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For more than 6 weeks now, I have been attempting to contact a post-doc or their (former?) PI to request access to either the source code or software of a tool that was published in BMC Bioinformatics. The authors did not provide the source as a supplemental file, but assure the reader in the article that it will be made available upon request. This is the first time requesting source code of a research group, but I have yet to receive any kind of reply to my polite requests.

I am unsure how to proceed. Pursuant to the guidelines for publication in the journal, "[i]f published, software applications/tools must be freely available to any researcher wishing to use them for non-commercial purposes, without restrictions such as the need for a material transfer agreement." This group is located in Europe, and it is highly likely that they should have a working knowledge of English, after all, the publication and their websites are in English, so I don't think there a language barrier exists.

Possible actions that I am considering:

  1. Contacting the managing editor for the publication to explain the situation, and see if his/her email attracts more of a response.

  2. Contacting any granting agencies who have provided supporting funding for the project to determine whether they have stipulations about providing source code.

  3. A phone call to the corresponding author.

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    I think both of the proposed actions can perceived as (extremely) hostile by the other group, so I would not do that. If you are familiar with how academic labs work: that code maybe is on a hard disk or a long-gone postdoc in an undocumented form or documented only in Russian/German/French, whatever is their mother tongue. It may be code written in LISP or Pascal, whatever that favorite of that guys was. Best case scenario is that someone trying to fix this for you, worst case scenario they just ignored and forgot your message. Your best chance is to have a normal relationship with them. – Greg Nov 5 '14 at 18:46
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    I highly disagree with the majority of answers. Most likely the research (and software) was funded with taxpayer dollars. The OP should not be a pushover. He should demand they fulfill their promises to taxpayers. There is no need to be polite. OP has already waited too long. – emory Nov 6 '14 at 1:03
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    To go along with @emory's answer, most funding (at least in the US) also has data retention policy requirements attached. I would think the same is true in Europe. They'd obligated to keep the source code around for several years after the funding ended. If they lost the source code then they'd probably in violation of the terms of their funding. – DaoWen Nov 6 '14 at 3:38
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    Have you considered simply giving them a phone call? – Roland Nov 6 '14 at 12:12
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I think contacting the editor of the journal is your best bet. Contacting grant agencies will most likely not warrant a reply, and I don't imagine many of them have stipulations for sharing code (yet).

That said, I have been in a similar position numerous times, and I have had very little luck every obtaining the code. The editor will most likely not be willing to retract a paper because the author's won't share, and they have little incentive to do so, since it will at most garner a single citation, but could lead to more problems down the road (e.g., the code is buggy and you can't reproduce their results, etc.)

Another tip would be that senior people (i.e., PIs) usually have more luck at this kind of thing because they are harder to ignore and/or have contacts, but it can be harder to get the to actually do it, because it can become political.

  • I agree that the editor will likely not retract the paper, but I am pretty sure that it will make him more careful handling the next paper by these authors. If the editor takes up on this, it should be a strong incentive for the authors to actually share the code. – silvado Nov 6 '14 at 13:26
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    It would be interesting to know how this went. – Captain Emacs Feb 15 '16 at 20:02
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Stop. Do not do any of the things you are thinking of doing.

The authors did not provide the source as a supplemental file, but assure the reader in the article that it will be made available upon request.

Have you thought that they need to polish the code before releasing it? The fact that I am planning to release my source code does not mean that I have to do it now or whenever suits you.

Pursuant to the guidelines for publication in the journal, "[i]f published, software applications/tools must be freely available to any researcher wishing to use them for non-commercial purposes, without restrictions such as the need for a material transfer agreement."

I have seen journals like that in my area (CS). Still, this initial rule proposed when those journals came out, might atone through the years. Since in certain areas, conferences are the main publishing venue, journals sometimes "relax" their original rules to get enough submissions to get them going. So, I would not count towards this rule to pressure the journal or the authors of this work. Check out some other works on this journal. Do they actually released the code? If not, then releasing the code is the exception and not the rule.

Also, "software applications/tools must be freely available to any researcher wishing to use them for non-commercial purposes, without restrictions such as the need for a material transfer agreement." does not necessarily mean releasing the source code but just the binary or a web-application created from the code. Where did you make the assumption that they should give their source code to you? The word "tool" refers to full apps and not original uncompiled source code.

Contacting the managing editor for the publication to explain the situation....

And what do you think the editor would do? Punish the authors because a random stranger on the internet tells him something bad about them? You can rest assure, this action will have little effect on the authors and only reflect bad on you.

Contacting any granting agencies who have provided...

Why do you assume that under the rules of their funding agency they should release everything as open source? I have worked in many research projects in Europe and I have never heard of such a strict rule. Perhaps there are some projects or agencies demanding that but I do not think it is the norm as you suggest it is. In many projects, participants are commercial companies and they are usually not interested in sharing their work with anyone else (except the project partners and only during the project's duration). Enforcing such a rule would make all commercial companies to not want to participate and that is against the policy of funding agencies.

Have you ever stopped to consider that the PI perhaps relocated and did not get those emails? Are you 100% sure that the authors did not reply your emails on purpose? And even if they do, are you sure that they broke some rule as you assume they did? In your shoes, I would not be too sure. And starting a full-scale war, will do more harm to you than them.

Also if you want something, be nice. Sometimes it does not work. OK. Bullying people into doing what you want is not an efficient long-term policy.

