SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools
Technical Analysis Library
Technical analysis library with indicators like ADX, MACD, RSI, Stochastic, TRIX... This is not an end-user GUI trading or charting application. It is instead targeted to application developers using either Excel, .NET, Mono, Java, Perl, Python or C/C++.
DD Thought Tickler is a thinking process recorder. It is a kind of vector graphics editor and idea processor. It has new function not ever known. It records your thinking process, by memorizing every steps that you've operated on this tool.
A project to increase free Arabic fonts on Unix/Linux
Arabeyes is a Meta project that is aimed at fully supporting the Arabic language in the Unix/Linux environment. It is designed to be a central location to standardize the Arabization process. Arabeyes relies on voluntary contributions.
AquaTerm is a Mac OS X grahics renderer. It allows command line applications written in ObjC, C, FORTRAN, Lisp, Perl or Python to display vector graphics, text and images using a simple API. Adapters for gnuplot, PGPLOT, and PLplot exists as well.
TinyOS is an operating system for embedded sensors and networks. Versions 2.0 and later of TinyOS should be downloaded from www.tinyos.net.
A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.
The Trinity RNA-Seq Assembly project provides software solutions targeted to the reconstruction of full-length transcripts and alternatively spliced isoforms from Illumina RNA-Seq data.
An automatic tool for binning metagenomics sequences
MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users could use MEGAN or similar software on MaxBin bins to find out the taxonomy of each bin after the binning process is finished. The most current version is 2.2.4. MaxBin was published on Microbiome journal (2:26)! Please cite the Microbiome paper if you use MaxBin in your work. More information can be found at the official MaxBin website: http://downloads.jbei.org/data/MaxBin.html to
MARF is a general cross-platform framework with a collection of algorithms for audio (voice, speech, and sound) and natural language text analysis and recognition along with sample applications (identification, NLP, etc.) of its use, implemented in Java.
Protein Kinase Identification and Classification
Kinannote identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. If the user inputs a complete proteome, additional modules evaluate the completeness of the kinome and place it in context with reference kinomes. Kinannote runs on a unix command line and depends on local hmmer 2 and Blast 2.24 installations. Citing Kinannote: Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily Jonathan M. Goldberg; Allison Griggs; Janet L. Smith; Brian Haas; Jennifer Wortman; Qiandong Zeng Bioinformatics 2013; doi: 10.1093/bioinformatics/btt419 http: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full pdf: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full.pdf+html
RandService is a Web Service which supplies pseudo- or true- random numbers through JAX-RPC API. Any random number generators can be used behind this Web Service.
GGI stands for "General Graphics Interface", and it is a project that aims to develop a reliable, stable and fast graphics system that works everywhere. We want to allow any program using GGI to run on any platform requiring at most a recompile.
IFEFFIT is a library and set of interactive programs for the analysis of x-ray absorption fine-structure (XAFS) data. IFEFFIT combines state-of-the-art analysis algorithms with graphical display of XAFS data, and general data manipulation. It can be
A simple command to convert calendar dates to julian dates. Quite useful in timing situations where you need elapsed time between dates. Also useful for astronomy applications.
The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites.
User-based CPU quota tool
CPU Balance is a Perl script to balance the CPU usage among users. It will allocate CPU resource to each user equally only by the command renice, no matter how many processes/threads a user runs. ################ # Basic Renice Goal ################ 1. User-based balance: every user get the same cpu percentage if they ask for more; 2. all the jobs of one user has the same NI; 3. NI of all jobs tend to move as large as possible when balanced; 4. No sudden change on NI. max change of NI of a proc <= 2. Only 1 user will be changed in a renice cycle. ################ # Advanced Features ################ 1. gid/uid/cmd based renicable filter 2. gid/uid based weighted cpu division: priority & punished user support
Pretty Damn Quick (PDQ) analytically solves queueing network models of computer and manufacturing systems, data networks, etc., written in conventional programming languages. Generic or customized reports of predicted performance measures are output.
Generate pdf diagrams for analemmatic sundial construction, papercraft sundial, and "plus" card game.
Middle level device drivers for the Ultraship U-2, a USB HID scale, no brand or company name available. Includes basic test scripts, drivers, example implementations and documentation. The output of this driver will insert it into applications.
This package aims to enable complex ideogram drawing in genetic applications for different species.
Join Finder helps locate joins by blasting contig end sequence probes and looks for link-supported joins. Probes are BLASTed against 2KB ends of contigs, strict matches are examined against link information and potential joins are outputed to file.
Trad4 is a fully concurrent, thread safe, graph-based programming language that scales linearly on multiple cores. It is initially intended for deployment in the financial industry to model real-time risk.
APEX Tools is a collection of utilities used in conjunction with the processing of airborne hyperspectral data developed for the ESA-Prodex supported Airborne Prism EXperiment (APEX).
Abra stands for 'A brain extension'. The core idea is to create personal mappings onto information space and share those mappings. Ajax-enabled bookmarklet allows users to 'say anything about any URI', outputs RDFa. Has simple category-enabled CMS.