Free biological science software for linux

American Political Science: Campaign Simulator project is a statistically based political campaign simulation game.
The Campaign Simulator is an attempt to statistically model and predict the outcome of an American presidential election.
Several users assume the roles of competitive candidates and inflict the repercussions of certain decisions on a GSS-based dataset.
The application is written in Java and supports all operating systems with a Java 1.5 VM.
Main features:
- Time is not the only limiting variable. In fact, time may not be the proper limit as most operations may be performed in tandem; an economic system that allows fund raising elements should be implemented.
- The current choices all utilize the same dataset algorithm to effect the populace in similar ways- this set of scripts should be broadened and deepened as they are too high level.
- The Python Architecture needs polishing- the internal IDE is not complete, and the ability to assign scripts to run at differing points in the lifetime of the application has yet to be created.
- The installer should place links on the desktops of Mac and Unix/Linux Systems.
- Some of the small features planned, such as a GUI for dialog creation, have been cut for the deadline and should be added.

Molecular Workbench project is a piece of free, open-source modeling software specifically designed for use in education. Powered by a set of real-time molecular simulation engines that compute and visualize the motion of particles interacting through force fields, in both 2D and 3D, it provides a simulation platform for teaching and learning science.
Many abstract concepts in physics, chemistry and biology can be dynamically visualized, and virtual experiments based on molecular simulations can be designed, limited only to your imagination.
The MW software consists of:
- a set of model builders, simulators and their associated scripting environments.
- a word processor for creating hypertext.
- an authoring system for constructing your own graphical user interfaces for your own simulations.
- an embedded-assessment system that allows you to design your own questions and collects student data.
- a special browser for you to deliver and for the users to access stuff created using the above sub-systems.
- Web services for collaboration among authors, students and teachers.
All these sub-systems are seamlessly integrated behind an easy-to-use graphical user interface. The customizability of models through the authoring system allows you to design user interfaces appropriate to your audience, without having to get them involved in the complexity of the modeling engines.

Bio::PrimarySeqI is a Perl Interface definition for a Bio::PrimarySeq.

SYNOPSIS

# Bio::PrimarySeqI is the interface class for sequences.

# If you are a newcomer to bioperl, you should
# start with Bio::Seq documentation. This
# documentation is mainly for developers using
# Bioperl.

# to test this is a seq object

$obj->isa("Bio::PrimarySeqI") ||
$obj->throw("$obj does not implement the Bio::PrimarySeqI interface");

# accessors

$string = $obj->seq();
$substring = $obj->subseq(12,50);
$display = $obj->display_id(); # for human display
$id = $obj->primary_id(); # unique id for this object,
# implementation defined
$unique_key= $obj->accession_number();
# unique biological id

# object manipulation

eval {
$rev = $obj->revcom();
};
if( $@ ) {
$obj->throw(-class => Bio::Root::Exception,
-text => "Could not reverse complement. ".
"Probably not DNA. Actual exceptionn$@n",
-value => $@);
}

$trunc = $obj->trunc(12,50);

# $rev and $trunc are Bio::PrimarySeqI compliant objects

This object defines an abstract interface to basic sequence information - for most users of the package the documentation (and methods) in this class are not useful - this is a developers only class which defines what methods have to be implmented by other Perl objects to comply to the Bio::PrimarySeqI interface. Go "perldoc Bio::Seq" or "man Bio::Seq" for more information on the main class for sequences.

PrimarySeq is an object just for the sequence and its name(s), nothing more. Seq is the larger object complete with features. There is a pure perl implementation of this in Bio::PrimarySeq. If you just want to use Bio::PrimarySeq objects, then please read that module first. This module defines the interface, and is of more interest to people who want to wrap their own Perl Objects/RDBs/FileSystems etc in way that they "are" bioperl sequence objects, even though it is not using Perl to store the sequence etc.

This interface defines what bioperl consideres necessary to "be" a sequence, without providing an implementation of this. (An implementation is provided in Bio::PrimarySeq). If you want to provide a Bio::PrimarySeq compliant object which in fact wraps another object/database/out-of-perl experience, then this is the correct thing to wrap, generally by providing a wrapper class which would inheriet from your object and this Bio::PrimarySeqI interface. The wrapper class then would have methods lists in the "Implementation Specific Functions" which would provide these methods for your object.

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating sequences, file parsers, DAS client and server suport, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.

