Biology Sequence

A Molecular Biology software that provides tools with an intuitive interface to assists you in DNA cloning, sequence analysis and visualization. Serial Cloner 2.1 handles Features/Annotations and now allows to define, import and export, customized lists of Features. User can annotate any sequence... Platforms: Mac

Creates a software environment enabling users to make basic bioinformatics analyses and smooth data management, combined with excellent graphical viewing and output options. Some bioinformatics features are: - GenBank searching and viewing (linear and circular views) - Multiple alignment of... Platforms: Mac

CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options. Bioinformatics features in CLC Sequence Viewer Multiple alignment of DNA, RNA, and... Platforms: Windows

TinkerCell is a Computer-Aided Design (CAD) tool for synthetic biology. Since synthetic biology is a rapidly evolving field, here are the issues which were taken into consideration when designing TinkerCell: -modeling techniques in biology are still at a developmental stage -experimental... Platforms: Windows

Researchers in quantitative systems biology make use of a large number of different software packages for modeling, analysis, visualization, and general data manipulation. The Systems Biology Workbench (SBW), is a software framework that allows heterogeneous application components-written in... Platforms: Windows

POSA (Perl Objects for Sequence Analysis) provides an easy-to-use perl interface to handling raw ABI sequence trace files. For example: fasta can be extracted, sequence contigs can be build and putative SNPs and SBE primers can be easily generated. Platforms: Windows, Mac, Linux

A fast and reliable tool, written in Java 5, for generating professional UML sequence diagrams from text. Supports actors, con-/destructors, threads, broadcasts, notes, and fragments. Can serve as a Javadoc taglet. Exports PDF, (E)PS, SVG, PNG, ... Platforms: Windows, Mac, Linux

The Systems Biology Workbench(SBW) is a simple framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. Platforms: Windows, Mac, BSD, Linux

The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more. Platforms: Windows, Mac, Linux

Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer. Platforms: Windows, Mac, BSD, Linux

TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological 'parts'. Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell. Platforms: Windows, Mac, Linux

Permutations and combinations are often required in algorithms that do a complete search of the solution space. They are typically rather large so it's best not to compute them entirely but better to lazily generate them.This script uses Python generators to create appropriate generator objects,... Platforms: Windows, Mac, *nix, Python, BSD Solaris

Generators, introduced in Python 2.2, can be used to work with infinite sets. This script is a simple example of a generator that creates the Fibonacci sequence.Running this produces the following result:c:python22>python fib.py1 1 2 3 5 8 13 21 34 Platforms: Windows, Mac, *nix, Python, BSD Solaris

Maximum length sequence assuming distinctvalues = baseVal^powerVal-1 [ms]=mseqSearch(powerVal,baseVal) OUTPUT: ms: generated maximum length sequence, of length basisVal^powerVal-1 such that all values occur with equal frequency=basisVal except zero, which occurs basisVal-1 times INPUT: baseVal:... Platforms: Matlab

Sequence Generator (file ID #24620) has been renamed to CORE - Constraint Randomization Environment. Interface and code structure of v0.91 are explained in this manual.Current development concentrates on these topics:- Performance related issues- Bug fixes (3 known issues)- Improved constraint... Platforms: Matlab

EMBOSS is "The European Molecular Biology Open Software Suite", it is a free Open Source software analysis package specially developed for the needs of the molecular biology user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of... Platforms: Most OSs

App::Session can represents a sequence of multiple events perhaps executed in separate processes. SYNOPSIS # ... official way to get a Session object ... use App; $session = App->context(); $context = $session->session(); # get the session # any of the following named parameters may be... Platforms: *nix

Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search. Parameters: fasta (Excl) Fasta program query (Sequence) Query sequence File pipe: seqfile seqtype (Excl) Is it a DNA or protein sequence (-n) protein_db (Excl) Protein Database nucleotid_db... Platforms: *nix

The STed is the high-performance MIDI sequence editor / Music composer system. It had been working on X680x0 old Japanese personal workstation. The STed was originally developed by Mr. Takayuki "TURBO" Toda. Through many volunteers good office the source code of the STed has been opened. Since... Platforms: *nix

AlignAid is a Perl module that easily run sequence alignments locally or on a cluster. SYNOPSIS use AlignAid; # create an AlignAid object # a single, locally run blast job is the default my $job = AlignAid->new( db => my_blast_db, dir => $dir, fasta => my_query.fa, prog_args => V=20... Platforms: *nix