Open Source Drug Discovery
Correspondence: (Login to view email address)
- Institute of Genomics and Integrative Biology
- Council of Scientific and Industrial Research
- Document Type:
- Poster
- Date:
- Received 19 November 2008 07:29 UTC; Posted 01 December 2008
- Subjects:
- Pharmacology, Bioinformatics
- Abstract:
Tuberculosis is a ravaging disease killing one person in every 1.5 minutes in India alone. Someone in the world is newly infected with TB bacilli every second. Overall, one-third of the world’s population is currently infected with the TB bacillus. Left untreated, each person with active TB disease will infect on average between 10 and 15 people every year. 450 000 new MDR-TB cases are estimated to occur every year. Estimated 5% of TB patients are HIV infected. Although the complete genome sequence of the causative pathogen Mycobacterium tuberculosis was published about a decade ago and many years of painstaking efforts have been invested, we are still far from having a good, fast acting drug and vaccine which confers long lasting protection. Despite increasing investment, led by charities including the Gates Foundation, no novel drugs for TB have entered the market for many years.
Novel mechanisms for attracting funding, particularly private sector funding, into this research area are desperately needed. We wish to bring in the power of genomics, computational technologies and participation of young and brilliant talent from Universities and Industrial partners with a strong inclination to apply a concerted effort to address this important scourge. All researchers contribute data on tuberculosis drug targets and active molecules through a copyleft agreement; anyone who is prepared to keep to this may participate. All the data is Clickwrap protected and credit sharing will be based on a novel and flexible micro-attribution system. This system is aimed at providing due credit through an active process. Various levels of investigators shall have appropriate levels of rights, recognition and responsibilities.
Another valuable aspect is the partnerships of Industry with belief in Open Source systems and models. We name this concerted effort to tackle this dreaded disease as Open Source Drug Discovery for Tuberculosis.
- Presented at:
- HUGO (Human Genome Organisation) 2008, 28 September 2008
Discussion
- Votes:
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1 vote
- Comments:
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6 comments
The term “Open Source” here appears to be used to refer to the collaboration model that is often (but not always) found in projects that distribute open source software. But given that it doesn’t seem likely that the Open Source Initiative (OSI) would approve the OSDD License with all its restrictions (which may be perfectly reasonable given the context), perhaps “Open Collaboration Drug Discovery” or just “Open Drug Discovery” would be a more accurate (though less exciting) title?
The word ‘open source’ is a generic one. The Open Source Drug Discovery is an open source model in the lines of Linux OS / Human Genome Project. There are various open source licenses. In any open source model, there will be collaboration at one level enabled by the open source code and a legal binding at another level which imposes a duty to contribute the improvement back and/or keep the source code open. In OSDD model, the entire information is available in the open for collaboration. All experimental results (wet-lab/dry-lab) both positive and negative will have to be posted online. The community is standardizing the metadata for OpenLabNoteBook. Also, the software used are open source and the source code is available. The portal itself is based on open source model with community participation in deciding the use cases of the portal. The license agreement of OSDD is different from traditional software open source licenses as it has to cover inventions in addition to copyright protection which is at the core of open source software licenses.
Sorry, I am posting my comment after quite some time.
Regarding Egon’s and Eric’s points, I wish to know the exact objection (points) – in your mind – of the OSI vis-a-vis the OSDD License.
Many Thanks and kind regards
Here is a list of points defining Open Source and this definition was taken straight from the site on Open Source Initiative:
Let me go through these points one by one in the context of what we are doing:
1. Free Redistribution:
We carried out a selected focused computational screening of chemical molecules with potential to bind to a given site (pocket) in a protein (whose structure is known) of M. tuberculosis. A list of 4 ligands were developed through some modifications involving our own thoughts and found these to bind to a selected protein using AutoDock algorithm. These results are posted at our site http://sysborg.osdd.net There are over 500 users on this site. We have posted all the results free. Users may also distribute these results to develop further as they may feel. we have charged no fee nor we have imposed any restriction
2. Source Code
In a work like this, the entire procedure describing the work we did and the results we got, is same as source code of a computer program. The source code of a computer program describes the full instructions required for the computer to run and execute designated tasks. Appropriate I/O files are also defined. Here in this work, we have described the input files, the computer programs used and the parameters, the output files with figures, and the entire process. Just as in the case of a Source code you would need a compiler or an interpreter, here we have mentioned the process along with the algorithms also available as open source, which can be used to process the procedure we have given.
3. Derived Works
Any future works derived from our postings also do not have any restriction. In fact they also can be shared and community peer reviewed as ours.
4. Integrity of The Author’s Source Code
We have done our own internal peer review to examine all the critical points and we have described the procedure in sufficient detail so that the same can be re-produced as such. My own driving philosophy is that “whatever we do we do it so well that, what we have done is reproduced as such in other’s hands”
5. No Discrimination Against Persons or Groups
We have not placed any discrimination at all against any one, regardless of their characteristics in the site http://sysborgtb.osdd.net
6. No Discrimination Against Fields of Endeavor
Our procedure has not done any discrimination against any field. If a user wants to use our procedure for any other system, such as any other protein, they can do it.
7. Distribution of License
Any user does not have to ask execution of any other agreement or any paper from us for using our procedure.
8. License Must Not Be Specific to a Product
No specificity attached to our procedure.
9. License Must Not Restrict Other Software
We don’t restrict users to use any other procedure with our results.
10. License Must Be Technology-Neutral
Users can use any technology meaning either windows or linux or any other to use our procedures.
Could you invent a drug without spending any money?” but “Could you invent a drug without making any money?”
Why would anyone work for free? and many now allow will their employees to participate on company time for OSDD?
All it takes to write open-source software is a laptop and an internet connection. With drug research, someone must pay for laboratory expenses and clinical trials. And the costs are high, at more than US$800 million for the discovery and development of a novel drug by most estimates.
Software is protected by copyrights that arise automatically as code is written, even if nothing is filed. Drug research is protected by patents that are costly to file and maintain, and for which meeting the legal standards that define innovation is much harder.
One sloppy programmer seldom jeopardizes the achievements of others, and errors can be patched without requiring the rewrite of the whole program. With drugs, one careless worker can compromise years of work costing tens of million of dollars.
To survive,OSDD will need to replenish their portfolios. There are also worries that, in some areas of science, the pool of contributors might be too thin to perform the work that must be done.
Raja Seevan
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Additional information
- License:
- This document is licensed to the public under the Creative Commons Attribution 3.0 License
- How to cite this document:
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Yadav, Jyoti and Consortium, OSDD . Open Source Drug Discovery. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2008.2537.1> (2008)
- Version info:
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Other versions of this document in Nature Precedings
None.
Other versions of this document elsewhere on the web
None known.
Egon Willighagen on 10 December 2008 19:59 UTC
Dear authors, I welcome this initiative as open source cheminformatician. I have a question, however, about the OSDD license and the use of the term ‘Open Source Drug Discovery’... is the OSDD license OSI approved, and if not, do you think it still appropriate to use the term ‘Open Source’ if the license would not be compatible with the ‘Open Source Definition’? Why did you not instead simply pick one of the many ‘Open Source’ licenses that already is marked as compatible?