How Open Source Could Benefit Academic Research 84
dp619 writes "Ross Gardler, of Apache Fame, has written a guest post on the Outercurve Foundation blog advocating that universities accelerate the research process through a collaborative sharing and development of research software while examining reasons why many have been reluctant to publish their source code. Quoting: 'These highly specialized software solutions are not rarely engineered for reuse. They are often hacks to answer a specific question quickly. ... What many academic researchers fail to understand is that this specialization problem is not unique to research projects. Most software developers will seek to provide an adequate solution to their specific problem, as quickly as possible. They don't seek to build a perfect, all-purpose, tool set that can be reused in every conceivable circumstance. They simply solve the problem at hand and move on to the next one. The difference is that open source developers will do this incremental problem solving using shared code. They will share that code in incremental steps rather than wait until they've built the complete system they need but is too specific for others to use. Other people will reuse and improve on the initial solution, perhaps generalizing it a little in the process. There is no need to share the details of why one needs a 'green widget' nor is there any reason to prevent someone modifying it so it can be either a 'green widget' or a 'blue widget.'"
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Maybe it is not as simple as pick zero / one / two. The purposes of writing software for research and engineering software for reuse are so different that it doesn't make sense to try and compare them. Going back to the summary:
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So for clarification, I think you missed the point of what the GP was trying to say. The statement in the summary as written suggests that highly specialized software solutions are commonly engineered for reuse.
Based on the context of the summary, it should probably say either:
1. These highly specialized software solutions are not engineered for reuse.
or
2. These highly specialized software solutions are rarely engineered for reuse.
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Yes - posts written in the middle of the night are not entirely coherent :)
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"What the author of the article fails to understand is that software is not the point of research - it is a side-effect, and I say that as someone whose field is CS."
(disclaimer: I am working as a postdoc for some US university)
The article in general is clueless. You are of course right. Researchers don't care about their code. I want to know if a design work, if an algorithm work or if it does not. That's why I end up writing code. Once my report/paper/thesis/grant application is written I do not care abou
Depends on the Field (Score:3)
None of the money that come from grants pays for software development. Even if it was, my career would certainly advance more if I do research instead of software.
This depends on the field. In particle physics where we have massive computational challenges grants can specifically fund software development. In fact when I was a grad student there were even permanent positions called physics programmers and software development certainly can be very good for your career as long as it is combined with physics analysis - at least it has not hurt me so far. As for "needing a postdoc or a professor to do it well" I very much beg to differ - and I say that as a professor!
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"What the author of the article fails to understand is that software is not the point of research - it is a side-effect, and I say that as someone whose field is CS."
(disclaimer: I am working as a postdoc for some US university)
The article in general is clueless. You are of course right. Researchers don't care about their code. I want to know if a design work, if an algorithm work or if it does not. That's why I end up writing code. Once my report/paper/thesis/grant application is written I do not care about the software anymore.
Well, there's s always the CRAPL [might.net] license that was made for exactly this kind of source code release, and IMNSHO publishing the source code with the paper should be a must, because it's only science if it is reproducible. I work in image processing and more often then not, papers are missing parameters, the description of the implementation is ambiguous, and as a result just reproducing the result of such a paper is impossible without contacting the authors. (The data used is yet another story.) I do not car
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I completely agree with you. And I try to publish code as often as I can. Though, I do not believe the original article is about getting the code out.
I think the original article is getting the code in the shape where it can be reused and built upon in the same way open source software is. Any code released under CRAPL is probably not in a shape where it can reasonably be built upon. Most of the code I published are not in a very good shape.
Just as long as a central body maintains quality (Score:2)
Open Source by default has the benefit of many eyes checking for errors, contributing ideas, but things get sour when too many people commit.
Too many chefs etc... etc...
I think this will change when there's an open record of who came up with an idea first. Wouldn't it be quite a bit harder to say "I came up with that" if we don't know
Shameless Plug (Score:1)
Sometimes publishing code loses you papers (Score:2)
Sometimes, when you publish the code you used to develop new Biochemistry or Genetics solutions, you find that other scientists in other countries use your code to reverse engineer what you are working on - your results, if you will - to eliminate dead ends and publish a paper on what you invested years finding a solution for, but before you submit your paper that they "effectively" stole.
