Free protein structure software for linux

queue_repair is a toolkit for dealing with the qmail queue directory structure; it can create a new queue, move and properly rename a queue, dynamically change the conf-split value, convert big-todo queues to non-big-todo and vice versa, and repair a corrupted queue.

AntiCMS is a minimalist content management system for small and simple websites. The main purpose of this system is to separate content, structure and layout.
Layout is defined using templates; content and structure are stored in XML file - database is not required. System is written in Python and released under the GPL.
Its still in early stage of development, so errors and unpredicted behaviour may occour. Currently a content editor is being developed, which will run on users computer and allow easy managent of content and structure of websites.
Enhancements:
- This release adds site configuration (it is now possible to change encodings, paths, and some other properties) and a new variable in the template engine.

atropine is a screen-scraping library built on top of BeautifulSoup.
atropine helps programmers make assertions about document structure while getting at the data they are interested in.
atropine library was developed under Python.
Special thanks to Piet Delport for the resolver, null resolver, chain-of-resolvers ideas.
Please note, using this library is not as complicated as it sounds, it consists of only 275 lines of python.
It is better to get no data than to get the wrong data.
The key to screen-scraping the right data is to make a painful amount of assertions about document structure
Enhancements:
- Some unused imports were removed.
- A text only version of the reference was added.
- Things were generally tidied up.

mcl-algorithm is a scalable cluster algorithm for graphs based on stochastic flow.
The flow process employed by the algorithm is mathematically sound and intrinsically tied to cluster structure in graphs, which is revealed as the imprint left by the process.
The threaded implementation has handled graphs of up to one million nodes within hours, and is widely used in the field of protein family analysis. It comes with a wide range of sibling utilities for handling and analyzing graphs, matrices, and clusterings.
The MCL algorithm simulates flow using (alternating) two simple algebraic operations on matrices. Its formulation is simple and elegant. There are no high-level procedural instructions for assembling, joining, or splitting of groups - cluster structure is bootstrapped via a flow process that is inherently affected by any cluster structure present.
The first operation used by MCL is expansion, which coincides with normal matrix multiplication. Expansion models the spreading out of flow, it becoming more homogeneous. The second is inflation, which is mathematically speaking a Hadamard power followed by a diagonal scaling. Inflation models the contraction of flow, it becoming thicker in regions of higher current and thinner in regions of lower current. The MCL process causes flow to spread out within natural clusters and evaporate inbetween different clusters.
- By varying parameters, clusterings on different scales of granularity can be found. The number of clusters can not and need not be specified in advance, but the algorithm can be adapted to different contexts.
- The issue how many clusters? is not dealt with in an arbitrary manner, but rather by strong internal logic. Cluster structure leaves its marks on the flow process simulated by the algorithm, and the flow parameters control the granularity of the cluster imprint.
- The limit of the MCL process (the process simulated by the algorithm) is in general extremely sparse, and the iterands are sparse in a weighted sense. This gives the means to scale the algorithm drastically, leading to a worst-case complexity of order Nk^2, where N is the number of nodes of the input graph, and where k is a threshold for the number of resources allocated per node.
- The rate of convergence of the MCL process, and projection of the iterands afterwards onto the resulting clustering, give hooks for unsupervised parameter adjustment.
- The iterands of the MCL process have structural properties which allow a cluster interpretation, and which generalize the mapping of MCL limits onto clusterings. The mathematics associated with the MCL process shows that there is an intrinsic relationship between the MCL process and cluster structure in graphs. This is very valuable given the many heuristic approaches in cluster analysis.
Enhancements:
- Numerous cleanups in much of the code.
- Improvements in caching intermediate results.

member_man project is designed as a management system for online organizations.
It allows the organization to manage its user base and committee structure through an online interface.
Main features:
- Member registration and self management
- Multiple Committee Management
- Committee Meeting Management

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

HTML Objects is a Perl module library for turning HTML tags into Perl objects. HTML Objects allows Web pages to be manipulated as a data structure rather than text.

Once manipulation is done, the entire page is generated via depth-first recursion.