Informatics for AllThe Open Source and FreewareRevolution in Chemical Biology Applications to Selected SRI           Proje...
Proprietary software: black box model● Exclusive code control● Exclusive development / customization controlUser-initiated...
Open source empowers users to pursue novelenhancements according to their needs and theirtimelines!
Open source = philosophically goodBut in practice: can you replace well established proprietary tools with open source and...
Sometimes it helps toYes!         have a guinea pig(mostly)                        = me                        July – Oct....
Synthesis &              Intellectual                 AssayProcurement               Property              Development    ...
Meta Data    Omics   Meta                    Data   Data      Chemical      Structures     Screening                      ...
Chemical specification, drawing & editing:Marvin (http://www.chemaxon.com/products/marvin/) functionality approaching     ...
Enumerate combinatorial librariesSmiLib (http://gecco.org.chemie.uni-frankfurt.de/smilib/) Efficient and flexibleMarvin (h...
Molecular Structure ConversionMolconverter (http://www.chemaxon.com/products/marvin/molconverter/)      FastOpenBabel (htt...
Store / analyze libraries and screening dataScreening Assistant SA2 (http://sa2.sourceforge.net/) Powerful, enterprise-lik...
WWWNeed                         Caveat:External               logged queryKnowledgebases         = disclosure!
Chemical Data / Meta DataChemSpider (http://www.chemspider.com/) structure, literature, suppliersPubChem (http://pubchem.n...
ADME/Tox profiling; target identificationPASS (http://www.pharmaexpert.ru/passonline/index.php) only offered online,     f...
ADME profilingiLab2 (https://ilab.acdlabs.com/iLab2/) good range of ADME endpoints,      online only, one compound at a time
Target DiscoveryNeed          Structure-Based DesignModeling,Informatics     SAR, ADME, Tox, PK
Molecular Structure Prediction / CharacterizationAvogadro (http://avogadro.openmolecules.net/)   Great builder; good graph...
Molecular Structure Prediction / CharacterizationVMD (http://www.ks.uiuc.edu/Research/vmd/)  Good graphics; excellent anal...
Molecular Structure Prediction / CharacterizationPyMol (http://www.openpymol.org)  Great graphics; Decent builder, good an...
Protein Structure PredictionSwissModel (http://swissmodel.expasy.org/)      good control, must have close homologModeller ...
Structure Based DesignPyRx / AutoDock (http://pyrx.sourceforge.net/)      easy to use; good predictionsSurflex (http://www...
QSAR: DescriptorsCDK (http://rguha.net/code/java/cdkdesc.html)          Good descriptor selection, easy to useSA2 (http://...
QSAR: modelingBuildQSAR (http://profanderson.net/files/buildqsar.php)                           Fast, flexible, easy to use
Toxicology profilingToxTree (http://toxtree.sourceforge.net/) fast, easy to use, clear logic,        good array of toxicol...
Synthesis &                                  AssayProcurement                            Development                 Targe...
Workflows (i.e., seamless process integration)
Thats enough for now .....  Thank you!Any questions?
Open source
Open source
Open source
Open source
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Open source

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In many research disciplines, including chemical informatics, open software is successfully challenging the age old paradigm of proprietary vendor software. Not only is this good for research vitality, but there are also avenues through which open source development can be lucrative and rewarding for developers themselves! This presentation discusses the open source philosophy and provides suggestions of useful open source tools covering nearly every practical aspect of chemical informatics.

Two important notes: the original presentation included practical applications that have been deleted to honor client confidentiality. Secondly, more details regarding key open source tools are being published periodically on my Tumblr and WordPress blogs:

