text:
How can I "time-stamp" my data without publishing it?
If I have a DB or set of data, and want to grant access to it to a limited group of experts in a field (not general access), and don't want others using it for their own publications, nor seeing the information being offered for free on the Internet.
What is the best approach to deposit the information somewhere to make sure, in a hypothetical future, that I can claim copyright over it?
Basically, I want to protect myself upfront against My research work stolen and published as his own by the co-author without my consent

I'm having trouble understanding your first sentence.  To me it sounds like you're saying that you both do and don't want to share a certain set of data.  Can you clarify?

I didn't really understand the question for the reasons provided by @PeteL.Clark but depending on the size, you may be interested in Proof of existence.

@Trylks That's fascinating.

Trylks: you are right on track. However, I still would need to know whether it would have any weight and a real copyright claim.

@QuoraFeans It would help if you stated clearly what your purpose is. Do you want to make money selling access to the data? Do you want credit for being the one to collect the data? Do you want to keep them secret for a short while to bid you time to conduct more research on them before they go public? Do you simply hate the world and don't want them to see them?

I don't think there should be a possibility to do this. In effect, you want to claim rights on some mysterious results you got, without others being able to know what it is. Then, in case someone else has the same results (maybe after years of work and as yours are mysterious they could not have known the results are already there) you would like to pull yours out of the back pocket and wave it at them, destroying all their hard work and still keeping the gain away from public knowledge? No. I don't think this is how science works. Neither how anything should work.

Basically, I want to protect myself upfront against My research work stolen and published as his own by the co-author without my consent

What you need is to convince the research community that this is your work, so that if anyone tries to steal it, then it will be considered professional misconduct, they won't be able to publish their theft, etc.  I'm not convinced copyright law is the right tool for this.  Sure, being able to sue someone for copyright violation could be useful in certain circumstances, but often it won't actually settle the academic issues.  For example, collaboration.  I might claim to have collaborated with you on the research contained in the database, in which case I would be entitled to be a coauthor on academic publications, and you would be considered to be acting unethically if you denied me coauthorship.  There's no way to defend against this using copyright registration, cryptographic time-stamping, etc.  You might be able to prove that you already had a copy of the database in the past, but it's much harder to prove that I didn't somehow contribute to it, except in extreme cases such as having had a copy before I first studied this field.
In practice, people often deal with this difficulty by telling more people.  If you tell just one person about your work, then they can steal it, and it's your word against theirs.  If you tell ten people, then it's much harder for a thief to get away with it, since there are nine other witnesses.  If you tell a hundred, then it becomes really difficult to steal your work.  Unless someone immediately tries hard to steal it, it will become impossible: the community will react by saying "Wait, Quora Feans told all of us about this database last year.  If it was your work, why didn't you say anything back then?"
Whether more publicity is a viable solution depends on your circumstances, but there's a fundamental trade-off here.  Ultimately, academia cares about credit for the ideas and research, not just who owns the copyright.  (If I write a paper about your work, then I own the copyright to my words, but I don't deserve credit for the ideas.)  The more you keep your work secret, the harder it is to prove anything about who deserves the intellectual credit.

Good. Your points are too often not at all understood by (especially) younger, nervous people.

I would add: telling via email may be especially good, as it leaves a trace.

@PiotrMigdal Cryptographically signed email might be even better. If practical, including hashes of the data normalized to some useful format might further make it possible to prove you had access to the data at that time.

@MichaelKjörling May point was to supplement details for a social, not technological, solution.

See this question on StackOverflow: Is there a way to digitally sign documents to prove they existed at a certain point in time.
The answer is yes.  Several solutions were suggested; my answer involves an Internet time-stamping service which signs a cryptographic hash of your document.  So if you keep that version of the document, you can prove that it existed on the date in question; but otherwise, nobody ever sees the document except you.
However, if you are actually expecting copyright or IP challenges, I cannot promise that this will stand up legally; you should consult a lawyer.

I don't believe the "sealed envelope to yourself" method would stand up in any court. It's simply too easy to fake it.

@Quora: If what you care about is standing up in court, then I'll repeat myself: consult a lawyer, not us random clowns from the Internet.

You can deposit the data in a research data repository that allows to restrict the access to the data while making the metadata available and citable, e.g. with a DOI. This could be your institutional research data repository (if your institution/institute has one and it has these features) or you could use Zenodo run by CERN which is open for everyone to register and deposit data and publications.

Restricted Access: Users may deposit restricted files with the ability to share access with others if certain requirements are met. These files will not be made publicly available and sharing will be made possible only by the approval of depositor of the original file. Source

Use ProofOfExistence.com to put a hash of your data on the Bitcoin blockchain. Blocks in the blockchain are time-stamped.
By putting a hash of your data on the blockchain, you are not publishing your data or making it in any way publicly available.* In the future, when you release the data, anyone can perform a SHA256 hash of it and verify that it matches the hash in the time-stamped block on the blockchain, thereby proving your priority.
Cf. the ¶ "Demonstrating data ownership without revealing actual data" of ProofOfExistence.com's about page.
*ProofOfExistence.com does client-side hashing (using a JavaScript library), so even that website doesn't ever access your data-set itself.

I've edited my answer with more explanation. I think not understanding how ProofOfExistence.com is the answer to the asker's question might be why my answer was down-voted.

It just proves you were in possession of the data (or at least the checksum of it) at a certain point in time, not that you are the owner or copyright holder.

@BlackJack It proves priority.

Maybe I have the wrong notion of „priority“ here, but if I steal a database or document from you and enter a hash of it into the bitcoin blockchain, does this really prove priority? It just proves that I was the first one to do this, not that I didn't steal the data or document from someone.

@BlackJack "if I steal a database or document from you and enter a hash of it into the bitcoin blockchain, does this really prove priority?" If you were the first to do so and if I can't prove I produced the document before the timestamp of the hash, how could I substantiate my case for priority?

Well, you can't. And that's where I wonder if I got the meaning of „priority“ right. But apart from that, timestamping with this technique seems useless to me in this case, as it can't be used to prove the data belongs to/originates from a specific person, but just who used the blockchain method first.

@BlackJack That's all that matters from the OP's perspective: They can prove that they used the blockchain method first.

This answer could be expanded beyond blockchain, e.g., a hash could be added to a website and that website could be cached by archive.org (which is now legally recognised---in at least one jurisdiction---as a timestamp).

@Geremia It allows you to prove that you had this data before the thief published it (and by implication before they claim to possess it). To make use of this, you likely have to have been loudly claiming to the relevant community that the data was yours, so that the thief has to claim that you've never been involved and never had the data before publication. Once they've done that, you can prove that they are lying.
If they admit in advance that you were involved in the data before publication, then they have to acknowledge as co-author, etc.

ProofOfExistence.com is too expensive since it costs 0.00025 BTC which amounts to $8.36 per proof. This cost can be reduced tremendously since one can use a blockchain with lower transaction fees (it does not matter too much which blockchain you use since the proof of one blockchains existence will eventually be posted on other blockchains), and one can also combine an unlimited number of timestamps into one proof using Merkle roots.

@JosephVanName Yeah, you don't need ProofOfExistence.com; you can do your own.

A good institutional data repository should be able to handle this for you. As an example, The Dataverse Network allows you to deposit data, gives that data a persistent DOI, and then allows you to manage permissions. So you could, for example, deposit the data to make it citable and immediately establish your authorship but then only make it available to specified users (who would need to create Dataverse accounts). In the future, you could make the data more broadly available if you so desired.
Other institutional data repositories should be able to handle this process as well.

This is country dependent and more of a legal question, but basically you have to register your work.
Most of the people in academia SE seem to be from USA, so you can check the process for USA. I was not aware of this, but the site is well ranked in Google and seems properly informing.
Your country should provide some similar mechanism. This kind of mechanisms are the best option if you want to be sure. Otherwise, you can use other kind of mechanism as proof of existence or CKAN and then use that as a proof to register the copyright if needed (but you may as well register in the office up front instead of worrying about doing something else and then registering).

I wonder whether we need country specific procedures here. If someone gets copyright granted in the US, this copyright should be valid everywhere. It's not like a patent, which indeed is country specific. Maybe we should just fill for copyright in countries which aren't too bureaucratic to work with, and maybe let you do everything online.

@QuoraFeans: But the concepts of copyright differ much e.g. between the US and the European Union, particularly with respect to the inalienable authorship rights, and also with respect to the treatment of data bases.

@QuoraFeans some countries completely disregard copyright. People who want to enforce copyright in one of those countries would require their own army (and an invasion). In the end you can prove that you had something at some certain date, but not much more.


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Do 90% of all German Chemistry graduates start a PhD?
Can someone corroborate the fact above? If it’s true, how did it come to such a high number, do they have some slots reserved, or is it easy to enter German PhD programs? Would it also be easy for foreign graduates (in my case chemistry) to join a German PhD program?
Source 1 (German Wikipedia):

Rund 91 % der frisch diplomierten Chemiker begannen nach ihrem Abschluss mit der Promotion.
91 % of the recent chemistry graduates enrolled in a PhD program. [This does not imply they completed it.]

