Search Results for "ofn-layer-modes"

Bowtie 2 is a fast, memory-efficient genomic read aligner used to map sequencing reads against long reference sequences such as mammalian genomes. It is especially effective for reads ranging from around 50 bases to hundreds or thousands of characters, and it supports modern sequencing workflows that require gapped, local, and paired-end alignment. The tool builds compact FM-index-based reference indexes, keeping memory usage low even for large genomes like the human genome. Bowtie 2 outputs...

Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. ...

...Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN. Due to its modular design fast development and addition of new converters is highly facilitated. SBFC can be executed in two modes: 1. standalone executable downloading the package provided in this website; 2. web-service at http://www.ebi.ac.uk/biomodels/tools/converters . For general discussion about SBFC, please use the forum sbfc-forum@googlegroups.com . A mailing-list is also available for developers: sbfc-devel@googlegroups.com Thanks for using SBFC! ...

---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. The assembly is driven by a perl pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a GE/SLURM-type cluster or a standalone multi-core server. ...

OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets.

iMet-Q (intelligent Metabolomic Quantitation) is an automated tool with friendly user interfaces for quantifying metabolites in full-scan liquid chromatography-mass spectrometry (LC-MS) data. It has a complete quantitation procedure for noise removal, peak detection and peak alignment. In addition to accurate quantitation, iMet-Q provides the charge states and isotope ratios of detected compounds. It accepts input data in netCDF, mzXML, and mzML format and exports quantitation results in csv...

The MAGE-TAB Utilities project provides a simple Perl SDK for parsing, manipulating, visualizing and exporting data in MAGE-TAB format. All file releases are now being made via CPAN.

cy2fluxviz - Cytoscape 2 Plugin for the visualization of flux distributions in networks. Latest releases from https://github.com/matthiaskoenig/cy2fluxviz

...This is a bioinformatics program. It performs faster than the existing PseAAC server. Reference: [1] Pufeng Du, Shuwang Gu, Yasen Jiao. PseAAC-General: Fast Building Various Modes of General Form of Chou’s Pseudo-Amino Acid Composition for Large-Scale Protein Datasets. International Journal of Molecular Sciences 15 (2014) pp.3495-3506 [2] Pufeng Du, Xin Wang, Chao Xu, Yang Gao. PseAAC-Builder: A cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions. Analytical Biochemistry 425 (2012) pp.117-119

The q utility is a platform for creating and managing data analysis pipelines. It expands the value of your existing job scheduler - either Grid Engine or TORQUE PBS - through numerous functions that help you organize, submit, monitor, manage and share your informatics work. Data processing pipelines require high-level organization and parallelization of work to optimize resource utilization and decrease the time to results. q (from queue) allows complex job sequences to be efficiently...

TopiaryExplorer has moved to GitHub. Find the new project info page here: https://github.com/qiime/Topiary-Explorer. If you need help or would like to add a bug/feature request, please do so there.

AutoMap takes a series of poses obtained from molecular docking and applies the site, epitope and conformational mapping techniques to the poses to select likely ligand binding modes.

C++ software which implements serial and parallel Nullspace Algorithm based on algebraic rank test for the computation of elementary flux modes.

SOCS performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences. Modes are available for detecting short sequence-space variants (such as SNPs) and for detecting unlimited numbers of bisulfite-induced nucleotide substitutions for 5mC methylation studies.

This project is the implementation of The Virtual Collaborative Environment (VCE) which supports clinical applications of 3D modeling in medicine. The system is based on three layer client-server architecture.

An SQL handler to interface multiple databases data to the OpeNDAP Hyrax (BES) server. Written in C++, it uses unixODBC to query DB and can be dynamically extended to use proprietary ODBC API driver in many easy ways. It is bundled with scripts to ge

Neurospaces is a development center for tools in computational neuroscience. See http://www.neurospaces.org/

ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models of signaling systems, according to the layer-based approach.

The Stem Cell Artificial Neural network project entails the analysis and integration of genomics data for extracting the stemness signature of several tissues by training a multiclass single-layer linear artificial neural network.

The Genomic Diversity and Phenotype Connection (GDPC) written in JAVA uses web services to make XML formatted data publicly available. The GDPC Browser (front-end GUI) can access these services, and other applications can use the API.

JPhysChem - a mathematical modeling toolbox designed to provide an abstract layer and a comprehensive graphical front-end for general model building and specific modeling and data processing in the field of mass spectrometry and physical chemistry.

Modware is an easy to use Perl library for querying and modifying genomic data in a Chado database. It provides a powerful link between BioPerl and Chado. This Chado API provides an intutitive way to use Chado from Perl.

Bio-SPHERE aims to create a flexible, secure and multimodal biometric platform for applications that require biometrics. Bio-SPHERE is formed by a network of interacting nodes that interface with biometric hardware and offer biometric functions.

The field representation projectis based on the Field Representation Language (FRL) and associated tools. Primarily this means the Abstract Field Layer (AFL) - a C++ API for reading, manipulating and writing FRL files.

...It provides efficient access to sequence data and gene features, a customizable command line interface to locally installed bioinformatic tools and flexible display of either text or images in different page modes.