Free developmental biology software for linux

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.

LON-CAPA is an Open Source Freeware Distributed Learning Content Management and Assessment System.
LON-CAPA is a full-featured, web-based course management system similar to commercial systems, see edutools.info for comparisons.
Main features:
- Content sharing and content reusability, including
- Network of shared resources from 27 participating institutions
- Shared repository of 61,000 resources including assessment questions and multimedia content
- Easy semester transition
- A large set of resources in physics/astronomy, chemistry, biology, mathematics/statistics, and geology
- Ability to add new resources to the existing content pool
- Creation and grading of randomized homework, quizzes or exams, including the ability to
- create sophisticated question types such as: click-on image, random label, random plot, or formula response
- reduce blind copying of answers by giving a different version of the problems to each student
- print randomized bubblesheet exams and quizzes
- configure the reporting of grades and feedback with a wide variety of options
- contextualize threaded homework discussions
- A development group based that sustains a twice-yearly LON-CAPA release cycle to insure rapid incorporation of instructor-requested enhancements.
- An open-source freeware system
Whats New in 2.4.2 Stable Release:
- This release correctly installs the jsMath fonts, which are used for TeX rendering.
- Symbolic math input now gets correctly compared to the instructor-prepared sample answer.
- Several issues regarding the printing, rendering, and grading of ".page" content assemblies were resolved.
- Teaching Assistants can now grade assignments that have an encrypted URL.
- The character "@" is now allowed in usernames.
- The German localization file was updated.
- Installation on CentOS and Scientific Linux is now possible.
Whats New in 2.4.99.0 Development Release:
- This release candidate supports personal response system ("clicker") registration and uploading of associated session data.
- It also offers new search functionality for users in and outside of classes, as well as optional coupling to institutional directories. User menu buttons can be switched off.
- Dynamics graphing in homework problems now supports linear/log, log/linear, and log/log plots.

BALL is Rapid Software Prototyping can significantly reduce development times in the field of Computational Molecular Biology and Molecular Modeling. BALL (Biochemical Algorithms Library) is an application framework in C++ that has been specifically designed for this purpose.
BALL has been carefully designed to be robust, easy to use, and open to extensions. Especially its extensibility which results from an object-oriented and generic programming approach distinguishes it from other software packages.
BALL is well suited to serve as a public repository for reliable data structures and algorithms. Based on BALL we have developed a stand-alone tool for molecular visualization, BALLView . BALLView makes the broad functionality available through an integrated user-friendly GUI.
BALL is distributed under the Lesser GNU Public License (LGPL), parts of it are under the GNU Public License (GPL).
Enhancements:
- This version finally brings full support for Python, DLLs, and nmake Makefiles under Windows.
- A large number of prominent fixes were made, especialy for g++ 4.x.
- Some new functionality was added to BALLView.

Bioknoppix is a customized distribution of Knoppix Linux Live CD. With this distrubution you just boot from the CD and you have a fully functional Linux OS distribution with open source applications targeted for the molecular biologist. Beside using some RAM, Bioknoppix doesnt touch the host computer, being ideal for demonstrations, molecular biology students, workshops, etc.

CLUTO is a software package for clustering low- and high-dimensional datasets and for analyzing the characteristics of the various clusters. The project is well-suited for clustering data sets arising in many diverse application areas including information retrieval, customer purchasing transactions, web, GIS, science, and biology.
CLUTOs distribution consists of both stand-alone programs and a library via which an application program can access directly the various clustering and analysis algorithms implemented in CLUTO.
Main features:
- Multiple classes of clustering algorithms:
partitional, agglomerative, & graph-partitioning based.
- Multiple similarity/distance functions:
Euclidean distance, cosine, correlation coefficient, extended Jaccard, user-defined.
- Numerous novel clustering criterion functions and agglomerative merging schemes.
- Traditional agglomerative merging schemes:
single-link, complete-link, UPGMA
- Extensive cluster visualization capabilities and output options:
postscript, SVG, gif, xfig, etc.
- Multiple methods for effectively summarizing the clusters:
most descriptive and discriminating dimensions, cliques, and frequent itemsets.
- Can scale to very large datasets containing hundreds of thousands of objects and tens of thousands of dimensions.
Enhancements:
- Support for Windows X86_64 was added.

Biomolecule Toolkit project is an Open Source library for the structural modeling of biological macromolecules. The toolkit provides a C++ interface for common tasks in computational structural biology, to facilitate the development of molecular modeling, design, and analysis tools.
Enhancements:
Documentation updates
- Addition of an extensive discussion of the leastsquares_superposition and RMSD-calculation methods, including a description of the mathematical theory behind their operation.
- Fully documented the rotation/translation methods
- Addition of a documented example program ("gyration_radius.cpp")
Bug fixes
- Fixed copy construction bug in PDBAtomDecorator that caused compilation errors in rare situations.
- Fixed a bug in PDBFileParser that caused a compilation error in the PDBSystem copy constructor.
- Fixed a const-conversion bug in GroupedElementIterator which prevented proper interoperation of const and non-const iterator types.
- Fixed a crash-producing bug in stream output for the TypeID class.
- Fixed a math error in RMSD and superposition methods that would corrupt molecule coordinates.
- Fixed a bug that caused all default-constructed PDBAtom objects to be treated as HETATMs.
Feature additions
- Added operator[] to AtomicStructure and PolymerStructure-derived classes.
- Added protected increment() and decrement() operators to TypeID class.
- PDBFileParser can now handle PDB files with ill-formed residue numbering (i.e. Files where residue numbers are repeated in successive chains).