Software Map

エントレーナーはバイノーラル ビート周波数と音と光と脳の波を連行の目的のためのアニメーションを作成する Java プログラム (JRE 1.7.0_07+ http://java.sun.com/javase/downloads/index.jsp から利用可能な必要) です。EntrainerFX ライト （http://entrainer.sourceforge.net/entrainerfx-lite.html） は、Java アプレット/機能のサブセットを含む JNLP プログラムで発見 EntrainerFX 配布。Http://entrainer.sourceforge.net に使用するための指示があります。

汎用個人ベース転送時間集団遺伝学のシミュレーション環境

SBSI (システム生物学ソフトウェア インフラストラクチャ) はシステム生物学のためのツールのスイートです、並列数値計算アルゴリズムや Java など Eclipse RCP ベース クライアントの結果を可視化するため、シミュレーションを実行してプラグインによる SBML の統合します。

並列のスペクトルのデコンボリューションは、分光画像ボケ解消のためのマルチ スレッド ImageJ プラグインです。

The vast number of data produced by next-generation sequencing (NGS) 
techniques poses significant computational challenges and many computational steps are required to translate this output into high-quality results. . Developing a workflow able to perform all stages in an automatic and reliable way is crucial to eliminate manual steps and to speed up result generation.
Here, we present a variant calling workflow executed in a HPC platform, which automatically executes all involved stages in this process using state-of-art software. Briefly, our process includes (a) short-read alignment with a combination of BWA and BFAST aligners, (b) a GATK-based variant calling protocol for indels and SNPs[3] (c) SNP effect predicto to annotate the variants. Our program accepts raw data in Fastq format from Illumina platform and generates a result file with the variants and its biological impact prediction ranked by detection quality score.

SwissParser allows you to define in a few lines a parser able to deal with the flat file format used in bioinformatics software such as UniProt, KEGG, etc.

The Samuel Lunenfeld Research Institute (SLRI)
Bioinformatics Toolkit is a mainly C-based
cross-platform toolkit for dealing with biological
information, especially protein structure/function
information. It is based on the NCBI Toolkit.

Molevolve is a library for running a genetic algorithm to
model the 3-dimensional structures of peptide chains from
amino-acid sequences. The client code can specify its own
peptide chain model, fitness functions, and GA operations.

BLAST on CD is a live CD distribution based on DNAlinux that
runs the NCBI BLAST server. It does not require installation
and comes with the SARS and smallpox genomes.

Drawtree is a program for visualisation of trees.
It reads in trees in the Newick format and outputs
them in a graphic format. Currently the only
supported output format is Encapsulated
PostScript, but other formats are planned.

PubCrawler is a script for an "alerting" service which scans daily
updates to the NCBI Medline (PubMed) and GenBank databases. When
PubCrawler is run daily, the results can keep scientists informed of
the current contents of Medline and GenBank by listing new database
entries that match their research interests.

Fura is a self-contained grid middleware that
allows enablement and distribution of applications
on heterogeneous computational platforms. It
features a Web-based GUI, wizard-guided
installation and configuration, and Web Service
compliance.

Ensembl is an open source project to create and automatically maintain annotations on DNA sequence.