What's New in Version Four
4.6692
- We now compute inst_energy with actual vector subtraction rather than converting between phase-magnitude and complex numbers.
- It's faster than ever thanks because Kidnap now caches free energy results.
- We renamed cumm_mag_phase and diff_vectors to cumm_energy and inst_energy to reflect their actual use.
- We removed stop detection due to its being obsolete.
- Performance increases as we continue vectorization and after buffering disp_shifts.m and implementing quick-fail Config.dire.
- quasiforce plots the wait times of a sequence. Don't ask me why.
- God 2.0: It's our new genetic algorithm that attempts to find the best TAV matrix given a yield criteria. In our case, we used it to find the optimal TAV values in an attempt to calibrate them according to bovine growth hormone biological data.
- Performance increases across the board as we vectorize GSPtools.
- Config.detect_stops and Config.detect_pauses controls the detection of stop codons and long wait times.
- sensitivity.m creates sensitivity plots, mainly used for Weiss genes.
- Travel2.mat replaces the old Travel.mat if you want the new values outputted from God 2.0.
- The harsher yield model is now gone, but in its place comes Deviation. You can switch back to probability via config.m.
- Extensive documentation for the Kidnap module ( Issue 3 )
- Optional arguments for megaunity and unity ( Issue 1 ); for usage, see in-file documentation.
- Model now detects stop codons and unusually long wait times (displacement.m) that we call ribosomal hyperpauses for short
- alopeciaunity.m saves polar plots in batches, similar to what opportunity.m and jejunity.m do for overlay and error bar plots
- impunity.m handles single files in addition to folders now. Try it out with impunity('prfb.txt', {'uga,25'}, {}, 100).
- free2bind, refactored to Kidnap, heavily edited (from 9000 lines to 400)
- Now extensible with other parameter modules and readable
- SantaLucia module depreciated due to lack of key subroutines
- free2bind.zip no longer a requirement for installation
- Performance increase in diff_vectors.m
What's New in Version Three
- Travel.mat memoizes nloopcalc.m and combines TAV.mat and Codons.mat, making it redundant. Huge performance increases resulted because nloopcalc was called so many times.
- dysentery.pl --rcheck
3.14
- Back frameshifts are now detected. Every function that took a forward frameshift parameter now takes a back frameshift parameter as well.
- dysentery.pl will convert amino acid primary structure sequences to codon sequences, randomly choosing codons. In addition, it verifies hand-customized codon sequences against a primary structure sequence.
- Sine and cosine in calculating window function now bounded for more accurate results.
- jejunity.m plots the average path taken by the codon in addition to error bars. It takes the same commands as opportunity.m, both displaying the same information about deviation.
3.1
- opportunity.m: Spits out superimposed displacement plots for rainy day family slideshows
- impunity.m: Puts the yields for all sequences in a folder into a results.txt file
- unity.m and megaunity.m and cornerstone.pl now web-enabled
- fabio.pl (web-enabled): Parses TAV frequencies and spits them back out in the order of Codons.mat, i.e. spits out new TAV.mat for new species
3
- Unused functions deleted but available from the archives
- fcalcmpx split up and megaunity now several times faster
- new cornerstone.pl parses Genbank search results and
- no more fudging with free2bind (Thanks, Scott!)
Why Version 1.1
We re-released with Lalit's deterministic model merged other changes we've made since 3.1, merely replacing 3.1's displacement.m. Therefore it's web-enabled and has 3.1's Perl tools and performance.