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Recent talk at the Open Science Summit in silicon valley. Should biotechnology be made open source? Pros and cons and is it a sustainable model?

From OpenBiotech Website / FAQ:

Aren’t you going to completely destroy closed-source companies’ business model?
We do think that the proprietary reagent industry managed to come into existence largely because so far, there were no open source players. After all, why would anyone buy products that they can’t make more of, with severe use restrictions, and pay extra for the privilege? When similar products are available in equally good or superior quality, in a form that can be copied, with no restrictions, and cost much less, then the proprietary business model will simply stop making sense.

It is not our intention to harm anyone’s business. We hope that these companies will adapt, ultimately acquire our open source DNA sequences and begin competing on manufacturing the same products. This will result in a business landscape where the key competitive trait stops being how well you keep your secrets, and starts being how efficiently you can make quality products. In the end, the main beneficiaries will be the world’s scientists and therapy developers, and with them, all of humankind.

Isn’t open source unprofitable?
Open source principles did indeed build a reputation of being unprofitable, largely due to the experience in software development. Any given piece of software can be copied indefinitely many times, for free, with zero skill required. Why would I pay for a piece of software, when its creator encourages me to legally copy it? Thus, it is at least a legitimate question how to make money in open source software.
In biotechnology, it is different. With access to the necessary DNA, biological sequences and objects can be copied, and doing so is much cheaper than, say developing a new sequence. However, it still does require some work, and significant technical expertise, to scale production, purify, characterize and fully validate the resulting biological products.

We find the situation more than sufficient to build a sustainable, innovative organization.

Why are you doing it?
We started primarily because we want open source biotechnology tools to use ourselves. We are a team of young scientists with a background in regenerative medicine. In trying to start our first regenerative medicine company, we perceived the use restrictions and, for lack of a better word, obscene profit margins seen in contemporary research tools products as extremely frustrating. So we set out to make our own research tools. In doing so, we were able to free ourselves from many types of use restrictions, remove most of the cost of doing our own research, and continue our work in regenerative medicine. But we also realized that we cannot make regenerative medicine happen all by ourselves. We decided to make our tools fully open source, and offer them to the world, so that other groups can join in the same benefits.

Open source databases in biology, chemistry, bioinformatics….

I can’t agree more about importance of open sourcing in biotechnology. Lack of money prevents lot of scientist and laboratories around the world from conducting experiments that could potentially improve human life either through faster drug development, or safer and more successful food production. Shared data could accelerate R&D by saving time and resources.

Here are examples of currently used open source databases:

Open source databases used in cheminformatics:

*Chemistry Development Kit (CDK)

This database is open source library for chemoinformatics and bioinformatics. It was developed at the University of Notre Dame in 2000. So far, 75 people contributed to the project. As from 2012, CDK is supported by InChI Trust (promotes and improves the International Chemical Identifier standard).

Main features:

• 3D geometry generation
• substructure search using exact structures and SMARTS-like queries
• QSAR descriptor calculation
• fingerprint calculation
• protein active site detection
• cognate ligand detection
• metabolite identification
• pathway databases


JOELib software is mainly used for conversion of chemical file formats. All Java supporting systems could use JOELib.

Main features:

• Query and substructure search
• Clique Detection
• Feature/descriptor calculation
• Fingerprint calculation
• Chemical file formats

Open source databases used in microscope image processing:


CellProfiler is free software designed to read and analyze microscopically obtained images (obtained through fluorescent microscopy, for example). When object of interest is identified, it could be further analyzed in more details.


ImageJ is developed by National Institute of Health. It’s Java based program designed for image processing. It’s used in 3D live-cell imaging and radiological imaging to edit, process and analyze obtained images. Also, ImageJ can be used for comparison of multiple imaging… It supports number of formats: TIFF, PNG, GIF, JPEG, BMP, FITS...

Open source databases used in molecular dynamics:

*Ascalaph Designer

Ascalaph Designer is software developed for molecular modeling and simulation. Some of the features are associated with molecular dynamics and quantum chemistry. It’s mainly applied in modeling and building of polymers like nano-tubes, proteins, nucleic acids, lipid bilayers….


GROMACS (GROningen MAchine for Chemical Simulations) is developed at the University of Groningen to be used in simulation of proteins, lipids and nucleic acids. It’s one of the fastest and most popular software in molecular dynamics field.

Open source databases used for viewing of molecules:


Jmol is Java based molecular viewer for 3D chemical structures. “Applets” is popular feature of Jmol that allows displaying molecules in a variety of ways: "ball and stick" models, "space filling" models, "ribbon" models…It supports a wide range of molecular file formats including pdb, cif, mol, CML....


PyMOL is molecular visualization system designed by Warren Lyford DeLano who wanted to incorporate open source practice in medical field as much as possible. This tool is used in molecular modeling and can produce high quality 3D images of various molecules. PyMOL is applicable in structural biology associated research. It’s free of charge for scientific and educational communities.

Open source databases used in biology:

*Systems Biology Ontology (SBO)

Systems Biology Ontology is set of terms commonly used in systems biology, especially in computational modeling. It’s part of the that define standards for model curation, vocabularies for annotating models and provide publicly accessible database of annotated, computational models in SBML and other structured formats. SBO is designed by Computational Neurobiology Group (UK) and the SBML Team (USA); it’s funded by European Molecular Biology Laboratory and the National Institute of General Medical Sciences.


Ugene is open source bioinformatics software with integrated (well known) biological tools and algorithms.

Main features:

• Creating, editing and annotating nucleic acid and protein sequences
• Multiple sequence alignment: Clustal, MUSCLE, Kalign, MAFFT, T-Coffee
• Restriction analysis with integrated REBASE restriction enzyme database
• Integrated Primer3 package for PCR primers design
• Search for direct, inverted and tandem repeats in DNA sequences
• Search for transcription factor binding sites with weight matrix and SITECON algorithms
• Search for ORFs
• Cloning in silico
• Protein secondary structure prediction with GOR IV and PSIPRED algorithms
• Building and viewing phylogenetic trees
• Local sequence alignment with optimized Smith-Waterman algorithm
• Visualization of next generation sequencing data using UGENE Assembly Browser

Number of open source databases is large and I hope that their number will increase even more in the future.