Source 2 (Universität Duisburg–Essen):

Wie jährlich durchgeführte Erhebungen der Gesellschaft Deutscher Chemiker (GDCh) zeigen, begannen in den letzten Jahren über 80 % der Absolventen nach dem Diplom bzw. Master mit einer Promotion.
According to yearly inquiries by the Gesellschaft Deutscher Chemiker (GDCh) [Society of German chemists], 80 % of diploma or master graduates enrolled in a PhD program in the last years.

can you cite the source of this information ?

@krammer: cannot find a source for all nat. sci., only for the Chemistry graduates. I adapted the question accordingly.

i don't have any data to confirm this, only three hypotheses: 1a) on the supply side, the funding for "wissenschaftliche Mitarbeiter" (research fellow) positions in the natural sciences is above average. 1b) equally on the supply side, there are less employment constraints, for example, positions don't have to be publicly advertised, perhaps because positions in the nat. sci. rely less on outside money (drittmittel) than average. 2) on the demand side, a PhD in the nat. sci. makes more of a difference in the labour-market, also for industry jobs, than, say, in the humanities.

According to the German Chemical Society, apparently 90% of master's recipients in chemistry do start doctoral studies afterwards.
Partly this is because PhD "admission" is largely not an admissions process at all in Germany. Individual faculty members who receive grants can hire master's recipients as "Wissenschaftliche Mitarbeiter" (literally "scientific worker," but "research assistant" is a better translation). They can do this without recourse to going through a department-level admissions process, and can skip outside advertising altogether if they have an internal candidate they can appoint instead. And, since many students follow the rule of "Was der Bauer nicht kennt, isst er nicht"—"What the farmer doesn't know, he doesn't eat"), many students do their entire education at one school.
So yes, it's much easier to get a PhD position if you're already in Germany.

this explains (very well) why many German students start a PhD. but since it applies across disciplines, it can't explain why the high number of PhD candidates only occurs in the natural sciences (rer nat.). or am i missing anything?

The system in Germany differs from the PhD system in some points:

Usually there are no (or very little) courses you have to take.
One assumes, you are capable of doing your own research projects (at least after a year or so)
You are mainly involved in projects running at one institute - and it's up to the chairperson to select the person.
You might have to do some work which is not (or just slightly) related to your PhD, like teaching courses, taking over part of the administrative work, etc. (this strongly depends on the group you are in).
Often it is requested that you write one or more grant poropsals (and be successful so that the person coming after you is financed). This also depends on the group you are in.

I know of several proessors who say "you are employee of the institute and you have the opportunity to use some of the time to work on your PhD". You should make sure, your "work for the institute" overlaps significantly with your PhD-topic, otherwise you won't succeed.
One reason why so many people in Chemistry have a PhD is, there are so many students and industry can just select the ones with the best qualification. I'm not very familiar with the situation in Chemistry, but I now some biologists and there is the same mechanism working.
In other fields, it is quite different, e.g. in engineering, computer science, etc. the PhD-rates are significantly lower (I don't have numbers, but my guess would be <15%).
One tipp at the end: If you can bring some money (e.g. a DAAD-scholarship), I expect your chances to be quite good.

While a lot of this is true, it doesn't answer the question.  And I disagree with your last point: one German professor I know rejected a candidate who came with their own funding.  All his other PhD students were employed at the university, and he didn't want a group where some PhD students were employed and unionised, and others at a (much lower!) grant from a foreign source.

Therefore I did not say "you will get ite position". But it helps (and of yourse it's good to ask in advance). I got very good PhD candidates this way.
The reason for my answer was, it explains a bit the underlying question of "how does the German PhD system work". I would rather consider it as a side note than an answer...

source: Stack Exchange

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

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Is it ethical to use proprietary (closed-source) software for scientific computation?
I have data from an ordinary scientific experiment. Now, in order to analyse the data, the most convenient way for me is to use some proprietary, closed-source software.
Is it ethical to use such kind of software in research?
If do use it then this part will be a big black-box in my research. So if someone cannot reproduce my data analysis with the same or with some other software, then it depends on the mercy of the software company if we can find out what went wrong. If the software company does not want to cooperate, then what went wrong might never be found out. I have the feeling that this opposes the principles of science.

Are you referring to software that is commercially available? Are the algorithms themselves proprietary or only the software that implements them?

If the methods are reproducibly documented (or else the software is gold standard and everybody uses it, believing it to be the measure-stick used in the field), probably it is ok. You could, for instance, have a software that does something "magically", in a non-documented way, but where it is easy to check how well it is doing (e.g. image recognition, alignment, etc.). More details?

See Popular proprietary program or obscure open source substitute for reproducible research?

This is absolutely standard in some fields - e.g. mechanical engineering where "gold standard" proprietary software is the result of hundreds of person years of development effort. If you reference the exact version of the software you are running, that is just as acceptable as any other reference in a paper IMO. Even if you use open source software, there is no guarantee that anybody can track down a bug retrospectively, unless you document and preserve absolutely everything in the tool chain that you used to build your version - not just "the application source code".

A literal interpretation of this would make it unethical to do calculations for publications using Excel, not to mention Stata or SAS.  I wouldn't care to estimate the penetration of R and Python into academia, but I'm still fairly certain this would disqualify the majority of published research over the last 20 or 30 years.

Related: Is it acceptable to use Mathematica to derive results in your research?.  I think what I wrote in my answer there mostly applies here too.

You could say the same about any hardware device you use, especially if it contains a microcontroler (which almost everything electronic does). You have no idea what that hardware is actually doing.

@David: Interesting to see, of the answers below, which of them their argument (if accepted)
would go through to show that it is unethical to use a patented tool (drug, lab equipment, computer hardware, screwdriver, pencil, etc)  in an experiment :-) This separates "unreproducible because obscure" from "unreproducible because dependent on the consent of the IP owner".

upvote to @DSVA for remining that, if you build from source, then you need to document every piece of software that you use to do so : what version of make, which compiler and what version, etc, etc. in properly done sotware projetcs, we put the tools, as well as the source code under version control

Lolx! But, preumably, there is accetped h/w, which has been proven to be properly calibrated & independantly tested? You would only get into trouble if you used a "non-name" h/w?

I do not think that this is an ethical question in the first place. Reproducibility is not harmed by the requirement that money needs to be spent on buying software or setting up an experiment (or are there open-source particle accelerators?).
While open source solutions are preferable for many reasons, there are clearly cases where using some proprietary software P is appropriate:

When it is known (and has been verified) that P's implementation of method M is correct while the known open-source implementations of M have not (yet) been established as reliable. Conversely, when open-source implementation O is known to give correct results whereas for P this has not been established, then clearly O should be used when there is a choice.
When one can reasonably expect that P is widely available in research institutions (and thus to researchers), like for example certain mathematical / computational packages.
When P allows for a much more (time-/resource-)efficient execution of experiments.
When P is a software package needed anyway to extract / process data from a big-ticket instrument.

Note that I am assuming that P can actually be bought by anyone. If P is not commercially available but rather a closed-source in-house solution then an open-source package is preferable.

+1. Reproducing a result might require writing software from scratch, or else we would have to worry that our research becomes invalid because some of the code used no longer compiles on modern systems. Plus, a lot of the time, software used in the discovery of scientific results is not actually needed for their reproduction (e.g., this happens all the time in mathematics).

The question says nothing about money.  It's about open vs closed source, not free vs non-free.

Surely it has a lot to do with money too. Sometimes one cannot afford to buy a license. Would it be acceptable to steal one?

"or are there open-source particle accelerators?" Well, CERN has been pushing for open-hardware since at least 2011... Keep in mind: open-source does not mean "free". The only difference is the ability to inspect how the "thing" (software/hardware) was designed and built, not how much you pay for it. In the same way nothing prevents you from writing a closed-source application and provide it for free.

@DimaPasechnik: To paraphrase a former supervisor: "the need to pay for a license is not a scientific argument" - you're paying for a tool here. If you cannot afford to buy a screwdriver, would it be acceptable to steal one?

@cbeleites - is it acceptable to steal food if you are dying from hunger?

@DimaPasechnik Morality is relative; scientific research presumes the first few levels of Maslow's Hierarchy are satisfied.

@DavidKetcheson I don't understand your argument. I am not aware of any closed-source but free-as-in-beer software packages for scientific computations with any sort of widespread traction. Perhaps you can furnish specific examples? Otherwise, the distinction you pose is entirely pointless.

@NReilingh well, here is more to the point example: is it acceptable to break an unfair rule to do scientific research? Examples: https://en.wikipedia.org/wiki/Victor_Ginzburg tells how he claimed the fence to avoid guards preventing unauthorised access to the building of Moscow State Uni., where I.Gelfand conducted his seminars.
https://en.wikipedia.org/wiki/Aaron_Swartz - was he actually a hero?

The particle accelerators and detectors at CERN are fully described in published documents (and the CAD files are probably online) to the extent that you could - given the budget - rebuild a similar machine.So pretty close to an open source software model. Proprietary software neither publish the internal design nor legally allow you to copy it.

