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Projects in category FOSS in science

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FOSS in science.

The available projects in this category, alphabetized.

Avida-base

Auto-adaptive genetic system for Artificial Life research

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Bioconductor

Provides tools for the analysis and comprehension of high-throughput genomic data.

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BioJava

BioJava is an open-source project dedicated to providing a Java framework for processing biological data.

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BioPython

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.

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CLUSTALW

Multiple Sequence Alignment Program

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ClustalX

Clustal X provides a window-based user interface to the ClustalW multiple alignment program.

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Critterding

Evolving Artificial Life

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DIALIGN2

Tool to perform multiple alignment of protein or DNA sequences.

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Insight Toolkit (ITK)

ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis.

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Muscle

A program for multiple alignment of protein sequences.

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Numerical Chameleon

The Numerical Chameleon converts numbers with a precision of up to 1000 significant figures!

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PHYLIP

A free package of programs for inferring phylogenies

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Scientific Applications

FOSS (Free/Open Source Software) programs are programs whose licenses give users the freedom to run the program for any purpose, to study and modify the program, and to redistribute copies of either the original or modified program without having to pay royalties to any previous developers. Thus open source is a development method for software that expresses the power of distributed peer review and transparency of process. The promise of open source is better quality, higher reliability, more flexibility, lower cost, and an end to predatory vendor lock- in [1]. The open standards and open contents are several other terms those are related to FOSS. The goal of this paper is to define these related terms in FOSS and show the use of FOSS in different scientific applications including construction of grid environment, solving bio-informatics problems, developing National Address Database (NAD) and so on.

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Scientific Computing

Free/open source operating systems and software constitute a major portion of the top 500 supercomputers [1]. Nearly 50 % of the top 500 supercomputers are used for Academic / Technological research which involves advanced scientific computations. Computational science (as opposed to computer science) is a relatively new methodology for scientific research compared to usual theoretical and experimental methods. It faces a crisis of confidence amongst the scientific community [2]. Adoption of better software engineering practices by researchers [3] and open standards for evaluation of research publications can help in alleviating many of the concerns. This paper puts in perspective the role of Free/Open Source software (FOSS) and Open Standards in scientific computing. It makes a case for the use of such software and more open standards in scientific software development and in the refereeing process of scientific publications. A need for introductory courses at the graduate and post-graduate levels on basic computational science and the available software using FOSS tools on a GNU/Linux platform is presented within the Indian context so that trained manpower for scientific computations is available.

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SciGraphica

Scientific graphics and data manipulation

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SciPy

SciPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering. It is also the name of a very popular conference on scientific programming with Python.

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Seaview

A multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny

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Tree-puzzle

Maximum likelihood analysis for nucleotide, amino acid, and two-state data

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TreeView X

TreeView X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms.

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UGENE

Bioinformatics software

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