http://geraldlushington.tumblr.com/

http://geraldlushington.wordpress.com/

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Open source

  1. 1. Informatics for AllThe Open Source and FreewareRevolution in Chemical Biology Applications to Selected SRI Projects
  2. 2. Proprietary software: black box model● Exclusive code control● Exclusive development / customization controlUser-initiated customization mustawait proprietor implementation Orreinvent all requisite wheels
  3. 3. Open source empowers users to pursue novelenhancements according to their needs and theirtimelines!
  4. 4. Open source = philosophically goodBut in practice: can you replace well established proprietary tools with open source and still sustain ● Effective ● Accurate ● Efficient science?
  5. 5. Sometimes it helps toYes! have a guinea pig(mostly) = me July – Oct. 16 distinct projects for 8 clients 98+% open source
  6. 6. Synthesis & Intellectual AssayProcurement Property Development WWW Meta Data Omics Meta Data Data Chemical Structures Screening Data Target Discovery Scope Structure-Based Design SAR, ADME, Tox, PK
  7. 7. Meta Data Omics Meta Data Data Chemical Structures Screening DataAcquire& managedata
  8. 8. Chemical specification, drawing & editing:Marvin (http://www.chemaxon.com/products/marvin/) functionality approaching that of ChemDraw; good drawing options; can embed into office documents
  9. 9. Enumerate combinatorial librariesSmiLib (http://gecco.org.chemie.uni-frankfurt.de/smilib/) Efficient and flexibleMarvin (http://www.chemaxon.com) Intuitive but slower
  10. 10. Molecular Structure ConversionMolconverter (http://www.chemaxon.com/products/marvin/molconverter/) FastOpenBabel (http://www.openbabel.org) Excellent functionality but slow
  11. 11. Store / analyze libraries and screening dataScreening Assistant SA2 (http://sa2.sourceforge.net/) Powerful, enterprise-likesoftware: capable of handling internal data management for serious operations
  12. 12. WWWNeed Caveat:External logged queryKnowledgebases = disclosure!
  13. 13. Chemical Data / Meta DataChemSpider (http://www.chemspider.com/) structure, literature, suppliersPubChem (http://pubchem.ncbi.nlm.nih.gov/) structure, screening dataSureChem (https://surechem.com/) patent searches
  14. 14. ADME/Tox profiling; target identificationPASS (http://www.pharmaexpert.ru/passonline/index.php) only offered online, free, and surprisingly accurate predictions on 300+ endpoints
  15. 15. ADME profilingiLab2 (https://ilab.acdlabs.com/iLab2/) good range of ADME endpoints, online only, one compound at a time
  16. 16. Target DiscoveryNeed Structure-Based DesignModeling,Informatics SAR, ADME, Tox, PK
  17. 17. Molecular Structure Prediction / CharacterizationAvogadro (http://avogadro.openmolecules.net/) Great builder; good graphics; built in molecular mechanics; hooks to free quantum codes
  18. 18. Molecular Structure Prediction / CharacterizationVMD (http://www.ks.uiuc.edu/Research/vmd/) Good graphics; excellent analytical tools; hooks to NAMD (molecular dynamics)
  19. 19. Molecular Structure Prediction / CharacterizationPyMol (http://www.openpymol.org) Great graphics; Decent builder, good analytical tools
  20. 20. Protein Structure PredictionSwissModel (http://swissmodel.expasy.org/) good control, must have close homologModeller (http://salilab.org/modeller/) use this for optimal control and efficient relaxation
  21. 21. Structure Based DesignPyRx / AutoDock (http://pyrx.sourceforge.net/) easy to use; good predictionsSurflex (http://www.jainlab.org/contact.html) fast; accurate; no free interface
  22. 22. QSAR: DescriptorsCDK (http://rguha.net/code/java/cdkdesc.html) Good descriptor selection, easy to useSA2 (http://sa2.sourceforge.net/) Better descriptor selection, but harder to navigate
  23. 23. QSAR: modelingBuildQSAR (http://profanderson.net/files/buildqsar.php) Fast, flexible, easy to use
  24. 24. Toxicology profilingToxTree (http://toxtree.sourceforge.net/) fast, easy to use, clear logic, good array of toxicological endpoints
  25. 25. Synthesis & AssayProcurement Development Target Discovery Structure-Based DesignInformationFlow SAR, ADME, Tox, PK
  26. 26. Workflows (i.e., seamless process integration)
  27. 27. Thats enough for now ..... Thank you!Any questions?
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