+1. I'd just add a bullet point (or rephrase the first): when it is expected that an independent implementation of method M in a different software would give identical results. Using P may not be only because P is the only software capable of doing the job, it can be that it's the only the authors are familiar with or it is the best available and supported in their institution and redesigning the analysis in another would be a waste of time when there's no expectation the results should change in doing so.

I see that all the time with Mathematica and Matlab which both have a plenty of free alternatives, but those are sometimes harder to install, less documented or just plainly less well-known to start with.

-1 for two reasons: 1. Reproducibility is harmed by the need to pay money for anything; and if it's a lot of money, then it's a severe harm to reproducibility. 2. It's not just about paying, it's about having to bind yourself by the license of the software vendor and promoting the use of such software.

This question has become an important one as the push for greater reproducibility in computational research grows.  Use of closed-source software is an acceptable part of research in most fields.
Nevertheless, the following viewpoint enunciated by John Claerbout is becoming more widespread:

An article about a computational result is advertising, not scholarship. The actual scholarship is the full software environment, code and data, that produced the result.

From this point of view, if you rely on closed-source code, you can't completely publish your research.
Issues with closed source software in science
There are multiple concerns:

As you mention, if someone else tries to reproduce your result and gets a different answer, it may be impossible to resolve the discrepancy.
The software implementation may have bugs.  Indeed, all software has bugs and any open source software you use will be susceptible to this too.  But with closed source software you do not have the right to inspect the code to find bugs yourself, nor can you fix them yourself if you discover them.

Both of these are matters of principle; in practice, resolving discrepancies and finding/fixing relevant bugs is also a major challenge with open source software (but is at least something you can conceivably do).
Suggestions for mitigating the impact of closed-source code on reproducibility

Publish all of your own code.  You probably have some scripts that call the proprietary software, or at least some input files that set up the problem for it to solve.  Usually, these scripts contain most of what is new in your research, so what is in them is often more important to other researchers than what is in the proprietary source.

Use multiple independent approaches to confirm your findings.  This reduces the likelihood of a bug affecting your results.  In my own research, this extra work has at times paid off by uncovering bugs (that led to erroneous results) in proprietary software.

Understand the algorithms encoded in the software, and their weaknesses.  Even if you can't see the source, you usually can learn what computational methods they contain.  Once you know the circumstances under which those methods are (or are not) reliable, you can check whether they are likely to give trustworthy results for your problem (e.g., by checking the condition number of a matrix that you feed into some linear algebra software).

Be aware that some commercial software is just a pretty interface to open-source code.  For instance, MATLAB's eigs function for computing eigenvalues of sparse matrices is just a thin wrapper around the open source package ARPACK.  If you use that, you're not actually relying on much (if any) closed-source code.

Of course, you should also follow best practices outlined in the literature (e.g., in this article, or the many references linked here) on reproducible computational science.

One could note that in practice, it is also basically impossible to ever provide a full environment allowing to replicate computational results. Using open-source software compiled with open-source tools and running it on an open-source OS is a very good start, of course, but you cannot usually go any deeper. Are there open-source/open-hardware CPUs, for example? What if someone fails to reproduce a result because his CPU performs a different approximation at some point? (No, I have never heard of such a case, but it's not really unimaginable...) "Mitigating the impact" is really the key.

@T.Verron There is work on that issue too (bitwise reproducibility). But for most applications it is not worthwhile.

"The actual scholarship is the full software environment, code and data, that produced the result."  But it isn't.  The scholarship is only in the code and data - the algorithm and the inputs to and outputs from that algorithm.  The software environment is purely a mechanical means for executing that algorithm.  Whether you use Mathematica, Matlab, Octave or a Babbage engine, all that matters is executing the algorithm.  There may be practical issues relating to ease of reviewing and reproducability, but that doesn't affect what counts as scholarship.

@T.Verron Some Intel Pentium chips famously had a bug and would sometimes produced bad results back in the 90s - they did floating point division incorrectly every once in a while.  The problem was actually discovered by a professor working on prime numbers.

Note that another important thing to publish, that people often forget, is the seed of your pseudorandom number generator. Even better, the script that runs the experiments should always reset it to 0.

@T.Verron: Yes, there is open-source hardware, but it's not very practical.  (e.g. open implementations of the RISC-V architecture.)  We usually just trust x86 (or other hardware) implementations.  The x86 architecture is very well documented by Intel, with the architecture manuals available as free PDFs (see SO's x86 tag wiki).

We're at the mercy of hardware design bugs, and of bit errors from inadequate cooling (e.g. overclocked CPU), but running the same code on different hardware designs can help verify things.  (e.g. AMD vs. Intel, or especially a different ISA like PowerPC or ARM).  IEEE floating point math is exactly specified for + - * / and sqrt, so a careful library implementation should be able to get bit-identical results even for other functions like pow, log, and sin across different architectures.  (But FP determinism is hard)

@DavidKetcheson and T.Verron: I just posted an answer to  Does any floating point-intensive code produce bit-exact results in any x86-based architecture? which I had started a while ago, but not finished until this discussion reminded me about it.  TL:DR: With the right tools, bitwise reproducible FP math is possible on modern computer hardware.  But C is usually not the right tool for that job, unless you stick to one compiler and one math library.

The link to ARPACK is a dead link.

Law is concerned with what you do; ethics is more about what is a better choice and why it is better. The answer to your question depends on why you use the proprietary software.

If this is the only way of achieving the result, then of course you can and should use it. It does not matter if the code is proprietary — if this is the only way to solve the problem, then everyone is possible either using it, or looking to use it. However, I am not sure such a software exists, so maybe this is a model example.
If you can choose between a proprietary software W, and free open-source software L, then the choice is yours to make. If your methods are well documented, your peers can either reproduce them in W (if they have it), or re-create an algorithm in software L (this happens a lot). There are some benefits of using W and some of using L. For academics as a large community it would be better if everyone uses the same open-source software and contributes to its development. However, your personal goals may be different, and it is not unethical to put them first. You can choose W because it is a better written software, it runs faster, it looks better, and you are more productive with it. This is fine.
However, if you chose W because you are paid by a company M which produces it, and you don't tell this, but instead advertise W in your papers and encourages everyone to buy it, then yes — this is unethical.
If you choose W because you know that your competitors, who are likely to review your paper, are from a third-world country with no access to W, and you don't particularly like W but use it to hide some dirty statistical voodoo in the code no-one can reproduce — yes, this is unethical.

An example of case #1 is that, in physics, we use Mathematica to do a lot of calculations because it's by far the most capable computer algebra system available. Some of these calculations cannot be done by any other (publicly available) software. Though it's not a perfect example because one can, in principle, reproduce the results by hand, but that could require years of work for something Mathematica can do in minutes.

@DavidZ: But Mathematica is full of nonsensical bugs due to incompetent programmers who know practically nothing about the mathematics behind what they attempt to implement. And scientists actually rely on it?

@user21820 Sure, but even best science literature has errors, and doing the computation by hand is error prone so its at par with that danger.

Note that "Proprietary" and "Closed Source" are not the same thing. For example, MATLAB (a proprietary commercial software) actually ships with readable code for most functions it implements. You're not allowed to reuse this code (hence "Closed Source"), but you can inspect it if you have calculation discrepancies that have to be explained.
Even when the source code is not available, it is usually documented which algorithm is implemented by a given closed-source function. So if somebody cannot reproduce your results using closed-source software, he can find open-source implementations of the algorithm he suspects are incorrect in the software you have used and compare results using those implementations. Sure, it's time consuming, but don't expect that using open source software will somehow make your results 100% reproducible with no effort at all. Your colleagues will still need to run the exact software version on the exact computer environment to be sure they will get exactly the same results, and those versions and environments will likely be unavailable in 10-20 years. After that, the same time consuming process will apply to open source software as well.
I'm assuming here that you don't use software packages which keep secret the algorithms used to implement it. You'll certainly want to avoid using those, not only for the sake of reproducible results, but because results obtained by unknown means don't have any scientific value.

Unfortunately, unless this has changed, the Matlab code for a lot of the algorithms that would be most important to access such as the statistics toolbox are from compiled code where there is no readable source included in the distribution.

The term is "source-available"

Dmitry, in many fields one cannot easily replace for-pay/restrictive-liencese/closed-source software with FOSS. This is especially true when we're talking about larger, more complex software systems, rather than small pieces of software implementing a single algorithm. There's the enormous effort of developing larger software systems, maintaining debugging and porting them; and there's the fact that the design spaces are so vast that it's unlikely that any two systems not recently-forked from the same parent are similar enough to be interchangeable.

Also, your assumption at the end is generally untrue for larger systems, since even if they publish the main concepts/aspects, there's just too much specific hackery to document.

