| 2015-07-27 |
Dariusz Murakowski | Add options for separate inverse temperature (beta... nonMC_send |
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| 2015-07-21 |
Dariusz Murakowski | Add option to initialize state completely randomly. |
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| 2015-07-16 |
Dariusz Murakowski | Uniform random integer generation (by rejection sampling). |
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| 2015-07-16 |
Dariusz Murakowski | Clean up trailing ^M characters. |
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| 2015-07-16 |
Dariusz Murakowski | Optionally track relative contribution to energy from... |
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| 2015-07-16 |
Dariusz Murakowski | Close file handles only when opened. Add make flag... |
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| 2015-07-06 |
Dariusz Murakowski | Add `make` rule for MC code. |
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| 2015-07-06 |
Dariusz Murakowski | Code for doing Potts Monte Carlo (optionally with fixed... |
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| 2015-06-26 |
Dariusz Murakowski | (minor) Don't build old Monte Carlo code. Print to... |
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| 2015-06-26 |
Dariusz Murakowski | Add secret help option (--help-rates) to show meaning... |
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| 2015-06-26 |
Dariusz Murakowski | Add command-line option/flag to flush each output line... |
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| 2015-06-26 |
Dariusz Murakowski | Counter (dummy species) for viruses that have escaped... |
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| 2015-06-26 |
Dariusz Murakowski | Only add reactions with non-zero rate constants. |
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| 2015-06-26 |
Dariusz Murakowski | Document goto/come-from(-like) behavior. Clean up junk... |
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| 2015-06-25 |
Dariusz Murakowski | Check number of inserted sites. Use unsigned int instea... |
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| 2015-06-25 |
Dariusz Murakowski | Proper indexing for multiple (>1) redundant sites. |
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| 2015-06-25 |
Dariusz Murakowski | Copy J matrix in blocks, padding with empty entries. |
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| 2015-06-23 |
Dariusz Murakowski | WIP attempt to insert dummy sites into J for degenerate... |
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| 2015-06-23 |
Dariusz Murakowski | Add some bounds-checking to the couplings-array accesse... |
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| 2015-06-23 |
Dariusz Murakowski | Define state2aa properly. |
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| 2015-06-23 |
Dariusz Murakowski | Implement write_mod and esc_all for non-epitope WF... |
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| 2015-06-23 |
Dariusz Murakowski | Numerical stability modification to sigmoid function... |
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| 2015-06-23 |
Dariusz Murakowski | Cosmetic changes to comments, format, and spacing. |
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| 2015-06-17 |
Dariusz Murakowski | Implement write_mod and esc_all for non-epitope WF... |
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| 2015-06-17 |
Dariusz Murakowski | Make only `wf` (Wright-Fisher code). |
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| 2015-06-17 |
Dariusz Murakowski | Numerical stability modification to sigmoid function... |
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| 2015-06-17 |
Dariusz Murakowski | Cosmetic changes to comments, format, and spacing. |
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| 2015-06-17 |
Dariusz Murakowski | Remove two-site Hamiltonian. |
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| 2015-06-15 |
Dariusz Murakowski | :retab (replace \t with normal whitespace). |
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| 2015-06-12 |
Dariusz Murakowski | Rescale rates by system volume ratio (parameter). |
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| 2015-05-14 |
Dariusz Murakowski | CTL killing reactions are smart about virus-changing... |
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| 2015-05-09 |
Dariusz Murakowski | Recalculate differently based on what reaction caused... |
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| 2015-05-09 |
Dariusz Murakowski | Test script for Potts code. |
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| 2015-05-07 |
Dariusz Murakowski | Clean up extra debug printing. |
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| 2015-05-07 |
Dariusz Murakowski | Fix some dependents. Modify total propensity instead... |
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| 2015-05-06 |
Dariusz Murakowski | Handle dependencies between reactions, only recalculati... |
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| 2015-05-06 |
Dariusz Murakowski | Option to print trajectory every N steps. |
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| 2015-05-01 |
Dariusz Murakowski | Allow passing script names into unit test runner. ... |
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| 2015-05-01 |
Dariusz Murakowski | Unit testing for Ising using compensatory landscape... |
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| 2015-05-01 |
Dariusz Murakowski | Copy constructor for Virus and NTVirus object to reduce... |
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| 2015-05-01 |
Dariusz Murakowski | Fix subtle rare bug involving next timestep = infinity... |
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| 2015-04-29 |
Dariusz Murakowski | Firing the viral growth/death reactions should probably... |
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| 2015-04-29 |
Dariusz Murakowski | Terminally differentiated effector cell needs additiona... |
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| 2015-04-28 |
Dariusz Murakowski | ctags -a -R |
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| 2015-04-28 |
Dariusz Murakowski | Reactions accounting for propagation of CTL divisions. |
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| 2015-04-28 |
Dariusz Murakowski | Framework for multiple divisions (i.e. generations... |
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| 2015-04-27 |
Dariusz Murakowski | Swap M and T in setting up CTL reactions (Ising). |
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| 2015-04-27 |
Dariusz Murakowski | Set up reactions for CTLs recognizing amino acids. |
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| 2015-04-27 |
Dariusz Murakowski | Import Potts epitope (amino acid sequence). Helper... |
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| 2015-04-24 |
Dariusz Murakowski | Save mapping of Potts state to amino acid as well.... |
