Search Results for "interface"

ProStack - a platform for image processing and analysis. It implements various image processing methods as separate modules, that can be joined in a complex image processing scenario by use of a graphical user interface. RPMs are available at https://build.opensuse.org/project/repositories/home:mackoel:compbio

APBSmem is a Java-based graphical user interface for Poisson-Boltzmann electrostatics calculations at the membrane. APBS version 1.2.0 or later is required.

'isotope' is a small command-line utility to calculate the isotope pattern for a given chemical formula. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.

hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.

bruread is a program to read and display NMR data in the Bruker XWIN-NMR format. The program has a command-line interface and a graphic display based on gnuplot. - Note that this is only an NMR spectrum *viewer*, not a full-fledged data evaluation suite

Epidaurus is a collection of epigenetic datasets including transcription factor ChIP-seq, histone ChIP-seq, DNase-seq, FAIRE-seq, DNA methylation, etc. It also includes commonly used genome features (GC content, conservation) and RNA-seq. A user friendly interface has been developed to interrogate and visuzlize these datasets.

...CAGE is prominently used in both the FANTOM and ENCODE project. MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. MOIRAI package comes with three main workflows allowing users to map, annotate and perform an expression analysis over multiple samples.

During the past few years, whole exome sequencing has imposed itself for genetic research, largely due to its use for detection of causative mutations responsible for Mendelian disorders. As a consequence of their power and of the rapidly decreasing cost of these technologies, massive amount of exome sequencing data are generated and becoming available to a broadening community of scientists. However, these data remain difficult to analyze and interpret by the general scientific community,...

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.

wEMBOSS is a Web interface for the EMBOSS software package for biological sequence analysis. Under wEMBOSS each user has a private workspace (UNIX home directory) on the server, where he can permanently store his data and organize them in projects. The companion suite wrappers4EMBOSS allows to integrate under EMBOSS a number of popular bioinformatic software suites as BLAST, CLUSTAL and MRS.

The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes.

The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. More at http://deconseq.sourceforge.net

CoactivationMap is a graphic user interface to browse through a map of functional co-activations of the human brain. Click on a region, and observe which other regions are likely to be connected

FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.

EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)

ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.

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.

A toolbox for quantitative morphometric analysis of early development in spherical embryos, such as Xenopus laevis (African Clawed Frog). The toolbox is developed for Matlab 6.5 and higher and combines C-Mex code with Matlab functions.

Gnome-EMBOSS is an open-source application to help scientists handle DNA, RNA and protein sequences. It uses Gnome/GTK for the user interface and EMBOSS libraries for sequence handling routines. (See www.emboss.org for further info.)