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I've been developing research software for +10 years and I experience this all the time. As one example, over a decade ago I wrote a biological simulation prog

I've been developing research software for +10 years and I experience this all the time. As one example, over a decade ago I wrote a biological simulation program called CompuCell3D it was the successor to CompuCell, a 2D simulator of cells as cellular automata. Since then many papers have been written based on research utilising this software. Not only have I not been credited in any of these publications but my name has been removed from the software, the website never mentions my original contribution and the current maintainers of said software are not responding to my emails. Granted this code has changed a lot over the years but there are still large parts of the code which are still verbatim from my original software. The researchers in this project see it as totally irrelevant that I wrote the original code because they value code creation MUCH less than their research. This particular case is especially egregious but it is a good anecdotal example of the problem. Sometimes code is not as significant or as breakthrough as raw research. It really matters what kind of coding you are talking about. You don't necessarily credit the construction crew when dedicating a new building but you do credit the architect. Coders are under valued in today's research environment.

dekhn 11y ago
What role did you have when you wrote the code? If, for example, you were a full time employee, grad student, or postdoc at a university, the copyright belongs to the university (not true for undergrads!) The website isn't required to list your contribution. That would be a courtesy. Also, if you have a problem with this where you think it's important to change the website or get another form of credit, your lawyer should be talking to your ex-employers lawyer. That should have been clear when the current maintainers failed to respond to your email.
dekhn 11y ago
The paper for citing CompuCell3D is Multi-Scale Modeling of Tissues Using CompuCell3D – M. Swat, Gilberto L. Thomas, Julio M. Belmonte, A. Shirinifard, D.Hmeljak, J. A. Glazier, Computational Methods in Cell Biology, Methods in Cell Biology 110: 325-366 (2012) I can't see that article online without paying, but I am certain it cites CompuCell, a Multi-Model Framework For Simulation of Morphogenesis – J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. Alber, G. Hentschel, S. A. Newman, and J. A. Glazier, Bioinformatics 20: 1129-1137 (2004) that original article includes your name on the author list. So your statement "I have not been credited in any of these publications" isn't really correct; your contribution is credited indirectly through citations. I don't see any problem with this; I doubt papers citing CompuCell3D have any text like "We acknowledge the efforts of <so and so>".
- jcoffland 11y ago
  I stand corrected I was credited in the original work. My main beef was that my name was dropped from the code itself and the website where it is hosted failed to mention me until recently.
3dresearcher 11y ago
You seem to be listed on the people page: http://www.compucell3d.org/People http://www.compucell3d.org/People
- jcoffland 11y ago
  You are right. They did add me. Perhaps they did get my emails but I didn't get the answer. I should have rechecked this before posting. Of course I did have to ask to be mentioned which shouldn't have been necessary.
coliveira 11y ago
> Coders are under valued in today's research environment. Exactly because it is a research environment. Coders are valued in a tech company environment because that's where they're the stars. In any other organization, such as a transportation company or a government bureau, a coder is just an assistant to the main tasks, and there is no reason it shouldn't be different.
- metaobject 11y ago
  Yep. I write simulation and data analysis software for a large company. My names appeared on ~5 papers simply because of the fact that I wrote the software used for the research.
  - spooningtamarin 11y ago
    You could have easily added a BSD derivative license where one would be required to cite your paper or just your authorship if they've used the software. I've noticed this being a good way to maximize credit.
    - Athas 11y ago
      This is both BSD- and GPL-incompatible, which has all sorts of potential ramifications. Particularly the GPL-incompatibility prevents you from including GPL-licensed code. Although both BSD and GPL already require attribution, so you could say that it's redundant.
- spacecowboy_lon 11y ago
  And in scientific computing the senior researchers are not paid very much so the supporting developers/tecnhnicians are badly paid. When I was a Research Assistant/Experimental Officer at a world leading Rnd organization I was paid about 1/3rd of what other jobs with similar entry requirements did.
  - jcoffland 11y ago
    That depends on who you work for. I've gotten paid well for research programming but only from top level universities and research institutions with money. Working for a state university usually won't pay well if at all.
jhbadger 11y ago
One problem is citation limits for many journals (which say that you can only cite 25 or 50 papers or whatever). As a computational biologist myself, I would prefer to cite every package that I use because I understand that the authors need this to get grants for further development, etc. But what happens when the more senior authors (who tend to be experimentalists) get the manuscript, they want to add a bunch of experimental citations and they see citations of computational methods as irrelevant and able to be sacrificed if there are too many citations.

