SOFTWARE

Computational biology

HumanGEMlib is a Python library for human genome-scale modeling. HumanGEM (1) comprehensive human reaction network, and COBRApy (flux balance analysis) power HumanGEMlib to simulate effects of genetic knockouts on human metabolism. Type 2 diabetes signature metabolisms simulated using HumanGEMlib are reported in (2).

HumanGEMlib is found here and its usage is documented here.

Bioreactor-Model Python library

Bioreactor-model is a Python package for bioreactor and biomass growth calculations. Read documemtation here.

Protocol Dex website

This website indexes commonly used biotechnology protocols in stem cell harvesting, cell differentiation, cellular agriculture and Planaria biology. Visit website.

Biotechdex mobile app

Biotechdex is a mobile application in development to explore biology and biotechnology natively on mobile, iPad and web.

1. Explore genes (NCBI gene)

2. Explore KEGG, BRENDA and other databases

3. Explore UniProt

4. Explore GEO (gene expression omnibus)

5. Upload RNAseq file for cell types by GEO match

6. Execute BLAST

7. Systems biology sim with whole-cell model. Tweak medium glucose, add differentiation factors, throw in challengers (antibodies, competing species) to grow simulated cellular life.

8. Connect your lab notebook for in silico experiments and data analysis from machine readouts

9. Share your biotechdex with other bioengineers

10. Run pre-existing scripts on datasets (cellular identity with scRNAseq data, immunology with CITEseq data)

Biotechdex is the starting point of mobile biotechnology. One day, ASBL machines will miniaturize to the point of sequencing and biomarker identification on phones. Spit on phone to decode saliva biology, powered by Biotechdex and ASBL under the hood.