We had that happen when we deposited ligand results a few times, until we learned to stop submitting such things until A
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Then too, there is a whole mash of what passes for "code" that is written, which is specific to which particular machines you have in your lab, and how you have
to extract data from those machines, followed by a lot more code that is off-the-cuff stuff to check some wild idea the researchers thought up over lunch.
On one lab we worked for there were several types of "software" being developed. One is automated data extraction from machines, some of which we had to sign NDAs to enable use access to their inte
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In my younger days I was involved im developing software for custom data acquisition and analysis. I can recall two instances where results were skewed and hypothesis were developed based on the skew. If the software had been looked at by more researchers, and used in more labs, the errors may have been more quickly
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Not arguing with you about publishing.
What I am describing is the use of publishing either data or software BEFORE actual publication.
The timing is what is in question, not the (eventual) publication.
In certain cases where we do genetic studies, we find that publication of inheritance trees too specifically identifies specific people, who are still alive, and so we may have to not specifically publish all of the tree, as that would publish data which one is not authorized to publish about the people who inh
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Submission of biochemical structures too early, prior to publication, can also result in similar things.
I can also confirm that this happens occasionally. Biologists are also reluctant to describe unpublished results at meetings unless the article is already accepted and scheduled for publication - it's a real shame, but I understand why they're reluctant. However, there is no requirement that they reveal any data before publishing; it's not like every crystal structure automatically goes into the PDB bef
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In order to publish a paper that includes a structure in any reasonably reputable journal, you have to provide the accession code (PDB ID) along with your manuscript. The only way you get that code is to deposit the structure in the PDB. You may also have to deposit diffraction or NMR data, depending on how the structure was solved.
When you submit the structure to PDB, you can indeed elect to have the coordinates held for publication. However, there is a ma
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"We request you to confirm release or withdrawal of your entry..."
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Sometimes, when you publish the code you used to develop new Biochemistry or Genetics solutions, you find that other scientists in other countries use your code to reverse engineer what you are working on - your results, if you will - to eliminate dead ends and publish a paper on what you invested years finding a solution for, but before you submit your paper that they "effectively" stole.
Fair enough, though sometimes getting out of the habit of 'releasing early, releasing often' can put academic developers on a slippery slope that ends with them closing the source. We use a well known (and excellent) suite of genomics software called GATK, originally MIT-licensed. Last year, the developers announced they were switching to a hybrid license, where the latest (unpublished) tools would only be available under closed source terms. The core (now 'lite') package would remain Open Source, and suppo
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They should open resource their research too (Score:2)
"Academic publishe
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The discoveries, algorithms and parameters generated by publicly-funded research is locked behind the paywalls of for-profit publishers.
Publishing the results has very little to do with the reason the code isn't open source. The copyright for code and data doesn't transfer to the publisher.
The most likely reason that code is not open-source or reusable is that it has been written by a graduate student to process a specific data set for a specific purpose. The grad student has little reason and no time to deal with creating an open-source project where others may make demands on his limited time to add/fix/change the code to make it usable
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You hit the nail on the head and I think what you wrote applies just as much to any researcher as it does graduate students. Journals are for the most part filled with papers of academics because institutions incentivize academics for the publication of papers through degrees and tenure and what-not. These institutions generally fail to incentivize the publication of a more complete set of data, code, and other useful things, so they are a low priority.
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The only reason these publishers have survived is because academics want their research published in the most prestigious (read 'expensive') journal they can find.
Not most expensive, most referenced. Your career as an academic is largely based on how many people reference your work. Your ability to recruit grad students, attract research funding (to pay those students) depends on how many papers you publish and how many people cite your work. Some funding agencies are a bit more lenient allowing the referees to assess the paper quality directly, but others have strict rankings of publishing venues and how much a paper in each venu is to be evaluated as. Until you br
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The discoveries, algorithms and parameters...
No, only the reports about them. Not only are the general facts uncopyrightable, a paper is not the same as the substance of the research. It's a report on the research. It's still important, but that's not controlled by publishers. (For that matter, algorithms and parameters are frequently not published in papers. Regardless, you can generally get it from the researcher themselves by asking, unless it's still an active area of research for them.)
