Free kingdoms biology software for linux

Defend the Kingdom project is a real-time strategy based game.

Defend The Kingdom, or Defender for short, is a real time strategy game dedicated to the fantastic world of LARP.

Its goals include the ability to build and control a complete fantasy world (with towns, poeple, etc.), control armies of knights and creatures to fight against your strongest enemies, gain power and resources by trading with your friends, and many more.

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.)

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.

ToBiX is a Morphix-based Linux live CD containing a range of specialist applications for bioinformatics. With this distrubution you just boot from the CD and you have a fully functional LINUX OS distribution with open source applications.
Besides using some RAM, ToBiX doesnt touch the host computer and is ideal for presentations, workshops or other learning or scientific activity on bioinformatics and computational biology.
ToBiX comprises some of the most useful and powerful bioinformatics tools such as:
- Blast 2.0 - Basic Local Alignment Search Tool for rapid searching of nucleotide and protein databases;
- Copasi - software application for simulation and analysis of biochemical networks;
- mpiBLAST - MPI based parallel implementation of NCBI BLAST;
- SimWiz - collection of Java tools for visualization of data resulting from different kinds of biochemical simulation processes;
- Cellware - tool to model whole cell biochemical reactions;
- Gromacs - molecular dynamics simulation package;
- SBML-Editor - tool for the quick creation and edition of SBML files;
- Stocks 2 - software for simulation of biochemical processes using Maximal Time Step Method

XMDS project is a code generator that integrates equations. You write them down in human readable form in an XML file, and it goes away and writes and compiles a C++ program that integrates those equations as fast as it can possibly be done in your architecture.
xmds - the eXtensible Multi-Dimensional Simulator - is a program for solving equations - fast. It is a tool to simplify the computer modelling of various systems, and is currently being developed within the Australian Centre for Quantum-Atom Optics at the University of Queensland.
There are many situations in many areas where a system of interest can be modelled by a differential equation or equations. Such areas include: physics, mathematics, engineering, physical and theoretical chemistry, theoretical and computational biology, finance, and economics. Modelling these systems involves writing a computer program to find a solution to the equations, which is not necessarily easy to do.
This is where xmds comes in. The advantage of using xmds instead of doing the same job by means of conventional programming is the same as ordering a pizza as opposed to making one yourself. The only thing you have to learn to become an xmds user is "How to order a pizza".
There are a couple of important differences here though: normally you have to pay for the pizza, while xmds comes for free; and xmds is like a gourmet pizza outlet - one has the option of exotic things like solving stochastic equations, which the chain-brand "pizza vendors" dont offer! xmds therefore makes writing complex computer simulations simple.
Another major advantage of xmds is that it is free. The source code and documentation can be freely downloaded from the xmds web site. xmds runs on Linux, Unix (including MacOS X) and the Cygwin environment on Windows, help for installing xmds on these systems is available both from the web site and the xmds distribution.
xmds is especially useful in solving complex problems requiring solving the problem over many different random parameters. Such problems can be parallelised (run on lots of computers at the same time) and xmds does this automatically with little user input, making the solution of these problems a breeze.
Often writing a computer program to solve complex problems can be very difficult, time-consuming, and error-prone. This is where xmds excels. One merely needs to write a script in a high-level form which is easy for a person to understand, and xmds goes off and writes the low-level code for you, producing code that is better for a computer.
This makes the writing of a simulation program significantly easier, reducing the development time, and almost eliminating bugs since xmds has written the vast majority of the code for you and has used thoroughly tested code and techniques in the production of the program.
The output program that xmds writes is still about as fast as code hand-written by an expert, so one can has the best of both worlds: quick development time, and quick execution.
So, if youre trying to model a bunch of atoms bouncing around together, the diffusion of an electrolyte solution, the reaction of enzymes with a substrate, or the volatility of stock prices, then xmds is the simulation tool for you.
Main features:
- An open-source XML based simulation package
- From Ordinary Differential Equations (ODEs) up to stochastic Partial Differential Equations (PDEs)
- Many applications:
- physics
- mathematics
- engineering
- finance
- economics
- chemistry
- theoretical biology
- Generates fast, C++ compiled code
- Documentation and source are free!
- Runs on Linux, Unix, MacOS X and Cygwin (Windows)
Installation
tar -xzvf xmds-1.3-5.tar.gz
cd xmds-1.3-5
./configure --with-user (or if logged on as root ./configure)
make
make install
Enhancements:
- This is another bugfix release of xmds-1.6.
- It is unlikely that anyone else has ever encountered these bugs, and now they never will. We are back to "no known bugs".

OpenTaxSolver (OTS) project is a free program for calculating Tax Form entries and tax-owed or refund-due, such as Federal or State personal income taxes.
An optional graphical front-end, OTS_GUI, has been added. Currently, TaxSolver has been updated for the 2005 tax-year for the following forms: US 1040 and Schedules A, B, C, & D.
As well as for California, Massachusetts, New Jersey, and Pennsylvania State Taxes for 2005 tax-year, thanks to contributors. Updates for the following additional states are expected to be posted soon: North Carolina, New York, Ohio, and Virginia. Preliminary versions for Canada and the United Kingdom were posted in previous years and may be updated with help from volunteers.
Motivations:
- To make tax preparation software available for all platforms.
- To provide insight into how our taxes are calculated in clear unambiguous equations/code.
- To avoid invasive, bloated commercial software packages.
- To avoid rewriting our own individual programs each year by combining efforts.
- To provide a simple reliable tax-package requiring only rudimentary knowledge to maintain.
Enhancements:
- Automatic phone credit was added to US1040.
- It will automatically calculate standard one-time phone credit, if not otherwise specified on US1040 line 71.
- The NJ State form F line 5 was fixed.

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.

ProxyTools is a package of Perl network utilities designed mainly to assist those whose Internet access is censored, unreliable, or otherwise damaged. Uncensored access is provided to any outside service required (Usenet News, Web browsing, IRC, Socks etc.). Setup requires installation of Perl and some modules; this is doable by even a novice MS Windows user with email instruction, allowing help to be provided to those inside these countries from expert users outside.

In pursuit of this rather non-specific goal, some interesting network utilities are already produced. We think the code is interesting in itself, useful in other areas, and would welcome contributions to the overall sum of ideas, concepts and ideals expressed in these tools.

The project is of interest to the following groups of people:

those who live in Internet censoring countries (or corporations, schools, universities) such as the Middle East (United Arab Emirates, Kingdom of Saudi Arabia, Kuwait, Syria), China, Burma, etc.
those who would wish to assist those in the group above.
those who are interested in Perl code dealing with many aspects of networks at the socket level, and transactions using HTTP proxies. One tool in this project offers a failover capability, and intelligent choice, between various censor-bypassing strategies and network paths, offering the user a robust, uncensored connection even in a low bandwidth, unreliable, packet filtered and proxy-poor environment.
those who administer the firewalls which do the censoring, and those who might be considering this.
those who are just curious about the current techniques used by the first group above.