I'll add one additional perspective here - if you manage to get a stunning result based on analysis done in a closed source package for which there is either no open-source implementation available, or for which the same is poorly developed, then you immediately provide a strong incentive for developers in the scientific community without access to that package, but with a desire to reproduce the results, to go out and start working on improving open-source alternatives to said commercial software.
This is a two-fold benefit.  In the first case, you are helping to encourage development of new open-source tools and, secondly, the parallel development of such tools help to provide mutual checks for both.  I'd say use what works, what is most appropriate, and whatever helps you get the job done best within your budget.  If you're not in a position to contribute better open-source tools to the community then let others take up that torch.  Producing useful, unique, and interesting scientific results is exactly the sort of thing that stimulates that type of development in the first place.
In a way, using a closed source package can actually be a catalyst for open source development - so you're still helping in an indirect way.  If there are, however, open source alternatives to the closed source package you have used then it should be trivial for others to reproduce your results with their own implementations with free tools and there is, therefore, no ethical problem at all.  If anything, it provides an opportunity to test the same result with two different tools and this is always better, in science, than reproducing the result using the same tool.  You get to check both the tools (against each other) and the science at the same time.  Bonus.

Although i couldn't bring myself to downvote, I really dont think "use closed-sourced software to incentivise open-source software!" really makes any sense at all. It's like saying go out an commit arson to incentivise the use of smoke-detectors.

@WetlabWalter There's always a SJW in the room, eh?  I wasn't aware that buying software was either criminal or destructive.  Really, if there isn't an open source alternative then there isn't one.  When you've got a job to get done and there's a tool available then you use it.  Simple as that.  Can't believe you'd spend a million bucks on an experiment and then squawk at paying a few dollars for software to analyze the data.  The point is that OSS shows up when there's good science to be done with it.  Chicken and egg...

lol, SJW, that's a new one for me. I was reducing your argument to absurdity - the benevolent evil is a common logical fallacy. S'ok we all make mistakes. Your other point is strawman - the question isn't closed-source or no analysis. It's closed-source or open-source. Regardless, the price of the software isn't the problem. It's that it's a black box.

@WetlabWalter Still, a black box that implements a known algorithm isn't entirely black.  It's a convenient automation of tedium.  I wouldn't say its use is undefensible.

Alright, have an upvote, jeez

@WetlabWalter lol, I wasn't fighting for a vote, but hey - I'll take it.

@WetlabWalter:  "the question isn't closed-source or no analysis. It's closed-source or open-source." I'd have said in this answer's scenario the question is: closed source analysis or open-source programming, and then analysis as it assumes no open alternative exists when analysis is starting. And while of course doing an open implementation plus data analysis is better than just analyzing data, it will also take more time... And depending on your field, programming a new implementation of a known algorithm may not be seen as having any scientific merits.

Unfortunately, while such results do create some mid-to-long-term incentive to develop FOSS software, they create immediate and stronger incentive to buy/license the non-free/closed/for-pay software, to not lose out in the competitive atmosphere of many (most) fields.

@einpoklum So what would you propose?  Wait until the group can get a developer... then wait 18 months for them to scratch together a buggy alpha version of something that might eventually get the work done?  Research is like a shark - you move forward or you die.  If you don't have the luxury of talent or time to contribute FOSS you've got to get the job done with the tools that are available.

@J...: Well, observing that something is more problematic/unethical than others suggest does not require providing a perfectly ethical alternative to it. It may very well be the case that all of our courses of action in some situation have undesirable (or even deplorable) consequences. In my own answer I conclude by suggesting we evaluate the pro's and the con's to strike the best balance possible (but I do mean all the cons).

If you write "results were processed with the software X v X.X using the following settings and the printed output was", this stops being science and becomes more like a magic. The algorithms must be fully documented somewhere and understandable for the research to be the science.
It is fully possible to satisfy this requirement for the proprietary software, if the algorithms are properly described in the user documentation, or the proprietary software just makes the platform of execution and algorithms themselves are coded on the top of it (Matlab, proprietary C compiler, etc). Ideally, also proprietary code should be available for review under restrictive license.
Unfortunately very often the proprietary tools tend to hide the exact algorithm details, keep the important parts of the code secret, and due that are disliked by the scientific community. Nobody wants to publish an article just to discover later results are only reproducible by the single version of the single proprietary tool, most likely due trivial bug.

Unfotunately, in many domains - that's almost the only kind of paper that ever gets published. DB architecture for example (VLDB, SIGMOD). And it's not just the commercial vendors like Oracle, Microsoft, SAP and others - even when people just modify a FOSS DBMS most often don't publish the code anywhere.

Most of publications important to me supplement the algorithm with source code that builds fine with GCC under Linux.

Well, ok, but it's not like that for every domain.

Yes, it is unethical*.
There are four aspects of the software you mention which raise ethical problems: Being closed-source, being proprietary and two aspects which you didn't mention but are characteristic of closed-source proprietary software - requiring (non-neglibile) payment and requiring agreeing to a restrictive license in order to use.
Issues with closed-source software:

Its use hampers reproducibility (see @DaveKetcheson's answer)
Its use hampers resolution of contradicting research findings/claims).
Use of closed-source software hampers the development of software - the specific kind of application you're using, and in general. IMHO.
It puts software vendors in a position of power over ourselves, and thus indrectly over our research and over the community interested in our research. Famous examples include government espionage, inter-state sabotage  and hardware tie-in.

Issues with proprietary software (and its typical licenses):

It creates artificial restrictions on our freedoms as researchers and users:

To run the software any way and any where that's beneficial to our research;
To apply lessons learned from studying the program in our own research work, and to possibly modify it to better fit our research (it might be technically possible with source access but legally forbidden);
To distribute copies for reproduction and further work to researchers within our group/institution and to others;
To distribute copies of our modifications and adaptations within our research groups and to others;

It often effects similar power-relations between vendor and users even without the source being closed. For example, a vendor affect hardware tie-in by forbidding legal installation on unauthorized hardware.

Issues with software requiring payment for use:

It creates an undue burden on other researchers who wish to (1) evaluate/review (2) illustrate limitations/flaws or (3) extend and improve your results.
If increases the pressure on other researchers to buy similar software in order to keep up - and this is an indirect effect on all researchers in your field.
If decreases the impetus and availability of funding for developing free ( = gratis, libre) software for doing the same.

(*) ... but with all that being said - these unethical aspects weigh against potential public benefit in obtaining and publishing research results. Make sure you fairly stack both sides of the scale when making your decision - and that you think about others as well as yourself.

I simply disagree.  Most objectors to closed source programs argue "not your best choice", or "try to avoid", but not "of questionable ethics".  While there are certainly valid reasons to use open source and free software, none of the arguments you offer rise to the level of ethical concern.

@ScottSeidman: First, you are certainly entitled to your opinion. However, you're making one implicit claims and one explicit claim with which I disagree: 1. An argument is discredited if most people use a different/weaker argument; 2. The "most objections" claim. For the latter, please link to some statistical evidence. In my experience, it's mostly corporate types make this weaker argument. As for the former - my arguments or claims stand for themselves, whether wrong or right.

@ScottSeidman: To the point, though, if you don't believe that causing the effects I listed is problematic, then with due respect I find your view to be unethical, and, in fact, immoral. And this is strengthened by your answer and a comment on another answer here, in which you claim that copied software is "stolen", that copying is "piracy" and that it should not be encouraged.

Are you really trying to assert that copying software is not intellectual property theft??  https://www.fbi.gov/investigate/white-collar-crime/piracy-ip-theft   There are certainly countries where the concept of intellectual property is much looser, but so far as I know, your's isn't one of them.  As to backing up positions, I'll put it back on you.  Name a reputable journal that will not publish a paper that uses close source software because the profession considers it ethically questionable.

By "most objectors", I meant answers to this question.  The statistical defense is simply counting the answers that say that using closed source software is of ethical concern.

Ah, ok, well - I gave my answer for basically the same reason - that other answers to this question don't reflect my views or those of a great many people (regardless of whether they're the majority).

@ScottSeidman: Also, the way US law defines things is not a basis for my definitions. Many states in the world (not sure about the US though) used to define homosexuality as being a form of rape, or an abomination, or a perversion etc.

Decide for yourself:
I can argue from my own experience that using closed-source software leads to shutting a considerable number of potential researchers out (or forcing them into getting illegal copies on a grey market). I worked for a number of years in an area where Matlab is a standard tool (still is, after 20 years :-(), and then I accepted a postdoc at a place which did not have Matlab licences (not all CS Departments have it even in good universities in Germany, as they might not have a campus-wide licence, and while at Engineering they surely have Matlab, it's quite questionable at CS).
I basically had to put on hold every ongoing Matlab-related project (as buying a sufficiently complete Matlab license on a postdoc salary was not an option...)
(And I have once basically stolen a Mathematica license at a department I was visiting, for the same reason. :-))
Another, even harder, case, is Magma (less well-known than Matlab, but still almost standard in areas related to algebraic number theory and group theory, and more), which makes it extremely hard to get a license for anyone outside an established circle of select universities, unless you are in the USA (which perhaps has to do with their biggest customer being NSA :-)).
EDIT: I am told that I am arguing for double standard (mentioning expensive tools for experiments), but I am not. Science software is often much close to scientific publications than it is to scientific tools. In case of a free alternative to an expensive tool, not choosing a free alternative is akin to choosing an expensive and exclusive publisher for your work, rather than  publishing on the web.
EDIT2: Also, issues of reliability of closed-source research software are well-documented in the literature; perhaps the most well-known at the moment is the story of a bug in a determinant computation in Mathematica.
It took the publication in such a high-profile source like Notices of the AMS for Wolfram Ic to fix it. With open-source normally fixing of such a bug happens much faster, or at least it would be publicly visible on a bug tracker.

