Ethical medical research/In papyro, in silico, in situ, and in vitro guide
This is a resource for non-animal medical testing. Pertaining to this are in papyro, in silico, in situ, and in vitro studies. An explanation of the tools and resources in virtual testing will be shown.
![](http://upload.wikimedia.org/wikipedia/commons/thumb/2/20/Jmol_screenshot_2hvy.jpg/200px-Jmol_screenshot_2hvy.jpg)
Software
editExternal multimedia: Computer aided drug design
Proprietary
edit- NONMEM - referred to as the gold standard in pharmacometrics.
Open-source
edit- OptFlux - metabolic engineering program.[1]
- Silico - molecular toolkit constructed in Perl.
- Little B - programming language for use in biology. [2]
- JBioFramework - chemical analysis program.
- GIMIAS - framework for medical applications.
- CMISS - mathematical biological environment.
- Jmol - 3d molecule viewer. Jmol video tutorial
- PASS (Putative Active Sites with Spheres) - Computes docking sites in proteins.
- RasMol - protein, nucleic acid and small molecule visualizer.
- TINKER Molecular Modeling
Databases
edit- Urine Metabolome database - Contains over 3,00 chemical compounds that can be detected in urine.[3]
- Pubmed International - PMC, Pubmed Europe, Pubmed Central Canada, PubChem
- Metabase - Wiki of biological databases
- EBSCO Host
- FAF-Drugs: Free ADME/tox Filtering - In silico molecule databases.[4]
- The Drug-Gene Interaction database (DGIdb) - Matches genes with interactions with drugs. Combines information from existing information into this database.[5]
Math
editElectronic hardware specific
edit- imaging and sensors
- hyperspectral imaging (HSI) device
- magnetic resonance imaging (MRI)
- nanosensors
Materials
editResearch chemicals, petri dishes, test tubes and other lab equipment can be bought online. Organ-on-a-chip is in plans to be manufactured by Sony with the co-development by Harvard's Wyss Institute to be accessible to the marketplace.[6] Several organ type organ-on-a-chips are in development. Currently cell cultures in petri dishes or test tubes are used, which has some limitations.
Analysis
editMicrodosing uses less than a salt grain size of a chemical to be tested.
References
edit- ↑ OptFlux: an open-source software platform for in silico metabolic engineering, BMC Systems Biology, 2010, doi:10.1186/1752-0509-4-45, PMC 2864236
- ↑ Biology enters 'The Matrix' through new computer language, Harvard Medical School; Eurek Alert!, 2008
- ↑ University of Alberta (September 5, 2013), "What scientists can see in your pee", PLOS One, doi:10.1371/journal.pone.0073076
- ↑ FAF-Drugs: free ADME/tox filtering of compound collections, Nucleic Acids Research, July 14, 2006, doi:10.1093/nar/gkl065, PMC 1538885
- ↑ Washington University School of Medicine (October 13, 2013), "Database of disease genes shows potential drug therapies", Nature Methods, Medical Xpress, doi:10.1038/nmeth.2689
- ↑ Harvard’s Wyss Institute teams with Sony to advance organs-on-chips, Boston Business Journal, 2013
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