Even so, access to papers is frequently more a theoretical pr
Most research in computer science is available (Score:2)
Citeseer and google scholar contain a large amount of scientific papers freely accessible. Many journals have open access policies. Many researchers publish their result on arxiv before sending it anywhere else. IEEE and ACM let their members access papers (IEEE policy at http://www.ieee.org/publications_standards/publications/subscriptions/prod/mdl/mdl_overview.html [ieee.org] . ACM's policy at https://campus.acm.org/public/qj/profqj/qjprof_control.cfm?form_type=Professional [acm.org] . SIAM's policy http://www.siam.org/member [siam.org]
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The government funds labs partially based on the number of publications they publish in "high impact" (almost always non-public) journals. Write your congressman (really!) that publicly funded research needs to be freely available, and that government needs to stop funding science based on publications in non-free sources.
Of course in that case you need to suggest a different metric for scientific success to allow the government to allocate limited funds between labs. This I think is the big sticking point
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Actually, not that many actually ask for transfer of copyright. And most academics completely ignore that anyway. Plus, if you really want to know, you have only to go to a library. Yes, I know it means leaving the basement.
many already do this (Score:3)
There are many open-source research software efforts already, and of course it would be good to see this become more widespread. These range from small-scale individual researcher one-off efforts to broad multi-institution efforts that are well-maintained over years. The software that I develop in the course of my mathematical research is available freely from our webpages, with intermittent downloads. And I still get inquiries about using it, to which I just say that it's all on our webpages already.
One barrier to broader efforts in the US is that science agencies (at least the National Science Foundation) generally support research proper, rather than development of tools. Oddly, I am much more likely to get a grant to work out research that perhaps 20 to 50 people may be interested in than I am to get a grant to develop research tools that may be useful in furthering research to a few hundred researchers. Nevertheless, it is more common that universities and funding agencies expect data and software from research to be freely available. Many people drag their feet on these requirements as they are worried that some other researchers will use their tools to scoop them, but I think these instances are very rare.
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I am a scientist who has made "code" (Score:5, Insightful)
The software I have written for my odd specialized purposes is similar to the software my colleagues write: It's spaghetti code written with custom libraries which are not better than common ones and it has no documentation at all.
We could open-source it, but then you'd just bitch about how poorly its constructed.
We don't have time to open-source our code. Heck, I've had people ask to use software I've made and I've regretted giving it to them because I then am obligated to explain to them how to use it.
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I've done research in Chemistry, and have heavily used open source quantum chemistry codes (mainly NWChem [nwchem-sw.org] and Quantum Espresso [quantum-espresso.org]. I am grateful to these guys for releasing these codes.
MY code on the other hand is not available. most of it is a bundle of scripts designed for one process that would make all the programmers on /. cry. the rest is in Fortran, which compiles using one compiler on one machine, and seg faults everywhere else. It's not open source because no one in their right mind would want it.
That
Re:I am a scientist who has made "code" (Score:4, Insightful)
I've had people ask to use software I've made and I've regretted giving it to them because I then am obligated to explain to them how to use it.
As someone who writes academic software specifically for distribution, I can confirm that this is a gigantic time suck, and one which the funding agencies generally do not support. We are judged both on scientific innovation and publication record, and on whether our tools are adopted by the community - but the latter frequently interferes with the former. I basically wake up to an inbox full of bug reports and feature requests every morning, and I have to find time to deal with these in addition to all of the actual science I'm supposed to be working on. Despite being an obvious sign of success (people actually use our software!), it's become so discouraging that it helped drive out one of my (very competent) ex-coworkers.
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I basically wake up to an inbox full of bug reports and feature requests every morning, and I have to find time to deal with these in addition to all of the actual science I'm supposed to be working on. Despite being an obvious sign of success (people actually use our software!), it's become so discouraging that it helped drive out one of my (very competent) ex-coworkers.
You're doing it wrong then. Just because you release source doesn't mean you have to maintain it. If you don't maintain it, and it's important enough, then some one else will. Typically I find that people who are in your position cling too tightly to the reins. If you love it, set it free. Check up on it from time to time, hell, even if it's forked and you want to add a feature you need to the code you have two options: a) modify the onsite version you keep and push out the source; Letting the forkers
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You're doing it wrong then. Just because you release source doesn't mean you have to maintain it.
