Free bioinformatics software for linux

The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems.

What we are trying to do is to create a framework for testing, and a core set of tests that all may download and use to probe specific elements of systems performance.

Moreover, the source to these tests are available under GPL, and are hosted on Bioinformatics.org and Scalable Informatics LLC The idea is to enable end users, consumers, systems developers, and others to easily build and use meaningful tests for measurement and tuning reasons.

Joe Landman from Scalable Informatics LLC conceived the idea and wrote the original codes. We are looking for additional benchmark code suggestions, tests, data sets, etc.

Current baseline tests are several NCBI BLAST runs, several HMMer runs, and a variety of others. We plan to include ClustalW, X!Tandem, various chemistry, dynamics, and related tests, as well as several others.

Tests such as LINPACK or HPL simply do not provide meaningful performance indicators or predictive models for high performance informatics. Unfortunately, nor do a number of more recent and focused tests.

This is a problem as LINPACK and HPL specifically test the performance on various matrix operations, where you have effectively regular memory access patterns, and specific mathematical operations.

These codes are most useful for comparison to codes with heavy floating point operations, and interleaved memory traffic. These codes were not designed for comprehensive systems benchmarking, where disk I/O, memory latency, and other factors all contribute to the performance issues.

The best tests are the ones that are most similar to the codes you will run on the machine. The tests themselves should be reasonable approximations to a real execution of your code, using real data. You may need to pare it back in order to get realistic run times.

You should have a reasonable subset of data sizes. A single test does not tell you how your system scales, and one of the reasons for the existance of this test is specifically to allow you to test the performance while you increase various aspects of the workload.

You rarely get a quiescent system in a cluster, so we would recommend that you try to run in as realistic an operating environment as possible. A baseline in a quiescent system is fine, but it may set your expectations unreasonably.
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NeoBio project consists of Bioinformatics algorithms in Java.

What algorithms? The current version consists mainly of (pairwise) sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch (global alignment) and Smith & Waterman (local alignment).

Anything else? Yes, a more efficient approach, due to Crochemore, Landau and Ziv-Ukelson is also available.

It uses Lempel-Ziv compression to speed-up the computation of the dynamic programming matrix. It also relies on the SMAWK algorithm, due to Aggarwal et al., that computes all column maxima of a totally monotone matrix in linear time.

Hum... And all sequence alignment algorithms support simple scoring schemes as well as substitution matrices such as standard BLOSUM and PAM matrices. But so far they support constant gap penalty functions only.

Future versions may contain related algorithms such as multiple sequence alignment, database search and protein structure prediction.

Wow...Last but not least, NeoBio also provides a simple GUI and command line based tools to run the sequence alignment algorithms on DNA and protein sequences.

Bioperl project is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS).
On the other hand, bioperl does provide reusable perl modules that facilitate writing perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.
In order to take advantage of bioperl, the user needs a basic understanding of the perl programming language including an understanding of how to use perl references, modules, objects and methods. If these concepts are unfamiliar the user is referred to any of the various introductory or intermediate books on perl.
Weve liked S. Holzmers Perl Core Language, Coriolis Technology Press, for example. This tutorial is not intended to teach the fundamentals of perl to those with little or no experience in the perl language. On the other hand, advanced knowledge of perl - such as how to write a object-oriented perl module - is not required for successfully using bioperl.
Bioperl is open source software that is still under active development. The advantages of open source software are well known. They include the ability to freely examine and modify source code and exemption from software licensing fees.
However, since open source software is typically developed by a large number of volunteer programmers, the resulting code is often not as clearly organized and its user interface not as standardized as in a mature commercial product.
In addition, in any project under active development, documentation may not keep up with the development of new features. Consequently the learning curve for actively developed, open source source software is sometimes steep.
Enhancements:
- Many bugfixes and enhancements were made, including support for parsing the latest NCBI BLAST text format changes, PAML 3.15 support, a Taxonomy (Bio::Species) overhaul, a Bio::Map overhaul, a Bio::SearchIO speedup, the introduction of a Build.PL installation system, and fixes for some memory leaks in Bio::Tree.
- This version requires Perl 5.6.1 or later.

RepeatFinder project is a console-based bioinformatics tool that searches for repeating stretches of DNA.

It allows mismatches, but enforces a one to one mapping between sections of DNA and a repeat motif, meaning that a section of DNA cannot be associated with more than one match.