This is no more true of closed source software than it is of other costly scientific tools. No-one is going to argue there's an ethical issue with using a confocal microscope, a nextgen sequencer, or a particle accelerator. So why apply the double standard to computer software?

@JackAidley :no,  in the case you cite there is simply no alternative. In case of software often there is: just like in the case of publishing - you can publish your book with a commercial publisher who would charge $$$ for it, or you can put it for free online (or do both). The choice is yours.

While many might argue about whether using closed source is "ethical" (I do not), violating license agreements and using stolen software is often illegal and goes beyond my ethical boundaries.

@JackAidley -- couldn't agree more.

Note, also, that there are perfectly viable open source options for just about every package you mentioned.  Octave is almost language compatible with Matlab.

@DimaPasechnik: You "stole" nothing. You used a copy of Matlab and circumvented an insidious mechanism restricting your ability to do so. Also - couldn't you just use Octave? Or rather - try to elaborate regarding why you couldn't use the free alternatives.

@ScottSeidman 15 years ago Octave didn't really do as much as it can now; IIRC there was no mechanism to link external C libraries, something quite crucial, or maybe it was different from Matlab's mex files too much to be of a value for me. There were no essential for the topic Octave equivalents of Matlab toolboxes available. Nobody in the community I am talking about bothered about writing Octave-compatible code, either.

@einpoklum - certainly circumventing a license of a commercial software package is stealing, as it deprives its vendor from extra revenue it would have gotten in case the licence had been properly bought.

@ScottSeidman I can easily name things not available (or available, but totally inadequate) in any open-source package, but available in Mathematica or Magma. E.g. tools for solving multivariate polynomial inequalities.

@DimaPasechnik: Arrgh, matey! Hand overrr yer imaginary profits, ya land-lover! Back to the pirate ship, men!

I think we need to go to the foundation of the question; the answer to ethical questions begins with morals (the science of right and wrong).
Specifically, we should ask ourselves...
* are we committing any deception of anyone involved? (e.g. have we disclosed everything related to the research, including all potential conflicts of interest?)  Put yourself in the position of others: what would I want someone else to do if faced with my situation, and I had a stake in the research?
* are we appropriating anything which does not belong to us?
If we can't identify a specific moral objection, we proceed to the field-specific ethics, namely:
* is there a field-specific code of ethics one has committed to, and would be violating? (E.g. the Hippocratic oath, in medicine, lawyer-client privilege, etc.)  Have you signed an agreement with your employer?
Finally, we should proceed to "value free" analyses: cost/benefit, relative practicality and availability of alternatives, reasonably expected outcomes.
Note that to place this last category in the highest position is to ignore ethics altogether, and run the risk of justifying questionable means with good ends--always a danger sign.
I hope this helps!
12/08/16 EDIT: I should add that according to the criteria above, and the information and opinions I have seen so far (including this thread), the answer is no, it is not unethical, per se (i.e., in itself).
There are circumstances in which it might become unethical, but that is different.  For example, if you chose the closed source software because that choice was to your personal financial advantage, that would clearly be unethical.  Or if you knew you could exploit a feature or bug in that software to disadvantage a scientific competitor, or obtain a more favorable result .  In other words, motives count heavily.
As an example, someone above mentioned a "marketing" motivation.  That would clearly diminish people's acceptance/trust in your results if that were disclosed.
As in politics, sunshine is the best disinfectant.  That is, disclose everything that you can reasonably expect would affect the acceptance of your results by non-trusting auditors.

I agree with the premise of your answer, but you're only asking one moral question, while in fact there are numerous questions to ask.

@einpoklum: sorry about my formatting--the asterisks were meant to flag separate questions. I wanted to suggest an approach to the original question, so the questioner could have some confidence in the answer.  FWIW, I'm pretty sure it's not inherently unethical to use proprietary S/W for a scientific research.

"Free" does not always mean "free" when considering time and effort.  Research can be expensive.  If someone can buy a package, and that package comes with good support and superb documentation that might save me time in a research project, it would be difficult to believe that it would be cheaper to use open source if it would take more time.  In fact, I would go so far as to say that if I didn't spend $2K to speed up my work, leaving my funding agency paying the same amount for less output, that's more ethically questionable than using the proprietary package. (Assuming, of course, that the open source is less convenient, and that the closed source is available to all who can pay -- and yes, I know that those aren't the only situations out there, so please don't bother pointing out exceptions where that's not true).
I run Matlab, and I run Octave.  They are similar, but I have a more trouble-free experience running Matlab, so that's what I tend to double click on.
... and yes, I use PLENTY of open source software, where it makes my life easier.  I also ONLY recommend open source to students (... except Matlab, which has generous student license), because every time I mention an expensive package to a student, they show up with a pirated version the next day, and I don't want to contribute to or encourage intellectual property theft.

I don't think this is an issue. Many research biologists use Photoshop to process their images, for example. I suppose open-source software is preferred by many since it is more in line with the principles of open research, but making sure your methodology is sound and reproducible is far more important in almost all situations.

But using closed/restrictive-license software prevents most people from checking whether your methodology is sound and from reproducing your results. And with Photoshop it's not even that bad, since it's pretty common - but think about software that requires special hardware and tens of thousands of dollars to use.

It should not matter.  Most but not all scientific calculators calculate sines the same way.  Do you know how your calculator calculates sines?
Some free software is simply inferior.  A specific example is OpenOffice.  As wonderful as it is it fails at some tasks that Microsoft Office handles with aplomb and doesn't even attempt others.
What if I use a Hewlett-Packard gas chromotograph because it's the only one I've ever used and someone else gets different results using another brand?  Am I responsible?

one should not process scientific data using MS office, or other office suites. Failures of Excel in this regard are well-documented in the literature.

Failures of closed source software vendors to fix reported bugs are well-documented; if you get incorrect results due to faulty closed source software then, well, you might get fired, or, worse, people might die

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

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


text:
How to convert Italian grades to American and U.K system?
I just graduated in aeronautical engineering (master of science) at the Polytechnic of Milan. In the Italian university system, students who finish their major get a final grade that that goes from 66 to 110 (plus honors). In my particular case, I got a 103/110.
Since I am writing my resume/CV in English, I would like to convert my Italian final grade to the American (GPA?) and U.K system.
Can anyone suggest me what conversion I should follow?

possible duplicate of How to interpret Italian grades for a grad school application

@jakebeal: I do not think it’s a duplicate. The other question is about interpreting Italian grades and so do the answers. This question is about converting grades.

Can you tell us who you are aiming your résumé at?

@Wrzlprmft I am thinking to send my resumè to Boeing, Embraer, Bombardier and Airbus

Why are you writing your CV in English?

Because not everybody speaks Italian outside of italy

Best thing to do is give your relative ranking, but Italian universities rarely provide relative rankings. I would either report as it is or simply do 103/110*4.0 and report the original grade as well. Your are somewhere between excellent and good.

@FedericoGentile I thought Boeing's commercial aviation efforts were centered in Germany. If you are planning to apply the military instury of Boeing, I believe the American law requires you to be at least a green card holder.

Don't even try.
There is no "American grading system".  There is a fairly common 0.0-4.0 scale for "grade-point averages", but the meanings of those GPA differ significantly among different US universities, among different departments at the same university, and in some cases, even between different instructors of the same course.
The only reasonable way to judge what Italian grades say about your potential for graduate study is to compare them against other Italian grades.

mmm... I see your point but you can understand that people in the US or UK might not know what grading system there is in italy... therefore if they see 103/110 they may have no clue of what I am talking about... would you raccomend not to send anything then?

I would not do a conversion, I would just give your score and the total possible score, as you did in your question.

For the UK system, a first class degree is generally awarded to those who achieve over 70% of the maximum mark. I think having got 103/110 you can safely conclude your degree is equivalent to a UK first. On the other hand, I think you could probably just explain how the grading works (perhaps in your cover letter) and anyone would understand that this is an excellent mark.