When I say "users", I do not mean "other programmers", I mean scientists who generally don't know a fucking thing about programming, except maybe rudimentary FORTRAN (which is not what I use), and are busy with their own research which does not leave them any time to fix other peoples' software. They are utterly incompetent to maintain our code for us, and the only people besides us who are qualified are our co
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When I say "users", I do not mean "other programmers", ... but the bulk of user support has to be done by us. Your response indicates that you've never had to support a non-technical user,
Don't worry. If you release a software library so it's only usable by other programmers, it doesn't get any better. Trust me on this. You'll wonder howhalf of them ever got past hello, world.
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One solution that leaps to mind is that someone other than yourself is given the responsiblity of supporting the users and maintaining the software.
If money is required to enable this, couldn't the users or the institutes that benefit from this software be conviced to chip in and fund the support?
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Typically I find that people who are in your position cling too tightly to the reins. If you love it, set it free.
For fuck's sake people, you make it sound like simple resource management is a form of rocket science.
I'm in a similar position to the GP and I have to say, you have no idea what you're talking about here.
I have released a number of things. One (most popular) is a C library requireing zero configuration and consisting of two functions. I've also released a decent sized library. The latter is al
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I'm a PhD student and this is completely true; mod parent up.
A small portion of the time, someone writes a tool with the intention of writing a tool for community use, and that can sometimes end well.
Other times, someone writes something and it ends up becoming popular, and is usually hacked upon and hacked upon when it should just be rewritten from scratch with the intention of being publicly consumed.
In any event, it is not often that academia will pay for either of the two above items; academia simply is
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I'm a scientist at a big national lab (SLAC). We do open source / collaboratively write some code. There is a real-time distributed control system "EPICS" that is developed and maintained by multiple labs. There are programs like LIAR, ELEGANT, GENESIS, etc that are widely used for accelerator design optimization. For widely used programs like these, it is wort the (very large) effort to support them and make them usable. Even with this effort through, I dare anyone to get EPICS running without help from
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The software I have written for my odd specialized purposes is similar to the software my colleagues write: It's spaghetti code written with custom libraries which are not better than common ones and it has no documentation at all.
Yes, I know the feeling of "source code like the underwear: if it's dirty, better not show it to anybody".
This is happening in statistics... (Score:3)
The Journal of Statistical Software is an electronic journal that publishes software. It tends to publish R packages because that's where the development is mostly happening these days, but it will publish any language. The refereeing process checks that the software works as well as that it is a good contribution. It has a reasonable reputation, far above the junk journals on Beall's list (Google it if you don't know what that is), though not as high as the better mathematical journals in the area. The R Journal has a similar goal, but it's newer, and the reputation isn't there yet.
I review grants, and I give a lot more credit to software published somewhere like JSS or the R Journal than to software available on someone's web site.
So some academics do get credit for this.
it's already out there (Score:2)
at least in the particle physics community, practically all anyone uses is open-source code. The most common are GEANT4 for simulating particles interacting with matter, and ROOT which handles data analysis. Both are maintained by dedicated people at CERN.
As to more specialized code, any time I've ever asked someone about their analysis, no matter what institution or relation (or lack of) to me, they've always been happy to share their code source with me. Usually with many caveats about quality, but it's
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they've always been happy to share their code source with me. Usually with many caveats about quality, but it's there.
I've been on the other side of that.
But when I say, "sure, but it was written when I was a student in 2003, against libraries that will not compile on a modern OS/compiler (the newer liberaries are incompatible), it's spaghetti code due to being research code, you'll need your data converted to this hard to convert to custom format and there are better, simpler algorithms out there now for
I blame the Bayh-Dole act (Score:3)
Most academics are under tremendous pressure to keep anything of potential commercial value closed; releasing code as open-source generally requires permission from above. (In fact, I know of one professor of biology who had to fight to get a line in his contract explicitly allowing him to open-source everything.) And it's not like most of them need encouragement; none of us are getting rich off NIH grants (well, most of us aren't) and we effectively hit a salary ceiling early in our careers, so the prospect of a few thousand dollars extra in licensing revenue is more than most can resist. In several cases that I'm aware of, the licensing money is used to support research activities - sometimes enough to pay for an entire employee, or pay for meetings that wouldn't happen otherwise. Note that in many cases the code itself is still available, just not under a license that allows distribution, which usually makes it difficult or impossible for anyone who wants to build on your work to do so.
