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.

Software

External multimedia: Computer aided drug design

Proprietary

NONMEM - referred to as the gold standard in pharmacometrics.

Open-source

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

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

Electronic hardware specific

imaging and sensors
- hyperspectral imaging (HSI) device
- magnetic resonance imaging (MRI)
- nanosensors

Materials

Research 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

Microdosing uses less than a salt grain size of a chemical to be tested.

References

↑ 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

[1] OptFlux: an open-source software platform for in silico metabolic engineering, BMC Systems Biology, 2010, doi:10.1186/1752-0509-4-45, PMC 2864236

[2] Biology enters 'The Matrix' through new computer language, Harvard Medical School; Eurek Alert!, 2008

[3] University of Alberta (September 5, 2013), "What scientists can see in your pee", PLOS One, doi:10.1371/journal.pone.0073076

[4] FAF-Drugs: free ADME/tox filtering of compound collections, Nucleic Acids Research, July 14, 2006, doi:10.1093/nar/gkl065, PMC 1538885

[5] 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

[6] Harvard’s Wyss Institute teams with Sony to advance organs-on-chips, Boston Business Journal, 2013

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