To be most accurate, you'd need to convert grades at the course level, weighting by credit hours, where, e.g., a strong grade in a longer course is worth more than it is in a shorter course. You could also ignore credit hours, or assume they're roughly the same across courses.
Either way, one approach is to convert the course grade or final grade on the Italian scale to a simple proportion of points earned over points available. You can convert to GPA based on the proportions for each score in the four-point scale. Wikipedia shows this conversion table for percentage to letter grade and grade point:
http://en.wikipedia.org/wiki/Academic_grading_in_the_United_States
Once you convert your Italian points to a proportion or percentage you should then be able to convert to any other grading system. There are apps online that will run the conversions for you. Here's one to try:
http://www.foreigncredits.com/Resources/GPA-Calculator/

The Italian equivalent of 2:1 is actually 100/110 - 104/110 according to Ca' Foscari University's website.
However, in the University of Torino, a 2:1 (3.5-4.49 on a 5 point scale), translates to 70% - 89% on the 100th and 77-98 on the 110th. I was denied admission because I didn't score 90% on the 100th or 100 on the 110th.
https://www.unive.it/pag/fileadmin/user_upload/inglese/pdf/Instructions_grade_conversion_cumulative_percentages.pdf

I've been through this for a while, searched official sites and so on, and I came to the conclusion that Italian grades are underestimated in the UK. I explain you why.
Note: for simplicity I will speak about exam grades since the graduation score in Italy is given by the average converted in 110th plus a variable score (depending both on the university and the course).
Both in USA and UK, scores are in percentage.
UK:

First class (1st): 70-100%
Upper second (2.1): 60-69%
Lower second (2.2): 50-59%
Third (3rd): 40-49%

US:

A (4.0): 93-100%
A− (3.67): 90-92%
B+ (3.33): 87-89%
B (3.0): 83-86%
B− (2.67): 80-82%
C+ (2.33): 77-79%
C (2.0): 70-76%
D (1.0): 60-69%
F (0.0): 0-59%

Now to Italy. Italy has exams votes in 30th, the minimum is 18/30 and the maximum is 30/30 plus honors. So it is:
Italy

A-, A, A+ (Excellent): 27-30/30 and 30/30 plus honors
B-, B, B+ (Good): 24-26/30
C-, C, C+ (Satisfactory): 21-23/30
D-, D, D+ (Barely passing): 18-20/30

Now, if you convert in percentages like the US system (as both have minimum at 60%) you get:

A (Excellent): 90%-100%
B (Good): 80%-89%
C (Satisfactory): 70%-79%
D (Barely passing): 60%-69%

That makes sense, right? In fact, if you convert between IT and US, you get the percentages above. But what happens if you convert IT to UK?
Well, it's kinda funny. As I said before, final score is made from the conversion in 110th PLUS a variable score. Now, let's pretend for a moment that you just have to convert the vote in 110th, according to math you have:

A (Excellent): 99-110/110
B (Good): 88-98/110
C (Satisfactory): 77-87/110
D (Barely passing): 60-76/110

I want to remark again that the score is lower than it should, because you should add points for your graduation. For my university, the points added were between 1 and 3, but other universities gives more or less points.
If you check requirements to enroll to an university, for example Manchester, you are required a score of 100/110 (link below).
If you are from USA, you are required a GPA of 3.0.
Too bad that if you convert from IT to US, you get that a GPA of 3.0 you need 25/30 or 89/110.
If you are from UK you need a 2:1, which is the correct translation for the US score but not for the IT.
Nice job UK.
Requirements for Italian students: http://www.manchester.ac.uk/study/international/country-specific-information/italy.htm
Requirements for USA students: http://www.manchester.ac.uk/study/international/country-specific-information/usa.htm?page=2
Requirements for UK students: http://www.manchester.ac.uk/study/international/english-education-system/

Downvoted.  The US scales are nowhere near universal. In particular, in the required classes I teach, B definitely does not mean "83-86%", but rather "between 1/3 and 2/3 standard deviations above the mean".

I don't get it. Speaking of percentage, in the UK if you take above 40% you pass, if you take above 70% you have an outstanding grade. In USA and IT you pass with 60%. This means that you need to know less to pass an exam and you are considered with great results with much less than IT. Basically, a 70+% in the UK is considered equal to a 90+% from IT

In USA...you pass with 60% — No, this is just not true. In principle, every instructor in the US has the freedom to set grade boundaries wherever they like (although in practice, some departments and some universities impose restrictions).

I think it is impossible to do the conversion. UK universities don't value students with a foreign bachelor's degree as much as those that obtained one at another UK university. Some universities only accept students with a 110/110 grade, which is much harder to obtain than a First (you only need an average of 70%). They underestimate grades from Dutch universities such as TU Delft, which is arguably better than any engineering university in the UK.
The grades vary a lot from university to university. For instance, at my university, the Polytechnic of Turin, the average grade for my course last year was 97.1 for a Bachelor's degree. In another Italian university, it was 101.3. Also, in response to another comment, "38% of the graduates get 105/100 or more" - that takes into account master courses where it is easier to earn a higher grade.
Edit: I see that some people were upset but having studied in both countries I have a better understanding than most.

What most people fail to understand is that a 70% in the UK scale does not mean you only got 70% of the exam correct. A score above 70% is something outstanding that very few people manage to achieve, that's why it's considered equivalent to much higher percentages in other countries. If you get everything correct on an exam you will get a 69% (happened to me). To get a score higher than 70, you have to not only answer the questions perfectly correctly but also insert new knowledge into your answers that you obtained from reading outside the course material. I have experience in both the portuguese and British system and I can tell you that a 70 on the UK scale is not your typical 70%. I would say it is equivalent to a 90% in the portuguese scale. Therefore, I don't think it's unfair that they ask for higher requirements for students from other countries.

I don't think this is universal. Suspect it varies within the UK

@Flyto absolutely, and even within each university/department/course.


text:
In which regions of the world do graduate programs typically require a GRE score?
I know that in most U.S. universities, most programs for graduate studies require a GRE score.
1- Are there any graduate programs in the U.S. which does not require this?
2- Is it required for graduate programs in Europe, Australia or other parts of the world?

ETS, which develops and administers the GREs, maintains a publicly available list of all of the institutions that are officially licensed to receive GREs.
If you look through, you will notice that almost all of these institutions are in the United States.
Now, there are a bunch of other universities around the world that at least are willing to receive a GRE.  As noted in the other answers, however, the fact that an institution is willing to receive a GRE does not mean that it is required or even particularly helpful.  It is primarily a US test, and even within the US it is not used by many departments and given little weight (unless one does horribly) in many others.

Besides the United States, I have not heard of any country and any topic requiring it.

I've studied in Australia and the U.K., and I believe that no universities require GRE for graduate admission. I don't believe that GRE is required in continental Europe either, but there may be exceptions.


text:
Do two-column format journals publish one column for special cases?
Sometimes a paper consists of lots of math equations which are too long so that they will look terrible in a two-column format. I was wondering:

Is is possible or even reasonable to ask the editor of a two-column journal to publish the whole paper in one column format due to containing lots of long equations?

Use a full-width figure?

@StuartGolodetz: I know that but there will be lots of these which will make it looking really bad!

Yes, with many long equations it is not uncommon to finds a good part of a page, or a full page, typeset as one column. If it is just one long equation they do an (ugly to me) splitting of the columns above and below the long equation. This is from my experience reading physics journals.

@JonCuster: So they don't agree to publish the whole paper in one column format?

Is it impossible for you to break the equations into multiple lines? Depending on the number of such equations it might make the paper too long for the journal’s constraints, but if it’s workable I often find that multi line equations are much more readable and aesthetically pleasing than one-line monsters.

@StuartGolodetz No, please (I mean, no to typesetting formulas as figures. Much better is to choose a journal which is less stupid than not to allow reasonable solutions.

Yes, you can ask, but you will almost certainly be turned down for such a request, because journals do not normally keep separate templates for single-column layouts. Moreover, at the type used by journals, a two-column format is essential because long lines of text are difficult to process. (Readability studies show that about 65 to 70 characters per line works best.)
That said, many journals do have to deal with long equations, and in such cases they will have equations that cut across both columns, and indicate how the text "flows" around the equation. As Jon Custer's comments indicate, if there are enough such equations in a row, the page in question may be set in a single-column format, before reverting back to two-column format after the "run" of equations is broken up.
As an example of how this looks, here's a page from a paper published in Physical Review D:

Thanks for your attention. It really looks ugly! :D Doesn't it?

Yeah it looks pretty ugly. And I always found the two column format very hard to process because I have to scroll up and down like an idiot.

It's not great, but given the column width, it still looks better than a single column would.

Some do, some don't. It depends on the journal in question. For example, Monthly Notices of the Royal Astronomical Society state in their instructions:

6.1 Layout
Papers should be formatted with two columns (except the abstract) and single line spaced. A single column layout may be used only if necessary for the display of numerous very long equations. The journal is printed on A4-sized paper.

One should always refer to the author instructions/guidelines and can usually contact the editor to ask for further information if something is not stated or is unclear.

I think that the instructions mentioned here is just for the equations and not the whole paper and the output would look like the one mentioned in aeismail's answer. right?


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Paper rejected based on one very short wrong comment
My paper is rejected based on a wrong (I am almost certain that it is wrong) comment of a single reviewer and the content is as below

The manuscript focuses on the problem of "Some Technical Things". This problem has been solved in several papers of "Mr. X" : See, for example "This Article".

But "This Article" of "Mr. X" is totally different from what we have done, and addresses a completely different problem. I don't know how I can show my objection to this unfair review that has wasted my time for two months!
I sent an e-mail to the journal's editor but he did not respond.
Do you have any suggestions that one can do in such situations?