Of course it's not always this simple - junior researchers have very little control, so many of us end up releasing code under proprietary licenses when we'd much rather open-source everything. I also know of many cases where paranoia and competitiveness, rather than avarice, are at fault - in these cases, the code itself is hidden and the software released as binary-only (which as far as I'm concerned should be unacceptable for anything published in a peer-reviewed journal, regardless of the license used). Regardless, there are simply too many incentives to retain full control.
This is a completely idiotic situation, of course, and it has been holding back science for years - I know of multiple cases where university researchers were effectively doing R&D for private companies (not always willingly!) with very little in return. I've also seen researchers prevent widespread adoption of their work (and hamper their career advancement) because of tight-fisted behavior. One asshole even charges other academics to obtain his software, with the result that some people avoid using it altogether. Frankly, since I have to deal with this bullshit on a near-daily basis, as far as I'm concerned a repeal of the Bayh-Dole act (and its equivalents in Europe), at least where software is concerned, would be a huge leap forward for academic computational research. The bonus I get from licensing fees is simply not worth the trouble and missed opportunities.
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In many fields, such as social sciences, most of the "code" is simply a bunch of MATLAB, Stata, or GNU R scripts, with virtually no commercial value. I'd be surprised the universities have any issues with releasing this. In fact, the faculty who want, simply post the code on their web page. The issue is that most people do not post either their code or data, and I know why. Most of the time, the code is just terrible. I know of smart tenure track faculty who rely on MATLAB to compute anything for their pape
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Nonsense. There is tons of academic open source. And Bayh-Dole doesn't apply outside the US.
The real reasons for not publishing source in academia are much simpler: it's ugly, people don't want to spend time support messy code, or they think you haven't finished publishing yet. Generally, if you ask, you get the code.
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There is tons of academic open source.
And there is just as much that is either closed-source, or not redistributable. It depends on the institution and the researchers involved - ultimately the professors have the most say in this; grad students and postdocs will do whatever they're told.
And Bayh-Dole doesn't apply outside the US.
Most other nations which can afford to fund basic research have similar provisions - I know this because all of our competitors outside the US have licenses which are equally rest
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You're engaging in circular reasoning: you conclude that other nations must have similar laws because they have similar licenses, but that's your hypothesis, namely that similar laws lead to similar licenses.
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I have a bunch of software I've been very willing to set free (it has already even GPL3 headers!) but I can't, because it might be publishable one day.
And so, it'll keep on being hidden...
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I have a bunch of software I've been very willing to set free (it has already even GPL3 headers!) but I can't, because it might be publishable one day.
And so, it'll keep on being hidden...
Sounds like you need to publish more often rather than whinging about the whether it "might be publishable one day" on slashdot. There's no point in sitting on stuff so long that it becomes irrelevant, and code that's just cowering in a dark corner of your disk might as well not exist at all.
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It doesn't help that I'm the only one doing this in my institution.
And to answer other replies, I had a *huge* flame with a Detroit professor because he wanted to keep other things closed - luckily I won that battle and the stuff went out as LGPL.
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Code can be the matter of a paper - and by releasing it, you may break the "novelty" aspect and never publish anything.
This has not been my experience - we release new features almost as soon as the code is written, sometimes years in advance of publishing anything, and we have never had a problem getting the eventual articles accepted. If anything it is beneficial to release early and often, because then we get credit for having come up with the idea first. Many of our competitors do the same. Again, it
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In MIDDLE SCHOOL, I took a science class.
Science is composed of:
Create a Hypothesis.
Write a Procedure.
Record Data.
Test the Hypothesis.
Other scientists independently reproduce based on your experiment.
So - if software (part of the procedure) is released closed source. . . then how in hell are other scientists supposed to reproduce the work?
This goes against the most very basic principles of science.
Why? (Score:1)
Why would researchers publish their code? They have only one target - to get their *papers* published in reputable venues. More often than not, such venues are closed and paywalled, so it is not surprising that they do not enforce (in fact they discourage it, to say the least) opening up bits of research.