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| 2015-04-24 |
Dariusz Murakowski | Initialize distribution of nt seqs from file. Print... |
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| 2015-04-24 |
Dariusz Murakowski | Start runtime framework for executing Potts system... |
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| 2015-04-24 |
Dariusz Murakowski | Fix the build: delete all the temporary testing stuff. |
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| 2015-04-24 |
Dariusz Murakowski | Define all the reactions for Potts virus, handling... |
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| 2015-04-24 |
Dariusz Murakowski | Map the nt enum to and from character representation. |
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| 2015-04-24 |
Dariusz Murakowski | Construct recognizer from epitope string (and starting... |
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| 2015-04-24 |
Dariusz Murakowski | CTL for recognizing arbitrary amino acid sequence as... |
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| 2015-04-24 |
Dariusz Murakowski | Potts state mapping+tracking complete. Fix bounds check... |
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| 2015-04-24 |
Dariusz Murakowski | Significant speed-up by inlining GSL RNG functions... |
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| 2015-04-24 |
Dariusz Murakowski | Copy over code to read seq2state file, which gives... |
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| 2015-04-24 |
Dariusz Murakowski | Start of Potts / amino acid / nucleotide-based virus... |
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| 2015-04-24 |
Dariusz Murakowski | Avoid multiple defs of translators by only declaring... |
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| 2015-04-24 |
Dariusz Murakowski | Scrap enum class definitions. Clean up seqTools. |
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| 2015-04-23 |
Dariusz Murakowski | Copy seqTools.cpp to seqTools.h for inclusion to main. |
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| 2015-04-23 |
Dariusz Murakowski | Break normal functionality for testing! Separate beta... |
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| 2015-04-23 |
Dariusz Murakowski | Solve warning about comparison between signed and unsig... |
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| 2015-04-23 |
Dariusz Murakowski | Copy John's Potts code from snip.{cpp,h}. |
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| 2015-04-23 |
Dariusz Murakowski | Decipher Potts encoding of sequence state/configuration. |
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| 2015-04-22 |
Dariusz Murakowski | WF: correctly use init pop frac. |
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| 2015-04-22 |
Dariusz Murakowski | Testing nucleotide <-> amino acid translation. Needs... |
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| 2015-04-22 |
Dariusz Murakowski | Remove mutation rate "mu" from Virus object; now exclus... |
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| 2015-04-21 |
Dariusz Murakowski | Update Makefile with header dependencies. |
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| 2015-04-21 |
Dariusz Murakowski | Multiple runs, more rate args, end simulation when... |
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| 2015-04-21 |
Dariusz Murakowski | Print virus species sequence when verbose. |
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| 2015-04-21 |
Dariusz Murakowski | Formatting: retab, clean whitespace. |
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| 2015-04-21 |
Dariusz Murakowski | Delete unused functions for SS. |
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| 2015-04-21 |
Dariusz Murakowski | Clarify dependencies. Copy hamiltonian.{cpp,h} to ham_s... |
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| 2015-04-21 |
Dariusz Murakowski | Virus reproduction reaction stores its own mutation... |
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| 2015-04-21 |
Dariusz Murakowski | Free memory from species and reaction arrays (to satisf... |
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| 2015-04-21 |
Dariusz Murakowski | Proper species names. Initial counts CTL counts for... |
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| 2015-04-18 |
Dariusz Murakowski | Output at intervals, remove more WF. |
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| 2015-04-17 |
Dariusz Murakowski | Clean out WF-only stuff. |
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| 2015-04-17 |
Dariusz Murakowski | Full system, including parameters. |
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| 2015-04-09 |
Dariusz Murakowski | Initialize multiple CTL clones+epitopes. Output at... |
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| 2015-04-09 |
Dariusz Murakowski | Separate function for running the dynamics. |
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| 2015-04-09 |
Dariusz Murakowski | Framework for killing by CTL. |
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| 2015-04-09 |
Dariusz Murakowski | Flesh out reactions for virus reproduction (with mutati... |
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| 2015-04-09 |
Dariusz Murakowski | Start of Gillespie test. |
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| 2015-03-20 |
Dariusz Murakowski | ctags -a -R |
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| 2015-03-20 |
Dariusz Murakowski | ctags |
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| 2015-03-06 |
Dariusz Murakowski | Code to read Potts coupling parameters and calculate... |
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| 2014-11-24 |
Dariusz Murakowski | Actually do (and document) multiple runs without epitop... |
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| 2014-11-20 |
Dariusz Murakowski | (cosmetic) Personalized RunParameters for stochastic... |
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| 2014-11-20 |
Dariusz Murakowski | Monte Carlo simulation of Boltzmann-distributed energy... |
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| 2014-11-12 |
Dariusz Murakowski | Fix sorted_vector compile errors (presumably due to... |
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| 2014-08-20 |
Dariusz Murakowski | STL compliant sorted vector class (std::map replacement... |
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| 2014-04-26 |
Dariusz Murakowski | Command line parameter for bonus/penalty applied to... |
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| 2014-04-17 |
Dariusz Murakowski | Print supplementary output file (*.sum) with CSV sequence. |
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| 2014-04-17 |
Dariusz Murakowski | Detect when escape from *all* epitopes (vs *any* immune... |
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| 2014-04-17 |
Dariusz Murakowski | GSL {headers,libraries} on lc2 are in default search... |
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