CamSketchpad is a modern recreation of Ivan Sutherlands seminal Sketchpad program. CamSketchpad is a 2D drawing / CAD program with support for geometrical constraints and the inclusion of instances referencing other drawings.
It was written as a group project for the Cambridge University computer science undergraduate course by a team of seven people: Tom Botterill, Matthew Brown, Tom Craig, Easlyn Kirupairajah, Amit Sarna, Andrew Smee and myself.
Most of my work was on the constraint satisfaction algorithm, which took perhaps 200 hours of staring at error gradient maps, and imbued me with an enormous respect for Sutherland, whose version of Sketchpad performed as well on 60s hardware as ours does on modern computers.
CamSketchpad is far from being as complete and efficient as the original Sketchpad, but it does have all the necessary components in a rudimentary form, and is finished enough to be usable. So weve decided to release it as open source under the BSD licence, so we or others are free to tinker with it and improve its algorithms and user interface.
Main features:
- Support for containing instances of other drawings in your drawings. Unlike copies, instances will change when the original drawing changes.
- Highlighting system for displaying what will be selected / snapped to / merged / created when you click.
- Very simple interface for creating new constraints - just write a function telling CamSketchpad how far away it is from satisfying the constraint. (So when the function returns 0, the constraint is entirely satisfied.)

Nihongo Benkyo is a Japanese dictionary and learning tool for Linux and Windows.
Its goal is to provide a comprehensive application that will help you learn Japanese. It is free software licensed with GNU General Public License and provided without any warranty of any kind.
Main features:
- Is available for Windows, Linux and other Unix operating systems.
- Imports JMDict, a word dictionary with a lot of interesting metadata.
- Imports JMnedict, a proper name dictionary.
- Imports EDICT, a format in which you can find many specialized dictionaries (science, computing, etc).
- Imports Kanjidic2, a kanji dictionary with over 10,000 entries.
- Finds words from Japanese (kanji, kana, romaji) or from a translation.
- Lists results in a table for quick overview.
- Shows further details about a selected result (part of speech, similar words, dialect...).
- Scans selection from other applications.
- Keeps an history of searched words so you can go back and go forward easily.
- Has its interface translated into bulgarian, english, french, japanese and spanish.

The goal of the Parallel Virtual File System (PVFS) Project is to explore the design, implementation, and uses of parallel I/O. PVFS serves as both a platform for parallel I/O research as well as a production file system for the cluster computing community. PVFS is currently targeted at clusters of workstations, or Beowulfs.
The PVFS project is conducted jointly between The Parallel Architecture Research Laboratory at Clemson University and The Mathematics and Computer Science Division at Argonne National Laboratory.
Additional funding for the PVFS project comes from NASA Goddard Space Flight Center Code 930 and The National Computational Science Alliance through the National Science Foundations Partnerships for Advanced Computational Infrastructure.
Main features:
- Compatibility with existing binaries
- Ease of installation
- User-controlled striping of files across nodes
- Multiple interfaces, including a MPI-IO interface via ROMIO
- Utilizes commodity network and storage hardware
PVFS supports the UNIX I/O interface and allows existing UNIX I/O programs to use PVFS files without recompiling. The familiar UNIX file tools (ls, cp, rm, etc.) will all operate on PVFS files and directories as well. This is accomplished via a Linux kernel module which is provided as a separate package.
PVFS is easy to install. The Quick Start page describes how to set up a simple installation. Scripts and test applications are included to help with configuration, testing for correct operation, and performance evaluation.
PVFS stripes file data across multiple disks in different nodes in a cluster. By spreading out file data in this manner, larger files can be created, potential bandwidth is increased, and network bottlenecks are minimized. A 64-bit interface is implemented as well, allowing large (more than 2GB) files to be created and accessed.
Enhancements:
- fixes to build under redhat 2.4.20-20.9 kernel
- checks for missing headers on ancient 2.4 kernels
- removal of unused fields from metadata and control messages
- updated pvfsd rc file
- handle various combinations of redhat kernel patches
- fixes to kpvfsd that had previously been fixed in user space
- fix for sftp directory reading problems
- fix to avoid oopses on clients when bad errno values returned
- adjustments to deal wiht gcc 3.4.0 issues
- fixes to work with redhat 9
- fixes to compile kernel code for xx86_64
- updated logging intrastructure
- fixes to error reporting
- update of makefile in pvfs core
- fix to bug in pvfs_open.c where pcount < 0 caused errors
- removed duplicated code in mgr
- fix for problem with bvrecv() optimization
- more unused code removal
- adjustments to keep portland group compiler happy
- removed sd_path from metadata
- new iod.rc and mgr.rc files
- fixes to chmod
- fixes to get correct fs_ino back to clients
- multiple mtime fixes
- streamlined pvfs file detection
- shared library building
- fixed closing socket bug in iod
- reordered messaging in mgr to iods to improve concurrency
- rename fix
- improved metadata file checking
- do_access permission fixes
- fix for "iod out of space" client hang
- cleaner dead socket handling, including special handling of case where mgr would close fds that clients were using
- noninteractive mkmgrconf