Comments deleted since they have either been addressed by edits or were answers as comments that are redundant to existing answers.

I say: submit to another journal.  Do not argue with the editor.

I removed the rant at the end. Please only edit the question to add more information or clarify existing info.

@GEdgar I have successfully argued with an editor to reverse a rejection, and encourage my students and mentees to do so when the circumstances of a review or an editor's decision warrant it.

@Alexis: Can you explain your experience as an answer please. :) Also, elaborate on how you made contact with the editor, e.g. by sending a direct email to him/her  or maybe by making a phone call or through the journal's  online submission system.

Wait. The editor has to assess if your claim is correct. People are busy. In addition, they may need to ask a more expert colleague for a quick opinion; this is not a full round of review, but still it will take several days. I would give them at least two weeks, personally (but publication times are heavily discipline-dependent).
If the editor agrees with the reviewer, consider seriously the possibility that they are correct and you are wrong. Ask privately for another opinion to a collaborator/colleague you are in good terms with, just to understand where the truth lies.
If you conclude that the referee is completely bonkers and their claim is ridiculously wrong, ignore their remark, submit somewhere else, and make a note for the future that this is not a good journal.
If you conclude that the referee is wrong, but their one is a reasonable mis-interpretation and someone else may get it wrong, too, then revise your introduction: mention mr. X's papers and explain in your manuscript why they don't solve your problem. Then, submit somewhere else.

(Note that case 4 is much more common than case 3.)

I moved the discussion about review times and other non-comments to chat. Please read this FAQ before posting another comment.

About No. 1, they can at least give an initial response to my email that they will consider this issue and will inform me in the next two weeks, for example. I have not received such a thing! Also, editors often check their email on a regular basis so it is likely that they have read my email and left it without response which is unfortunately the most common and probable case.

I wonder if case 3 may be more common if the mysterious Mr. X happens to be the reviewer...

You know what the referee said in the part of the review meant to be seen by the authors, and you know that the paper was rejected.  You don't have necessarily have access to all the communication between the editor and the referee.
In particular, there are often check boxes for the referee indicating how she or he ranks the importance of the topic of the paper, the relevance of the topic with respect to the journal and the readership, and the priority for publication.
You also don't necessarily know what's already in the hopper for this journal.  They might have a backlog of extremely high quality papers, and are only accepting the best of the best.  There are certainly enough papers that receive good reviews that don't get published -- just like there are tons of good grants that don't get funded.
So, there's a chance that your paper was an excellent paper, and just not a high priority for that particular journal at this particular time.
There's also the possibility that the referee is right about how applicable the work of Mr. X is, and you just don't see it.  (No offense meant -- all we know about you are your initials, and that you say you've had a paper rejected).  Maybe what the referee is trying to say is that Mr. X's work is solid enough, and even though you have a new approach, the conclusions drawn are similar enough that a revisit isn't high enough priority for publication in that journal.  We have no way of knowing.  If you feel this isn't on the mark, when you resubmit elsewhere, be sure to include the work of Mr. X in your discussion, and show the reader why your work is different from that work, and why your current efforts are important to consider.
The best advice I can offer is to depersonalize the process.  You'll hear a lot of stuff during peer review, and it's real easy to let it get to you.  Don't let it get to you.  With experience, you'll learn what your referee pool wants to see, and you'll give it to them, and have an easier time pushing your papers through.

The dumb reviewer is a common problem, and fits Occam's razor much better than the dangerous conspiracy that would destroy a prestigious journal's treasured reputation if the truth got out.
The dumb reviewer is especially problematic because not only are they not qualified to provide a helpful review of your paper's technical content, the fact that they got themselves in over their head by accepting it means they are doubly motivated to find a way out. Besides of course actually putting in the (especially hard for them) effort of comprehending the paper. The easiest and most frustrating response one gets from such reviewers is to seize upon a "fatal flaw" which would make the paper completely unsuitable for the journal and not worth trying to fix... or finish reading, fortunately for them.
Sending an email to the editor may make you feel better (I've done it) but won't accomplish anything. You certainly shouldn't rant at them.
What you can do that actually matters is write a better paper. If the dumb reviewer hadn't gone for the easy out, they instead could have demanded you to explain far better what your novel results are and how they fit into prior research. This needs to be something even a dumb reviewer can immediately understand when they read your abstract and intro. If they are guessing, wrongly or not, you didn't do your job well enough.
Two months is nothing, by the way.

I don't agree with the last sentence "Two month is nothing, by the way". These lengthy useless peer reviewers really need a revision! Maybe a mechanism by the publisher to report such issues be useful or any other measures that can be taken into account. We should value people's time.

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


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Can a poorly done second degree ruin one's academic record?
Currently I have a BSc degree in Computer Science, and in the future I plan to get a Master degree in Computer Science. In my opinion, my BSc grades are good enough to help me be accepted at good universities in my country.
Also I'm considering doing a second BSc degree (in Electrical or Mechatronics Engineering), but I don't think I'll have enough time to study in order to get very good grades.
Could this ruin my academic record? Would it lower my chances of being accepted in a Master's course in the area of Computer Science?

What are graduation grades? Do you mean the grades you received for your BSc?
What is a graduation course?

Regardless of my above questions, I don't see how another course can "ruin [your] academic record." If your results are bad, then you can always omit them.

Exactly. By graduation course I mean the course you take to get a BSc degree.

@user2768 Indeed. But would it be more beneficial if you didn't omit the fact that you've taken a second BSc degree, despite the not so good grades? I don't know if the fact that you've managed to complete another BSc course would compensate for the medium grades.

I've attempted to improve the question based upon these comments. Hopefully, they'll be visible after peer review.

A second degree will take a lot of time, so it seems unlikely that you'll complete it prior to enrolling on your Master's course. Thus, I don't see how it will impact your chances of getting a place on a Master's course. Perhaps I'm missing something.

@user2768 I wouldn't be able to do both at the same time. I would have to finish the second BSc first.

I suggest that you enrol on the Master's course, that qualification appears to be your goal. In parallel, you can study a second BSc part-time; perhaps you drop the second BSc, perhaps you eventually finish it. One question you should ask yourself: why do you want the second BSc?

See also some of the related questions (in the bar to the right). Link any truly related questions here, so that they can be used by others in the future.

@user2768 Thank you for your advice. I didn't find any truly related question here.

There seems to be little point in taking the second BSc if you don't expect to study enough to get at least acceptable grades. Engineering courses tend to be cumulative - you will be lost in later courses if you have not fully absorbed earlier material.

@PatriciaShanahan I just fear that the lack of time won't allow me to study hard enough to keep up with the grades I had in my first degree, thus lowering my "average" grades (considering both degrees) together with the chances to be accepted in a Master's program. I'm aware that an engineering course demands a lot of effort, which I'm willing to undertake, but I'm also aware that it will be a lot harder than the first time, because back then I was full-time dedicated to the graduation.

@user2768 - RE: If your results are bad, then you can always omit them. Not necessarily so. Many graduate schools want to see ALL transcripts as part of the admissions process, and clearly state so. If the O.P. got a second degree from the same institution, it might be impossible to get a transcript with just the good grades and not the bad ones. If the second degree was from a different institution, that would be easier to omit, but it's still a risk – a violation that could result in a revoked admission.


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Publishing research software that was developed by professional programmers - attribution ettiquette
I wish to publish a software platform that was developed for a research project. The usage-logic and user interface design were largely specified by the academic team, but the code was written by professional software engineers.
Is there known precedence for this? (citations)
And how would the community tend to handle attribution?
EDIT (due to request for more information):
Software engineers did not make 'creative' contributions, in other words they received a brief and executed it. One could argue that they acted much like a physical research service provider, for instance technicians who install/manage research equipment in labs. The main confusion is that the publication directly concerns the software. The research for which it was built is reported in another paper.
What I was hoping for here was some reference to existing publications with a similar focus, to see guiding examples.

Thought experiment: substitute "professional software engineers" with "undergraduate students", and assume the same level of involvement of these students in the design and logic as your programmers. How would you handle attribution in that case? Is this case different? If so, how?

Ever heard of Linux? :)

I don't think you've given enough information for anyone to answer this question. Is the code and other work of the engineers part of the intellectual contribution of the paper?

Designing the user interface is easier than actually implementing it. So, if designing the GUI is your main contribution you should not be an author either (if building the GUI is not sufficient to warrant co-authorship according to you).

@Alexandros that is true, thankfully designing the GUI was not the only contribution the authors made ;)
In case it was unclear, the engineers were paid for their work - they are not interested in academic credits, and would not do extra work to receive them. In this part of the world it is expected that authors should contribute also to writing the paper.

If the software engineers made a direct contribution to the research product, then the should be listed as authors on the paper.


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How is Google Scholar changing academic evaluation?
Google Scholar is making it very easy to track (their measure of) citation counts, h-index, etc. for individual researchers. Is this changing how academics are evaluated? Do tenure committees now bring up google scholar profiles, or do they continue to prefer other sources for citation data? Is there pressure to make your Google Scholar profile public?

