Open Tools for Synthetic Biology Jenny Molloy | University of Cambridge | @jenny_molloy | jcm80@cam.ac.uk
What
does
“Open” mean?
A piece of data or content is if anyone is free to use, reuse, and redistribute it subject only, at most, to the requirement to attribute and/or share-alike. opendefinition.org
Open
data tools
What is content?
1982 “Automatically generating logical representations of text passages... by means of an analysis of the coherence structure of the passages.”
Jerry R. Hobbs, Donald E. Walker, and Robert A. Amsler. 1982. Natural language access to structured text. In Proceedings of the 9th conference on Computational linguistics - Volume 1(COLING '82), Ján Horecký (Ed.), Vol. 1. Academia Praha, , Czechoslovakia, 127-132. DOI=10.3115/991813.991833 http://dx.doi.org/10.3115/991813.991833
What is mining? 2008 “The use of automated methods for exploiting the enormous amount of knowledge available in the biomedical literature.” Cohen, K. Bretonnel; Hunter, Lawrence (2008). "Getting Started in Text Mining". PLoS Computational Biology 4 (1): e20. doi:10.1371/journal.pcbi.0040020. PMC 2217579.PMID 18225946.
Mining Examples Building bacterial supertrees Mining chemical reactions Better genome annotation
Supertrees Only ~4% phylogenetic analyses make underlying data available.
Content Mining enables AUTOMATED extraction from daily literature and conversion to NeXML: - Machine-readable - Open - Reuseable RAW data would be optimal!
PLUTo: Ross Mounce & Peter Murray-Rust
Chemistry Open software reads and recognises chemicals structures. Can even create reaction animation. Natural language processing can be used to analyse chemical methods. These are FACTS but the paper itself may be copyrighted.
Potential to improve quality and efficiency of genomic research.
Annotation
Many applications: -
Find primers Enhance positive controls Find novel sequence information More detailed and accurate annotation
Open
hardware
expensive!
proprietary
difficult to source
Science requires TOOLS a black box
difficult to customise
hard to maintain
Makers make tools easier to maintain
ope n
-sou rce
easy t o
custo mise
cheap
openly documented manufactured hyper-locally
There are a lot out there...
Commercial examples of open hardware
Open
biology
Transaction Costs
Tech Transfer
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Design goals for the OpenMTA ACCESS. Materials available under the OpenMTA are free of any royalty or fees, other than appropriate and nominal fees for preparation and distribution. ATTRIBUTION. Providers may request attribution and reporting for materials distributed under the OpenMTA. REUSE. Materials available under the OpenMTA may be modified or used to create new substances. REDISTRIBUTION. The OpenMTA does not restrict any party from selling or giving away the materials, either as received or as part of a collection or derivative work.
NONDISCRIMINATION. The OpenMTA supports the transfer of material between researchers at all types of institutions, including those at academic, industry, government, and community laboratories.
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The OpenMTA will … Eliminate or reduce transaction costs associated with access, use, modification, and redistribution of materials; Provide an avenue for researchers and their institutions to be credited for materials and data made openly available; Support collaboration among researchers across institutional and international boundaries; Promote access to materials for researchers in less privileged institutions and world regions; Facilitate translation of biotechnologies into commercial products and services that benefit all people and the planet. 20
A simple, standardized legal tool that enables individuals and organizations to share their materials on an open basis.
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Visit OpenMTA.org