Ignored Requests Open-Source Software from a Research Group

Question

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.

Answer 1

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.

Answer 2

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.

Answer 3

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).

Answer 4

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.

Answer 5

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.