In silico analysis

• In silico = "performed on computer or via computer simulation.“

• coined in 1989

• in vivo, in vitro, and in situ,

– experiments done in living organisms, outside of living organisms, and where they are found in nature, respectively.

• Defn : “Analysis performed using computers in conjunction with informatics capabilities”.

• first used in public in 1989 in the workshop "Cellular Automata: Theory and Applications" in Los Alamos, New Mexico.

– "DNA and RNA Physicochemical Constraints, Cellular Automata and Molecular Evolution“

• Pedro Miramontes

• In silico has been used in white papers written to support the creation of bacterial genome programs by the

• Commission of the European Community. The first referenced paper where "in silico" appears was written by a

• French team in 1991.[6] The first referenced book chapter where "in silico" appears was written by Hans B.

• Sieburg in 1990 and presented during a Summer School on Complex Systems at the Santa Fe Institute.[7]

• The phrase "in silico" originally applied only to computer simulations that modeled natural or laboratory

• processes (in all the natural sciences), and did not refer to calculations done by computer generically.

Drug discovery with virtual screening

• Potential to speed the rate of discovery reducing expensive lab work and clinical trials.

• Producing and screening drug candidates

• Using EADock, -potential inhibitors to an enzyme associated with cancer activity in silico.

• Differs from use of expensive robotic labs to physically test thousands of diverse compounds a day, following further testing

Cell models

• Efforts to establish computer models of cellular behavior.

• In silico model of tuberculosis to aid in drug discovery -faster than real time simulated growth rates

– phenomena to be observed in minutes rather than months

Genetics

• Digital genetic sequences obtained from DNA sequencing may be

– stored in sequence databases, be analyzed

– digitally altered and/or

– used as templates for creating new actual DNA

Using artificial gene synthesis.

Other examples

In silico computer-based modeling technologies have also been applied in:

• Whole cell analysis of prokaryotic and eukaryotic hosts

– E. coli, B. subtilis, yeast, CHO- or human cell lines

• Bioprocess development and optimization

– optimization of product yields

• Analysis, interpretation and visualization of heterologous data sets from various sources

– genome,

• transcriptome or proteome data