During the last evaluation at our department, all staff members were encouraged to make their Google Scholar profiles public.

many colleagues in my field do not have Google Scholar profile so it is hard to switch to it fully.

Google Scholar is useful even for people without profiles.

Yes, promotion and hiring committees look at Google Scholar, especially in fields like computer science where Google's citation data is more comprehensive than other sources like Scopus, which misses many citations of and by conference papers.  In this respect, Google Scholar hasn't really changed the way people are evaluated, though; we've just replaced one unreliable (and expensive) source of questionable statistical data with a slightly less unreliable (and free) source for almost (but not quite) the same data.
Much more importantly, though, Google Scholar makes it easier to find electronic copies of papers, which makes it easier for committees to judge each candidate's work directly.  In this respect, Google Scholar has had a significant impact.

Is Google Scholar really that accurate in your fields? I am in applied mathematics, and I find lots of duplicate, bogus or grossly misformatted (completely wrong title and/or authors) entries in its "citations". It overestimates my citations by roughly a factor 4, at the moment, and my publications by roughly a factor 2 (before I corrected it by hand).

Sadly, in theoretical computer science at least, Google Scholar is more accurate than any other source.  Yes, there are lots of false positives, and duplicates, and problems with merging authors with common names, and citations from things (like lecture notes) that aren't publications, but other sources miss large swaths of the literature entirely.

It's also handy for people who work across fields that don't normally talk to each other. For example, one of my papers is just never going to show up in say, a PubMed search for me.

Since the criteria is the same (citation count, H-index, G-Index...) I think Google Scholar is not changing anything, just making much easier to find/evaluate; therefore it might have a considerable impact.
But should be noted that, due to many errors like mixing authors with similar names and counting citations that shouldn't be counted, Google Scholar can't be used as a definitive source of evaluation.
Recently I have found Microsoft Academic Search more useful.

+1 for MS academic search. It shows the citation contexts also, which I believe, Google scholar doesn't show.

Having looked at it, I find MS Academic Search to be a rather chaotic tool, and one that still needs a lot of refinement. Most of my own papers are missing or mischaracterized.

I find the same as aeismail: MAS has far more errors than GS, and a far lower citation count/h-index.

Agreed, MAS in many cases I have seen underestimates the number of publications (to say nothing of citations) by a factor of 5 or more.

At my place, people who are doing well have public Google Scholar profiles, while those who shouldn't and probably wouldn't get tenured hide their profiles, probably because their publication — and thus citation — records stink.

Correlation is not causation… and even if it were, which way does it go?


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Policy regarding grouping of papers in Google Scholar
Using Google scholar, a researcher can generate a public webpage where all his papers and citations are presented.
Because Google is far from perfect, it is possible to group some papers. For instance if the same paper is (wrongly) seen as two papers by Google scholar, it is possible to make a fusion : the two papers are now a unique one, and the citation are recomputed accordingly.
My question : when there is a conference version, an extended journal version and possibly a invited conference version of the same work, is it best to merge all the versions or all the papers are to be considered different ?

One rule of thumb would be that any set of related papers that would be considered separate for a paper CV should be considered separate in what amounts to an electronic CV. Especially if one version clearly contains more material/data/argument than another one.

authors: ʇolɐǝz ǝɥʇ qoq


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What are the current standards for plagiarism?
At the first day of the 2016 Republican National Convention in Cleveland, Melania Trump gave a speech including these words:

"From a young age, my parents impressed on me the values that you work hard for what you want in life, that your word is your bond and you do what you say and keep your promise, that you treat people with respect. They taught and showed me values and morals in their daily lives. That is a lesson that I continue to pass along to our son. And we need to pass those lessons on to the many generations to follow. Because we want our children in this nation to know that the only limit to your achievements is the strength of your dreams and your willingness to work for them."

This seems strikingly similar to Michelle Obama's speech when her husband was nominated as the Presidential candidate about eight years earlier:

"And Barack and I were raised with so many of the same values: that you work hard for what you want in life; that your word is your bond and you do what you say you're going to do; that you treat people with dignity and respect, even if you don't know them, and even if you don't agree with them.
  And Barack and I set out to build lives guided by these values, and to pass them on to the next generation. Because we want our children -- and all children in this nation -- to know that the only limit to the height of your achievements is the reach of your dreams and your willingness to work for them."

Trump campaign chairman Paul Manafort characterized the possibility of plagiarism as "crazy" and "just really absurd," an attempt by Clinton to "demean [Melania Trump], and take her down."  Apparently "what she did was use words that are common words;" "these were common words and values."  Gov. Christie said "There's no way that Melania Trump was plagiarizing Michelle Obama's speech." After all, most of the speech was not the same as Obama's (or Astley's).  The speaker herself claimed, "I wrote it ... with (as) little help as possible."
The campaign could have said something like "Yeah, we copied those bits; so what? Our party will unite the country behind those values this November and we can see they've got proven electoral success.  We're going to be winning so much,..."  Instead, they chose not to do that and took a strong position that this kind of copying is not plagiarism and is so far from it that even the suggestion is absurd.
In a situation unsettlingly common for modern American politics, it seems like people with opposing views don't even understand why there's any question here.  On the one hand, widely respected voices say there's no way this could even possibly be plagiarism, while others taking a different perspective think there's no way it isn't.  I wouldn't be surprised if folks from both sides vote to close this under the reasoning that there isn't even a real question about this topic, since their own view is so obviously the only right one.
Maybe standards have diverged so much because plagiarism is usually handled quietly and it's rare to have any large-scale public discussion or catalyzing event that would prompt such a discussion.  Here is such an opportunity.

If it's now "crazy" or "just really absurd" to think that this might be plagiarism, what are the standards?
They've apparently shifted (or gotten on a plane and flown halfway around the world) quite a bit since I learned them.  If I'm going to be writing, reviewing, and grading work of politically diverse authors, I need to learn the modern standards, quickly.
So, what are the standards, especially around reusing "common words and values," tweaks to original phrasings, and percentages of a work that's mostly original?
Are they a lot different with an audience tens of millions strong than when it's a handful of specialists?  If so, how?

Sounds the same as any other politician's speech. I feel you're wasting your time with a plagiarism debate. It's not intended as original research.

If she'd said "yeah, I ripped that off Obama, because I agree with it" then it wouldn't matter [to me].  It's the claim to originality and the claims by prominent leaders about what the standards are for plagiarism nowadays that are a bit more alarming - have I really missed some drastic shift?  Are my views on this topic antiquated enough to now be "crazy" and "absurd?" What exactly are the modern standards?  Also, this question evaluating Barack Obama's JAMA paper by academic standards was well received here.

Politicians have a vested interest in appearing to be reasonable, fair, relatable, and in agreement with the people whose votes they hope to win. The strategy they have chosen towards that goal is to underscore how "crazy" it is to even think this might be plagiarism.  They seem to think a lot of people agree with that view, and that agreement has significant implications for the modern standards around plagiarism as well as for the kinds of pushback and defenses one should expect in a situation like the second sentence of user37208's most recent comment.

I'm voting to close this question as off-topic because it is about ethical standards in politics, not about academia at all.

The question is not about the ethics of political plagiarism.  It's about the standards for what constitutes plagiarism, a topic usually relegated to the shadows which is now in the limelight for large-scale discussion. Academia should have a good answer (or set of answers) on this, if anyone does.

The standards for what is considered plagiarism depends on the context. Your question is about plagiarism in the context of a political speech, which is out of the scope of this site. If you have a question about plagiarism in an academic context, on the other hand...

@ff524 I think a lot of people assume that the same word has the same meaning across contexts, that they might come here looking for an answer to better understand what academia thinks plagiarism means, and that "the answer is X in one context by Y in another" would be a decent answer to go below.

If we look at Wikipedia, these seem to be relevant parts here:

Plagiarism is considered academic dishonesty and a breach of journalistic ethics.

For political speeches of the kind we're discussing, there are near zero expectations regarding academic correctness, or journalistic integrity (not to mention honesty and ethics, which are also part of the quoted sentence).
Any standards are valid only in their respective context. Academic plagiarism and journalistic plagiarism have vastly different standards and consequences. As far as I am aware, there is no standard for plagiarism in the context of political speeches.
and

Plagiarism is not in itself a crime, but can constitute copyright infringement

Copyright (usually) allows derivative works, which seems to be what we're dealing with here.

In other words: You can't plagiarize a political speech.

There is a significant history of politicians copying, sometimes word for word, other politicians, even those of the opposing party.  Sometimes they get called out for it, but that disappears very quickly in the 24/7 news cycle.

This comment and the part of the answer above the line explains why folks would not care if a political plagiarizer just admitted it and said "so what?" The Republicans easily could have done that and moved on to focus on the substance of the speech and how they plan to unite the country behind those values, etc.  Instead, they chose not to do that and took a strong position that this kind of copying is not plagiarism and is so far from it that even the suggestion is absurd.  The last line of this answer seems to be the clearest rule the answer presents.