Free optimization software software for linux

Optimization Algorithm Toolkit is a workbench and toolkit for developing, evaluating, and playing with classical and state-of-the-art optimization algorithms on standard benchmark problem domains; including reference algorithm implementations, graphing, visualizations and much more. The project was developed initially by Jason Brownlee as a part of his Ph.D. program.
The goal of this project is to deliver obscure-and-prevalent, old-and-new optimization algorithms from research literature to both research scientists and algorithm practitioners alike. Algorithms include biologically inspired approaches such as evolutionary algorithms (genetic algorithms), swarm algorithms (ants and particle swarm), and immune system algorithms.
Also included are more conventional approaches such as approaches inspired by physics including simulated annealing and extremal optimization. Problem domains include numerical function optimization, traveling salesman problems, and protein folding all with many standard benchmark instances taken from research literature.
A user-friendly graphical interface is provided to rapidly evaluate and compare algorithm and problem configurations, visualize algorithm behavior, and graph algorithm performance over time. A robust, modular, and extensible framework underlies the platform to facilitate the easy addition and modification of algorithms, addition of new problem domains and problem instances as well as facilitate more advanced algorithm experimentation.
The algorithm implementations are extensible and easily support modification and applicaition to varied problem domains. Please report any bugs, feature requests or include your own algorithms by accessing the services on the project home website. This is an open source project (released under the GPL) so the source code is available. The project was compiled with Java 1.5 (update 9).
Enhancements:
- This release includes many framework and graphical interface fixes, as well as a few new algorithms to play with.

Fruit Show is a minimalist forum package based on the forums at joelonsoftware.com. Fruit Show is based on the philosophy that social atmosphere is a by-product of software design.
Theres no registration and very few features for visitors. Its skinnable and easy to install. It also contains some unique moderation features.
Fruit Show is intended for small sites that need an easy to use and accessible forum.
Enhancements:
- This release of FruitShow fixes a large number of issues and makes a few improvements to IIS support and support for PHP5.
- Smarter topic locking and improved optimization were added.

PIC USB Framework is a USB application framework dedicated to Linux (on the host side) and to the PIC 18F4550 family of microcontrollers (on the device side).
PUF includes: a bootloader that can flash the PIC application through the USB, a PIC demo and its corresponding application on the host side, and docker, the host-side flash programming utility.
The PUF also contains gputils and sdcc as cross-building tools, and odyssey 0.4vasco as a parallel port PIC programmer.
Enhancements:
- sdcc optimization flags are now switched on by default.
- A component library (including a console mechanism and a small real time scheduler) has been added to help building user applications.
- Tools have been upgraded to automake 1.9.6, autoconf 2.59d, sdcc snapshot 4482, odyssey 0.5, and gputils 0.13.4.
- The applications size has been optimized.

Combean project is a Java framework for combinatorial structures like graphs or linear programs and optimization algorithms working with these structures.
The objective of Combean is to integrate existing proven optimization packages as well as new implementations through a set of lean Java interfaces. Using a JavaBeans-based configuration mechanism, solvers for real-world optimization problems can be generated by plugging together the best-performing components.
Combean as glue between optimization packages leads to more interoperable, adaptable and flexible solutions.
Main features:
- You develop software that uses optimization technology. You would like to use existing optimization codes and you are looking for a possibility to easily integrate your code with them. You want to be flexible to exchange one solver with another as your project moves forward.
- You have written a library that provides data structures or algorithms for optimization problems (combinatorial optimization or mathematical programming). Now you are searching for a way to integrate your library with other existing frameworks and to improve the interoperability of your library.
- You want to use linear programming to solve a real world application and you would like to transform your optimization problem into a linear programming model that is easy to use and compatible with many existing solvers (both open source and commercial).
- You are teaching optimization algorithms and you are searching for a programming framework which integrates standard data structures and algorithms and a way that captures the essence of the optimization problem and results in clear code.

TuxGuitar is a multitrack guitar tablature editor and player. TuxGuitar project can open GP3 and GP4 files.
Main features:
- Fixed a bug in tTablature editor
- Multitrack display
- Autoscroll while playing
- Note duration management
- Various effects (bend, slide, vibrato, hammer-on/pull-off)
- Support for triplets (5,6,7,9,10,11,12)
- Repeat open and close
- Time signature management
- Tempo management
- Imports and exports gp3 and gp4 files
If you make use of TuxGuitar, youll find it to be a complete program for editing, listening, learning or even writing a complete song... youll be able to realize your dream of playing with style and accuracy all the stuff that you ever wanted to.unning when you select a percusion track
Enhancements:
- Piano editor
- Lyric editor
- Music Scales
- Simple Score edition
- Custom Chords
- Customize ToolBars
- Metronome
- Memory Optimization when song is playing
- Print layout changes: Tablature and Score enabled/disabled options, Measure range.
- Dynamics
- Increment-Decrement Semitones.
- Shift Up/Down
- New Effects: Tremolo Bar, Harmonics, Grace note, Trill, Tremolo Picking, Ghost note, Accentuated, Heavy Accentuated, Palm mute, Staccato, Tapping, Slapping, Popping, Fade In.

Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search.

Parameters:

fasta (Excl)
Fasta program

query (Sequence)
Query sequence File
pipe: seqfile

seqtype (Excl)
Is it a DNA or protein sequence (-n)

protein_db (Excl)
Protein Database

nucleotid_db (Excl)
Nucleotid Database

break_long (Integer)
Break long library sequences into blocks (-N)

ktup (Integer)
ktup : sensitivity and speed of the search (protein:2, DNA:6)

optcut (Integer)
OPTCUT : the threshold for optimization. (-c)

gapinit (Integer)
Penalty for gap initiation (-12 by default for fasta with proteins, -16 for DNA) (-f)

gapext (Integer)
Penalty for gap extention (-2 by default for fasta with proteins, -4 for DNA) (-g)

high_expect (Float)
Maximal expectation value threshold for displaying scores and alignments (-E)

low_expect (Float)
Minimal expectation value threshold for displaying scores and alignments (-F)

nucleotid_match (Integer)
Reward for a nucleotid match (-r)

nucleotid_mismatch (Integer)
Penalty for a nucleotid mismatch (-r)

matrix (Excl)
Scoring matrix file (-s)

X_penalty (Integer)
Penalty for a match to X (independently of the PAM matrix) (-x)

frameshift (Integer)
Penalty for frameshift between codon (fast[xy]/tfast[xy])(-h)

frameshift_within (Integer)
Penalty for frameshift within a codon (fasty/tfasty)(-j)

threeframe (Switch)
Search only the three forward frames (tfasta) (-3)

invert (Switch)
Reverse complement the query sequence (all tfasta) (-i)

genetic_code (Excl)
Use genetic code for translation (tfasta/tfast[xy]/fast[xy]) (-t)

band (Integer)
band-width used for optimization (-y)

swalig (Switch)
unlimited Smith-Waterman alignment for DNA (-A)

noopt (Switch)
no limited optimization (-o)

stat (Excl)
Specify statistical calculation. (-z)

random (Switch)
Estimate stat parameters from shuffled copies of each library sequence (-z)

histogram (Switch)
No histogram (-H)

scores (Integer)
number of similarity scores to be shown (-b)

alns (Integer)
number of alignments to be shown (-d)

html_output (Switch)
HTML output (-m)

markx (Excl)
Alternate display of matches and mismatches in alignments

init1 (Switch)
sequences ranked by the z-score based on the init1 score (-1)

z_score_out (Excl)
Show normalize score as (-B)

showall (Switch)
both sequences are shown in their entirety in alignments (fasta only) (-a)

linlen (Integer)
output line length for sequence alignments (max. 200) (-w)

offsets (String)
Start numbering the aligned sequences at position x1 x2 (2 numbers) (-X)

info (Switch)
Display more information about the library sequence in the alignment (-L)

statfile (OutFile)
Write out the sequence identifier, superfamily number, and similarity scores to this file (-R)

filter (Switch)
Lower case filtering (-S)

outfile (OutFile)
pipe: mview_input

html_outfile (OutFile)

CGI::Minimal is a lightweight CGI form processing package.

SYNOPSIS

# use CGI::Minimal qw(:preload);
use CGI::Minimal;

my $cgi = CGI::Minimal->new;
if ($cgi->truncated) {
&scream_about_bad_form;
exit;
}
my $form_field_value = $cgi->param(some_field_name);

Provides a micro-weight alternative to the CGI.pm module
Rather than attempt to address every possible need of a CGI programmer, it provides the _minimum_ functions needed for CGI such as form decoding (including file upload forms), URL encoding and decoding, HTTP usable date generation (RFC1123 compliant dates) and basic escaping and unescaping of HTMLized text.

The :preload use time option is used to force all sub-component modules to load at compile time. It is not required for operation. It is solely a performance optimization for particular configurations. When used, it preloads the dehtmlize, param_mime, param_filename, date_rfc1123, url_decode, calling_parms_table and parameter setting supporting code. Those code sections are normally loaded automatically the first time they are needed.

The form decoding interface is somewhat compatible with the CGI.pm module. No provision is made for generating HTTP or HTML on your behalf - you are expected to be conversant with how to put together any HTML or HTTP you need.