Some researchers would be happy to publish their code anyway (as a matter of principles, or to promote themselves through non-academia channels) but at best they would be frowned upon by their superiors
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Actually, the copyright issues you are mentionning are important. I frequently end up mashing together code found god knows where. When we finally wanted to publish our code, we had to go through the various files and decide which ones we can publish and which one we can not publish because of copyright. We use them internally (and probably we actually should not, but nobody cares about that). But putting it on your website opens potential lawsuits.
We ended up scrapping auxilary functions and reimplementing
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Why would researchers publish their code? They have only one target - to get their *papers* published in reputable venues. More often than not, such venues are closed and paywalled, so it is not surprising that they do not enforce (in fact they discourage it, to say the least) opening up bits of research.
Well conference cost is normally paid by the university or institute. Therefore, this is an bad excuse. And in addition, if you have "proofen" something and publish it in a paper. How could I reproduce your study with out your data and software? It would be nearly impossible. Therefore, publish it. A good starting point is "e-science".
Some researchers would be happy to publish their code anyway (as a matter of principles, or to promote themselves through non-academia channels) but at best they would be frowned upon by their superiors for mis-allocating their resources. At worst, they would be accused of undermining team efforts (by disclosing too much information or exposing inconvenient assumptions to competing researchers) or risking legal conflicts with publishers (copyright).
What field are you working in? In CS code publishing in almost mandatory, otherwise no one will believe you. In geo sciences and marine research (as far as I can see), publish
oh my (Score:2)
People should perhaps have a look at where open source actually started. In any case, there are reasons not to publish source that aren't nefarious: you haven't written up all the papers yet and don't want to get scooped, you don't want to spend a lot of time answering questions about it, etc. I think most academics really have these tradeoffs under control.
research uses a lot of open source (Score:2)
Not sure what the intent of this article is, since academic research already uses a lot of open source software, far beyond use in industry. Knowing how to navigate a posix system is practically a requirement. Researchers also produce a lot of open source software. In my experience, software mostly falls into two categories: quick, hacked together scripts for analyzing data in a specific way, and complex simulations. The quick scripts generally aren't shared because it would take just as long to explain it
The small fish do share. (Score:3)
"Sharing can’t hurt the small fish. Almost nobody sets out to beat Daniel Lemire at some conference next year. I have no pursuer. And guess what? You probably don’t. But if you do, you are probably doing quite well already, so stop worrying. Yes, yes, they will give you a grant even if you don’t actively sabotage your competitors. Relax already!"
The big fish (and I've worked for them) don't, and it's likely they got that way by protecting their turf. Science is cut throat.
Comment removed (Score:3)
Here's hoping. (Score:2)
I've developed quite a bit of code in the process of my PhD that I'm in the process of open-sourcing on github (backed with a website here [abl.es] I've developed with open-access scientific protocols - no code there yet; getting clearance).
As others have mentioned the big anti- to this is the problem of publication. If I put my software up there free to use, there is nothing to stop someone else swooping in and using it to pre-empt the results I've spent time writing the software to accomplish (I'm helped slightly
What we do (Score:2)
We release all of our code (if not written for a company) used in our projects, or created during research. However, we are a software engineering group, and computer scientists more often open source their work. In recent years it has become mandatory to do so, as otherwise your claims are not backed. If you publish results and do not provide the means to reproduce the results, you are a blabber.
But, most of code produced in research is lousy, as it is just used to proof something not to actually use it. I
I don't know what academic world you guys are in.. (Score:2)
...but writing OSS software for education and academia and distributing it to other universities around the country and world has been my job for the last few years.
To All Grantmakers On Copyright & Post-Scarcit (Score:2)
http://www.pdfernhout.net/open-letter-to-grantmakers-and-donors-on-copyright-policy.html [pdfernhout.net]
"Summary: Foundations, other grantmaking agencies handling public tax-exempt dollars, and charitable donors need to consider the implications for their grantmaking or donation policies if they use a now obsolete charitable model of subsidizing proprietary publishing and proprietary research. In order to improve the effectiveness and collaborativeness of the non-profit sector overall, it is suggested these grantmaking org