dekhn 11y ago

What role did you have when you wrote the code? If, for example, you were a full time employee, grad student, or postdoc at a university, the copyright belongs to the university (not true for undergrads!) The website isn't required to list your contribution. That would be a courtesy. Also, if you have a problem with this where you think it's important to change the website or get another form of credit, your lawyer should be talking to your ex-employers lawyer. That should have been clear when the current maintainers failed to respond to your email.

dekhn 11y ago

The paper for citing CompuCell3D is Multi-Scale Modeling of Tissues Using CompuCell3D – M. Swat, Gilberto L. Thomas, Julio M. Belmonte, A. Shirinifard, D.Hmeljak, J. A. Glazier, Computational Methods in Cell Biology, Methods in Cell Biology 110: 325-366 (2012) I can't see that article online without paying, but I am certain it cites CompuCell, a Multi-Model Framework For Simulation of Morphogenesis – J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. Alber, G. Hentschel, S. A. Newman, and J. A. Glazier, Bioinformatics 20: 1129-1137 (2004) that original article includes your name on the author list. So your statement "I have not been credited in any of these publications" isn't really correct; your contribution is credited indirectly through citations. I don't see any problem with this; I doubt papers citing CompuCell3D have any text like "We acknowledge the efforts of <so and so>".

jcoffland 11y ago
I stand corrected I was credited in the original work. My main beef was that my name was dropped from the code itself and the website where it is hosted failed to mention me until recently.

3dresearcher 11y ago

You seem to be listed on the people page: http://www.compucell3d.org/People http://www.compucell3d.org/People

jcoffland 11y ago
You are right. They did add me. Perhaps they did get my emails but I didn't get the answer. I should have rechecked this before posting. Of course I did have to ask to be mentioned which shouldn't have been necessary.

coliveira 11y ago

> Coders are under valued in today's research environment. Exactly because it is a research environment. Coders are valued in a tech company environment because that's where they're the stars. In any other organization, such as a transportation company or a government bureau, a coder is just an assistant to the main tasks, and there is no reason it shouldn't be different.

metaobject 11y ago
Yep. I write simulation and data analysis software for a large company. My names appeared on ~5 papers simply because of the fact that I wrote the software used for the research.
- spooningtamarin 11y ago
  You could have easily added a BSD derivative license where one would be required to cite your paper or just your authorship if they've used the software. I've noticed this being a good way to maximize credit.
  - Athas 11y ago
    This is both BSD- and GPL-incompatible, which has all sorts of potential ramifications. Particularly the GPL-incompatibility prevents you from including GPL-licensed code. Although both BSD and GPL already require attribution, so you could say that it's redundant.
spacecowboy_lon 11y ago
And in scientific computing the senior researchers are not paid very much so the supporting developers/tecnhnicians are badly paid. When I was a Research Assistant/Experimental Officer at a world leading Rnd organization I was paid about 1/3rd of what other jobs with similar entry requirements did.
- jcoffland 11y ago
  That depends on who you work for. I've gotten paid well for research programming but only from top level universities and research institutions with money. Working for a state university usually won't pay well if at all.

jhbadger 11y ago

One problem is citation limits for many journals (which say that you can only cite 25 or 50 papers or whatever). As a computational biologist myself, I would prefer to cite every package that I use because I understand that the authors need this to get grants for further development, etc. But what happens when the more senior authors (who tend to be experimentalists) get the manuscript, they want to add a bunch of experimental citations and they see citations of computational methods as irrelevant and able to be sacrificed if there are too many citations.