projects / VirEvoDyn.git / shortlog
? search:
summary | shortlog | log | commit | commitdiff | tree
first ⋅ prev ⋅ next
VirEvoDyn.git
2015-04-23 Dariusz MurakowskiCopy seqTools.cpp to seqTools.h for inclusion to main. commit | commitdiff | tree | snapshot
2015-04-23 Dariusz MurakowskiBreak normal functionality for testing! Separate beta... commit | commitdiff | tree | snapshot
2015-04-23 Dariusz MurakowskiSolve warning about comparison between signed and unsig... commit | commitdiff | tree | snapshot
2015-04-23 Dariusz MurakowskiCopy John's Potts code from snip.{cpp,h}. commit | commitdiff | tree | snapshot
2015-04-23 Dariusz MurakowskiDecipher Potts encoding of sequence state/configuration. commit | commitdiff | tree | snapshot
2015-04-22 Dariusz MurakowskiWF: correctly use init pop frac. commit | commitdiff | tree | snapshot
2015-04-22 Dariusz MurakowskiTesting nucleotide <-> amino acid translation. Needs... commit | commitdiff | tree | snapshot
2015-04-22 Dariusz MurakowskiRemove mutation rate "mu" from Virus object; now exclus... commit | commitdiff | tree | snapshot
2015-04-21 Dariusz MurakowskiUpdate Makefile with header dependencies. commit | commitdiff | tree | snapshot
2015-04-21 Dariusz MurakowskiMultiple runs, more rate args, end simulation when... commit | commitdiff | tree | snapshot
2015-04-21 Dariusz MurakowskiPrint virus species sequence when verbose. commit | commitdiff | tree | snapshot
2015-04-21 Dariusz MurakowskiFormatting: retab, clean whitespace. commit | commitdiff | tree | snapshot
2015-04-21 Dariusz MurakowskiDelete unused functions for SS. commit | commitdiff | tree | snapshot
2015-04-21 Dariusz MurakowskiClarify dependencies. Copy hamiltonian.{cpp,h} to ham_s... commit | commitdiff | tree | snapshot
2015-04-21 Dariusz MurakowskiVirus reproduction reaction stores its own mutation... commit | commitdiff | tree | snapshot
2015-04-21 Dariusz MurakowskiFree memory from species and reaction arrays (to satisf... commit | commitdiff | tree | snapshot
2015-04-21 Dariusz MurakowskiProper species names. Initial counts CTL counts for... commit | commitdiff | tree | snapshot
2015-04-18 Dariusz MurakowskiOutput at intervals, remove more WF. commit | commitdiff | tree | snapshot
2015-04-17 Dariusz MurakowskiClean out WF-only stuff. commit | commitdiff | tree | snapshot
2015-04-17 Dariusz MurakowskiFull system, including parameters. commit | commitdiff | tree | snapshot
2015-04-09 Dariusz MurakowskiInitialize multiple CTL clones+epitopes. Output at... commit | commitdiff | tree | snapshot
2015-04-09 Dariusz MurakowskiSeparate function for running the dynamics. commit | commitdiff | tree | snapshot
2015-04-09 Dariusz MurakowskiFramework for killing by CTL. commit | commitdiff | tree | snapshot
2015-04-09 Dariusz MurakowskiFlesh out reactions for virus reproduction (with mutati... commit | commitdiff | tree | snapshot
2015-04-09 Dariusz MurakowskiStart of Gillespie test. commit | commitdiff | tree | snapshot
2015-03-20 Dariusz Murakowskictags -a -R commit | commitdiff | tree | snapshot
2015-03-20 Dariusz Murakowskictags commit | commitdiff | tree | snapshot
2015-03-06 Dariusz MurakowskiCode to read Potts coupling parameters and calculate... commit | commitdiff | tree | snapshot
2014-11-24 Dariusz MurakowskiActually do (and document) multiple runs without epitop... commit | commitdiff | tree | snapshot
2014-11-20 Dariusz Murakowski(cosmetic) Personalized RunParameters for stochastic... commit | commitdiff | tree | snapshot
2014-11-20 Dariusz MurakowskiMonte Carlo simulation of Boltzmann-distributed energy... commit | commitdiff | tree | snapshot
2014-11-12 Dariusz MurakowskiFix sorted_vector compile errors (presumably due to... commit | commitdiff | tree | snapshot
2014-08-20 Dariusz MurakowskiSTL compliant sorted vector class (std::map replacement... commit | commitdiff | tree | snapshot
