AB's repositories
hpcleap_dnds
Sliding window dN/dS vs. functional protein domain comparison tool. Given VectorBase gene id inputs it will aggregate various useful Bioinformatics information available, then allow the user to compare selective pressures acting along the protein sequence vs. an overlay of functional protein domain annotations.
kaks_error_bars
A simple script and example data file to draw barplots of multiple protein's pairwise dN/dS values, with error bars!
HPCLEAP_SWE-MPI
Tsunami simulations in 3D (with 2D visual output showing +1D via colour).
nonRedCRE_tested
Thoroughly tested prototype of multi-species, non-redundant, de novo CRE discovery pipeline. Publishable database and web-service in progress.
SWE_localtimesteppingscheme
local time stepping scheme for solving shallow water equation
vigilab_intergeneShareGFF
(1) Parse in a GFF file, (2) Filter only rows matching a specific type (e.g. transcript), (3) Then print a new GFF file whose "start" and "end" fields are expanded to include intergenic regions whose sharing distribution differs according to pairwise strand orientations: (i) 1/3:2/3 ratio for tail:head (+,+) strands, (ii) 2/3:1/3 for head:tail strands (-,-), and (iii) 1/2:1/2 for head:head (-,+) and tail:tail (+,-) strands
hpcleap_md
Molecular Dynamics simulation (HPC-LEAP workshop 1)
hpcleap_neuro
Neuroscience practical excercises in HPC-LEAP Thematic workshop: Computational Biology
hpcleap_ppi
Protein-protein interactions predicted between proteins of Anopheles gambiae, Plasmodium falciparum and between the proteins of the two species
isatab-generators
parsers for third-party PopBio data to munge into ISA-Tab, original author Andrew Brockman
microbiota
Microbiome analysis
SplinterBotPPI
Scrapes iPfam and Uniprot for co-complex protein-protein interactions in Anopheles gambiae and Plasmodium falciparum.
T-SNE_testing
Testing dimensionality reduction techniques useful for VB Expression map, turning into a 1D indexable vector
AK-DE-biGRU
Improving Response Selection in Multi-turn Dialogue Systems by Incorporating Domain Knowledge