RepeatFinder, after a couple of years of private lab use, is now available for public consumption!

RepeatFinder is a tool for finding repeating segments of DNA called motifs and then parsing them so that no repeating segments overlap - it is an exclusive matching algorithm where any part of the original DNA string is associated with one and only one match.

RepeatFinder has been written to compile and run on Linux and Windows. The source code has been designed to have a minimum of requirements so if you can compile a C program, then hopefully RepeatFinder will work for you even if your OS isnt one of the above. Let me know if you succesfully compile RepeatFinder on another platform.

Further details about the algorithm and how to use the command line tools will be added to this site in due time. In the mean time the first release, 1.0.0, is available for download here. Only source, x86 and x64 linux binaries are currently available. Windows binaries coming soon!

CLC Free Workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management, combined with excellent graphical viewing and output options.
Main features:
- GenBank searching and viewing (linear and circular views)
- Multiple alignment of DNA, RNA and proteins (2 alignment algorithms)
- Open reading frame determination
- Translation from DNA to proteins (all genetic translation tables)
- Reports with residue composition, molecular weight and iso electric point (for proteins)
- Neighbor-joining and UPGMA phylogenies
- Restriction site analysis and viewing
- Other reporting facilities
- Import/export to a number of data formats
- Launch of external files
- Detailed History Log

Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry.
It has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling software. VigyaanCD v0.1 is based on KNOPPIX v3.3.
At present the following ready to use software comes on VigyaanCD: Artemis, Bioperl, BLAST (NCBI-tools), ClustalX, Cn3D, EMBOSS tools, Garlic, GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, Jmol, MPQC, NJPlot, Open Babel, Octave, PSI3, PyMOL, Rasmol, Raster3D, SMILE, TINKER, XDrawChem, Xmgr and Xfig. GNU C/C++/Fortran compilers and additional Linux tools (such as ps2pdf) are also available.
VigyaanCD also provides tools required to compile and install other applications (from source). Therefore, making testing of Linux applications possible on computers with other OS.
Enhancements:
- This release is based on KNOPPIX 3.7.
- Most software packages have been updated and new applications added.

EnsEMBL::Web::Record is a family of modules used for managing a users persistant data in a database.

SYNOPSIS

Many web sites now encourage users to register and login to access more advanced features, and to customise a site to their needs.

The EnsEMBL::Web::Record group of Perl modules is design to manage any arbitrary type of user created data in an SQL database. This module follows the Active Record design pattern, in that each new instantiated Record object represents a single row of a database.

That object can be manipulated programatically, and any changes made can be stored in the database with a single record->save function call.

Because arbitrary Perl data structures can be stored in this manner, EnsEMBL::Web::Record allows user preferences to be easily saved, and allows developers to implement new featurs quickly.

This module was first used (and has been abstracted from) the Ensembl genome browser (http://www.ensembl.org).

New user data can be added to the database:

use EnsEMBL::Web::Record;

my $bookmark = EnsEMBL::Web::Record->new();
$bookmark->url(http://www.ensembl.org);
$bookmark->name(Ensembl);
$bookmark->save;
...

The Record can be associated with an user id:

$record->user($id);

The same record can also be removed:

$bookmark->delete;

EnsEMBL::Web::Record also provides a number of methods for getting collections of records from the database, using a field selector.

EnsEMBL::Web::Record::find_bookmarks_by_user_id($id).

DNALinux is a Linux distribution with bioinformatics software pre-installed.
We believe that this distro fills an empty niche. Specialized biotech software usually is released as source code only and its not packaged for easy installation on "mainstream" Linux.
Most scientific software is "author software" and it is not easy to install (that is particulary true for Biotech people). As we told before, all the software is pre-installed. Since the distro works from CD, you dont even have to install the operation system.
Since is a live-CD, no permanent changes can be made to your system (unless you make a hard disk install). Its not easy to apply a security patch to this kind of distros, thats why you shouldnt used under a "raw" (unprotected) Internet conection.
So you are advised to use it inside a trusted network.If you want a Linux distro to act as a firewall, we recommend SmoothWall.
Enhancements:
- The server edition features a live NCBI BLAST server.
- The H5N1 genomic sequence is included, but you can install you own sequence database.
- This version is based on Slax 5.10 and Apache 2.