Free optimization software for linux

Electronics Optimizer project is an electronics design tool for advanced optimization and design of electronic circuits - with Monte Carlo, Optimizer and Worst Case Analysis.

Electronics Optimizer helps you to quickly design a circuit (choosen from a standard library of circuits) to match your specified design parameters without drawing a schematic. Moreover Electronics Optimizer has a calculator for first-cut estimates for designers.

PDFlib is a widely used programming library which allows the programmer to generate and manipulate files in Adobes well known Portable Document Format (PDF) and integrate this ability into any application or server environment.

The project is available for all major operating environments (12 different packages) and development environments.

The new release offers a variety of new and improved functions, including a new table formatter, PDF/A output for longtime archiving, AES encryption, integrated pCOS analyzing tools, a repair and optimization mode for input PDFs, and numerous other new features.

Table formatting. The new table formatter in PDFlib 7 creates complex tables automatically. The new table formatter simplifies the process of generating PDF files with tables on the fly, such as catalogs, invoices, or database reports.

PDF/A for archiving. PDFlib is one of the first tools worldwide to generate output according to the PDF/A-1a and PDF/A-1b standards. Existing PDF/A documents can be imported by PDFlib and combined or split.

StrBio is a set of Java classes and libraries useful for development of software for computational structural biology research.

They are licenced under the LGPL.

he strbio.org classes are the basis for several published research projects, including the Pred2ary secondary structure prediction program and the ASTRAL database of protein domain sequences.

The most interesting structural biology applications included are:

Pred2ary protein secondary structure prediction
JThread protein fold prediction
ConvertProtein for interconversion of protein file formats (FASTA, PDB, MSF, ALN, CASP, DSSP, HSSP, YAPF)
Filters to exchange data with commonly used molecular biology applications (e.g., BLAST, MinArea, MODELLER)
MakeRAF tool to create the Rapid Access Format sequence maps for the ASTRAL database.

Other more general-purpose functionality that is included:

Neural network library, including Scaled Conjugate Gradient or Steepest Descent optimization
Hooke and Jeeves derivative-free global optimization algorithm
Misc mathematical objects and algorithms (vectors, matrices, etc)
Efficient string formatting using Printf-based syntax (printf, atoi, atof, etc.)

JOpt.SDK library is a routing software for Java that uses specialized genetic algorithms to calculate an optimized allocation of orders and stops to mobile resources.
The algorithm not only provides tours at minimum costs but also considers an arbitrary set of constraints for each tour. You may define your own constraints and optimization goals in order to customize JOpt.SDK to your specific planning needs or you decide to use one of our best practices addons in order to achieve a fast application of our optimization algorithms to selected industries.
JOpt.SDK can solve nearly any problem that can be classified by one of the following types:
TSP - Traveling Salesman Problem. JOpt.SDK finds the shortest or fastest path for your mobile resources
VRPTW - Vehicle routing problem with time windows - like TSP but for a set of vehicles. JOpt.SDK finds an optimal allocation of orders and stops within a vehicle fleet. It may also consider different constraints for vehicles, drivers and stops.
JOpt.SDK functionality can be accessed via Java API and thus fits seamlessly into any JAVA application. Software developers may integrate the JOpt.SDK component into their application in order to offer their customers a consistent solution including optimization of mobile workforce schedules.
Enhancements:
- The tutorial has been revised to reflect some major API changes introduced since JOpt 2.0.0.

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)

ROCK is a Distribution Build Kit. You can configure your personal build of ROCK and easily build your own distribution (see the screenshots). Rock Linux is software for managing operating environments. In a way it is a software development toolkit for building OS solutions.
The available config options include, but are not limited to:
Package Selection
You can select the packages you want to have in your Distribution. So packages you dont want or need are not build at all. A list of available packages can be found here.
Compiler and Optimization
You can select a compiler (by default gcc3) and optimization options for building your distribution. That enables you to highly optimize for your hardware. You can also build your entire distribution with the GCC Stack-Smashing Protector enabled for enhanced security.
Dietlibc
You can use dietlibc instead of the GNU LibC as your C library. That can be very useful e.g. for embedded systems.
And much more ...
Other options are: selection of an init-style, custom GNU configure options, cross-building, and much more. A major focus in the ROCK development always has been to make adding new features and config options as easy as possible.
Enhancements:
- Packages can be forked (gcc=gcc3, gcc=gcc4) to reduce code duplication.
- Packages can be split (gcc, gcc:doc, gcc:dev) to reduce necessary filesystem space after installation.
- Postinstall scripts can be run to setup the application after installation rather than after compilation.
- Every ROCK script now has a -help text.
- udev has replaced devfs.
- Toolchain compilation for cross-builds has been made easier.
- Cluster Builds, Pseudonative Builds, and Cross Builds have been made easier.
- Lots of other improvements were made, and practically all of the 1600 packages were updated.