2014-04-26 Dariusz MurakowskiCommand line parameter for bonus/penalty applied to... commit | commitdiff | tree | snapshot
2014-04-17 Dariusz MurakowskiPrint supplementary output file (*.sum) with CSV sequence. commit | commitdiff | tree | snapshot
2014-04-17 Dariusz MurakowskiDetect when escape from *all* epitopes (vs *any* immune... commit | commitdiff | tree | snapshot
2014-04-17 Dariusz MurakowskiGSL {headers,libraries} on lc2 are in default search... commit | commitdiff | tree | snapshot
2014-04-17 Dariusz MurakowskiAllow calculating energy without including epitope... commit | commitdiff | tree | snapshot
2014-04-11 Dariusz MurakowskiUpdate unit tests. Add new one with simple two-site... commit | commitdiff | tree | snapshot
2014-04-11 Dariusz MurakowskiPrint sequence as CSV (comma-separated). commit | commitdiff | tree | snapshot
2014-04-10 Dariusz MurakowskiUpdate unit tests. commit | commitdiff | tree | snapshot
2014-03-20 Dariusz MurakowskiSpread total immune pressure strength uniformly over... commit | commitdiff | tree | snapshot
2014-03-13 Dariusz MurakowskiStart of Monte Carlo (static epitope calculation),... commit | commitdiff | tree | snapshot
2014-03-13 Dariusz MurakowskiDon't fflush population-writing each time. commit | commitdiff | tree | snapshot
2014-03-06 Dariusz MurakowskiPrint generation number on each line. (Need to update... commit | commitdiff | tree | snapshot
2014-02-17 Dariusz MurakowskiTest all one- and two-epitope cases of WT/mut site... commit | commitdiff | tree | snapshot
2014-02-17 Dariusz MurakowskiMore comprehensive test framework. commit | commitdiff | tree | snapshot
2014-02-17 Dariusz MurakowskiCorrectly parse multiple epitopes per file (using C... commit | commitdiff | tree | snapshot
2014-02-17 Dariusz MurakowskiUnit test for multiple-epitope input file. commit | commitdiff | tree | snapshot
2014-02-17 Dariusz MurakowskiMultiple epitopes; one per line in .ep file. All have... commit | commitdiff | tree | snapshot
2014-02-17 Dariusz MurakowskiUse '|' as epitope mut/WT field list separator (on... commit | commitdiff | tree | snapshot
2014-02-17 Dariusz MurakowskiUpdate unit tests for separate .st and .ep files. commit | commitdiff | tree | snapshot
2014-02-17 Dariusz MurakowskiRead population state and epitopes from separate files. commit | commitdiff | tree | snapshot
2014-02-13 Dariusz MurakowskiExtra output and tests for debugging. commit | commitdiff | tree | snapshot
2014-02-13 Dariusz MurakowskiStart framework for targeting multiple epitopes. commit | commitdiff | tree | snapshot
2014-02-04 Dariusz MurakowskiBasic unit testing framework. commit | commitdiff | tree | snapshot
2014-02-04 Dariusz MurakowskiCheck for file-opening / existence errors (vs segfault... commit | commitdiff | tree | snapshot
2013-09-26 Dariusz MurakowskiAdd write_mod option to write population at regular... commit | commitdiff | tree | snapshot
2013-09-16 Dariusz MurakowskiLocate segfault for small N (population size = 0).... commit | commitdiff | tree | snapshot
2013-05-17 Dariusz MurakowskiSpecial two-site + two-allele (two-locus + binary)... commit | commitdiff | tree | snapshot
2013-05-15 Dariusz MurakowskiMore output for non-epitope runs. Assuage compiler... commit | commitdiff | tree | snapshot
2013-05-14 Dariusz MurakowskiWright-Fisher code by Tom Butler (via John Barton). commit | commitdiff | tree | snapshot
2013-05-14 Dariusz MurakowskiJust use the GNU Scientific Library (GSL) for RNG.... commit | commitdiff | tree | snapshot
2013-04-05 Dariusz MurakowskiAdd Mersenne Twister RNG library/header. Generalize... commit | commitdiff | tree | snapshot
2013-04-05 Dariusz MurakowskiPrint mutset_t (to stream using operator<<) as CSV... commit | commitdiff | tree | snapshot
2013-04-05 Dariusz MurakowskiStart of Wright-Fisher dynamics using STL. Mutations... commit | commitdiff | tree | snapshot
VirEvoDyn simulates viral evolutionary dynamics with a full fitness landscape.