Immunology and Biology Resources and Basics

A generic Agent-Based Model (ABM) simulator (very easy to use) (by Christy Warrender and Drew Levin)

Here is a sample definition file and a sample init file. To execute simply download cycells and save the

two files in the same folder and type the following in the command line:

./CyCells -d mys29.def -i mys29.init -t 10000

The -t specifies the number of time steps that it has to run.

The simulation produces a file (test.history) which has the data from the run.

Notes by Dr. Alan Perelson on the immune system

http://sites.google.com/site/neelsoumya/immunology-resources/Perelson_Notes.pdf?attredirects=0

More notes (by yours truly) taken during a lecture in immunology modelling by Dr. Alan Perelson

http://sites.google.com/site/neelsoumya/immunology-resources/Perelson_lecture_immunesystem_modelling.pdf?attredirects=0&d=1

Yet more notes (again by yours truly) taken during a lecture by Dr. Ruy Ribeiro on mathematical modelling of Tcell labelling

http://sites.google.com/site/neelsoumya/immunology-resources/LectureRuyRibeiroTcellLabellingModels.pdf?attredirects=0&d=1

Excellent presentation and compendium on viruses (by Kimberly Kanigel at UNM, zipped file)

http://sites.google.com/site/neelsoumya/immunology-resources/Viruspresentation.ppt.zip?attredirects=0

Great resource on Dendritic Cells

Cell maturation/lineage charts

Immunology papers (great compendium)

Resources (learning material and code) for artificial immune systems

Compendium of complex networks papers

Epidemic and immunological datasets (MIDAS website, link1 and link2)

GWAS (link)

Biology basics (link)

Genetics basics (link)

List of data fitting software

1) Berkeley Madonna