacking some information, and I am also not sure if my implementation is correct at all (I am working with a numerical approximation method, they wrote, that their error changed while calculating (and therefore they had to implement a intelligent error algorithm), but my error never changes.
I am currently the person with the biggest knowledge both in numerical computation and in solving the GNLSE at my chair, so my supervisor can't help me, either.
So, when should I write the responsible author a mail and ask him about the missing parts in the paper? I don't want to annoy him with stuff like "oh look, I forgot a bracket", or similar things which I never saw. Is there a line to draw? How do I check if my questions are "clever" enough to ask?

I think a good general rule of thumb, when you don't know the authors in question, is when you've convinced yourself you can understand some piece of the paper (or resolve an apparent contradiction) with your current resources.  Once this is the case, try to craft a simple, brief and direct email which addresses the primary issue(s). Then sleep on it before sending it, as often things will be more clear the next day.
In your particular case, it seems reasonable to ask about details of the algorithm, but I would not ask about your implementation.  However, they may be willing to share their code with you if it is non-proprietary and not a complete mess (like most of my code!), which you can then use to understand the details of their algorithm and check your implementation.  (Have you already checked their websites to see if they made the code available?)

Checking websites is a good idea!