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    Very detailed reply. Let me rebut: 1) The article is >18 months old now. How much "polishing" can the code still require? This claim makes sense in a recent publication, but not one this old. 2) The software in this case is a python script, so releasing the tool is the source code. Not only is that the journal policy, which they should be adherent to, it is quite common in bioinformatics to release the software (not necessarily source code, but a binary/web interface at a minimum). Further, their abstract and paper state the software is available upon request, thus, my request. – user479 Nov 5 '14 at 18:43
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    While this advice is generally sound, for this particular journal, availability of software described in a software article is a hard requirement. – ff524 Nov 5 '14 at 18:50
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    @ff524 If the journal would take this requirement seriously, they would have asked the code submitted in a repository just like crystal structure files required e.g. for Chemistry papers. Making that optional is a sure way the many authors will not have a reliable solution for code sharing. It is poor practice. Academics are very bad at development / management of code. – Greg Nov 5 '14 at 19:05
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    So you would advise being a pushover and not caring about scientific accountability. A scientific article must give the reader the knowledge required to retrace the steps leading to the result. That is why the journal requires that the software is available, without it, one of the steps is missing, and the result cannot be verified. And the code most certainly should not be changed before release, the version that the article is built upon is the version that will most accurately retrace the steps. If the author has a newer better version, he can release both. – aaaaaaaaaaaa Nov 5 '14 at 23:32
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    The idea that they need to polish the source code before releasing it is not compatible with a commitment (according to the journal guidelines) to provide the software "upon request". If it is requested before it is polished, it needs to be released in its unpolished state. – BrenBarn Nov 6 '14 at 3:47
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It's perfectly possible that your polite request is sat in a queue of jobs behind several others. If you mailed them six weeks ago, then that would just about coincide with the start of the teaching term at many institutions (such as my own). That time of year is quite crazy, so it might just be that they haven't got around to it yet.

Failing that, do you know of anyone else who might need to use the software, and might also send a request? If people feel that their "product" is actually in demand, that might act as a spur to further action...

And, to reiterate the points already made, do not contact the journal - at this stage - and absolutely do not contact the funders until all other possibilities have been tried (and, even then, think very carefully about taking this action).

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    What I don't understand is why this should be a logistical problem for the original researcher - what is there to "get around to"? This is exactly why the web was developed in the first place: to facilitate the sharing of academic materials of this sort. Drop a tarball on a server and it's done and dusted. This doesn't take more than two minutes, and should have been done when the paper was published. – Jon Kiparsky Nov 6 '14 at 16:46
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I think you need to forget about how you do things on the internet and remember how you do them in the real world. The fact that you do not think they have treated you with the courtesy and respect you believe you deserve does not justify you treating them any worse then you would hope to be treated.

You have asked for something, you didn't get it. Move on.

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    Or, he has asked for something, but hasn't gotten it yet. It isn't like an email requesting that I dig up something and send it off is the highest thing on my priority list... – Jon Custer Nov 5 '14 at 22:01
  • @JonCuster: well, that's a matter of how you relatively prioritise different promises you've made to different people. Yeah, the promises you made to your employer (and students) out-rank the promises you made to the scientific community at large, but only because eating (and students) are more important than your scientific contribution ;-) – Steve Jessop Nov 6 '14 at 12:17
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    Well, that plus how many random emails one gets asking for stuff to be done! Right now I have waaaaaay too many emails in my in box, most of which are high priority to the sender... A few weeks or months to dig up some old code and package it neatly to ship off to someone I don't know at all? That would be a pretty fast response, actually. – Jon Custer Nov 6 '14 at 14:01
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    @JonCuster Do you expect your papers to be read only by people you personally know? Preparing the software together with the paper before actually publishing and then keeping it accessible online seems a more sensible solution that also allows others to verify your work. Otherwise it's asking people to take your results by your word. – Svalorzen Nov 6 '14 at 15:23
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    My tone is exasperation with the attitude of entitlement that pervades both your original post and your subsequent responses. Who gave you the right or the authority to keep them honest? Have you entered into some sort of personal or financial contract with them? Having access to their material will benefit you, but you are doing nothing to benifit them in return, instead, you are proposing barely disgused threats to get what you want. – Paul Smith Nov 11 '14 at 15:24
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Do you absolutely need the source code or the tool they created to reproduce their work? If so, then I think them coughing up the code would be paramount for you and any other group wanting to pursue or validate their work. If not.. then try coding your own solution.

I know, I know, your logic may be that it would be easier to start with their source code and build from there. IE: see how they did it. But, what programmers since the dawn of time have learned is it's easier to start and build your own code then it is to take on and learn someone elses. That's why programmers love to go into new things saying "we need to start from scratch". It can be a royal hairball trying to untangle someone elses' code.

If their research provides a basic process that their code simply helps expedite, then try coding your own solution and see if it also works. If they said they would provide code-upon-request, contact them again, but remain friendly. This isn't something to burn a bridge over. Research teams can sometimes get pulled different directions (esp. depending on who they work for), and a past project may get filed away and all the resources they used for it (hard drives, email addy's, etc) may get mothballed. So, asking for the code may require someone spending time digging through archives and such. (In retrospect, if they say the code is available they should have tossed it on a publicaly available repo, so folks like you could grab-n-go without having to pester them). Research goals also change over time. The person writing up the thing you read may have though the code would be available upon request.. but, the folks that funded the research may have changed their minds ... perhaps they want to patent the code as a tool to sell later?

I think you should contact them again, and simply ask that you requested the code, haven't heard from them, could someone please let you know if the code availability has changed, and if so, why? Be polite about it. At this point you just want a response saying whether you might get the code or not.

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