Search Results for "export"
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Showing 28 open source projects for "export"
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Jmol
An interactive viewer for three-dimensional chemical structures.
...Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export). -
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SPINA
Structure parameter inference approach for endocrine feedback control
SPINA is software for the rapid, reliable and accurate determination of constant structure parameters of endocrine feedback control systems. It is a class of static function tests that require nothing more than steady-state concentrations of hormones or metabolites obtained in vivo. The first version of this cybernetic approach had been developed for the evaluation of the functional status of the thyroid gland, i.e. thyroid's secretory capacity (gain of thyroid, GT or SPINA-GT) and sum... -
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SimThyr
A simulation program for thyroid homeostasis.
SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients. -
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dualword-chem
chemical viewer
chemical viewer written in C++ (Qt, RDKit) Source code: http://github.com/dualword/dualword-chem -
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NOVA
Analysis and visualization of complexome profiling data.
...Several hierarchical clustering algorithms (e.g., single linkage, average linkage, Wards linkage), different distance measures (e.g., Euclidean distance, Manhattan distance, Pearson distance), and various normalization techniques are implemented. Many additional functions like zooming, searching for proteins, image export, and automatic file format recognition support intuitive handling for biologists. Giese, et al. NOVA: a software to analyze complexome profiling data. Bioinformatics, 2015, 31(3): 440-441 -
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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.
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RDML stands for Real-time PCR Data Markup Language and is the standard file format for export, storage and exchange of quantitative PCR (qPCR) data. This project focuses on the development, implementation and enhancement of the RDML file format and its description (XML schema).
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CoverageAnalyzer
RNA modification detection by RT signatures in deep sequencing data
...Recent studies yielded high-resolution RT signatures relying on both, sequence dependent mismatch patterns and RT arrests. Common alignment viewers lack in specialized functionality, such as filtering, tailored visualization, differential analysis and export. Consequently, the community will profit from a platform seamlessly connecting detailed visual inspection of RT signatures and automated screening for modification candidates. CoverageAnalyzer was developed in response to the demand for a powerful inspection tool, running on all 3 OSes. With SAM standard as input and an intuitive GUI, even non-experts can accomplish a variety of tasks, from visualization of RNA Seq data, up to sophisticated modification analysis with significance-based candidate calling. -
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The complexity of cellular networks is an outstanding challenge for documentation, visualisation and mathematical modelling. In this project, we develop a new way to describe these networks that minimises the combinatorial complexity and allows an automatic visualisation and export of mathematical (ODE/rulebased) models.
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ChelomEx
Isotope assisted discovery of metal chelating agents from LC-MS data
ChelomEx identifies chromatographic features of metal complexes and associated free ligands or other related adducts in high-resolution LC-MS data. A built-in graphical user interface and compound library aid in the efficient evaluation of the results. If you use ChelomEx for your research, please cite our Analytical Chemistry paper that describes the software (http://dx.doi.org/10.1021/ac503000e). To comment, send bug reports or suggestions for additional features to be implemented... -
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fast_count_multi
Extremely fast NGS read counter
.../fast_count_multi num_threads gtf_file bam_file(s) > output Requires bamtools API library at run time, and c++0x for compile. git clone https://github.com/pezmaster31/bamtools cd bamtools mkdir build cd build cmake .. make export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path to/lib g++ -I bamtools/include/ -L bamtools/lib/ -o fast_count_multi fast_count_multi.cpp -lz -lbamtools -fpermissive -pthread -std=c++0x -
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A Tool for Retrieval, Visualization and Analysis of biological Pathways. Import a Gene or Protein Set from any Excel file. Automatically find signaling Pathways from KEGG. Integrate your Data in Seconds with a live interactive Force-directed Layout.
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qPMerge
phospho-peptide merge tools for Galaxy
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Protospacer
Rapid gRNA design and validation for CRISPR
...Protospacer then allows the user to sub-select targets from the database by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. From here, users are able to evaluate potential off targeting, to export results in FASTA format or tabulated (e.g. for Microsoft Excel), and to connect to the Integrative Genomics Viewer (IGVref) and view target-sites in the context of genomic annotations, amino acid translations, and HT-Seq data (for off-target validation). We provide online video tutorials and a toy database from our main website. -
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Arcadia is a light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways.
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cy2fluxviz
cy2fluxviz : Cytoscape 2 plugin for flux distribution visualization
cy2fluxviz - Cytoscape 2 Plugin for the visualization of flux distributions in networks. Latest releases from https://github.com/matthiaskoenig/cy2fluxviz -
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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.
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AJT is a set of utility classes for Java for handling some bioinformatics data, graphics file export, GUI widgets, and classes that should long have been added to the official Java API.
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BioDare
BioDare is Biological Data Repository focused on timeseries data
...The main features of BioDare are: - an online repository for experimental data accompanied by extensive metadata - generation of secondary data (normalized, detrended, averaged …) - graphical output of data, secondary data and rhythm analysis - simple text-based search throughout metadata - biology- and conditions-aware search for data - data aggregation and export - group-based privacy settings for collaborative research -
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ClinStudyWeb is designed to provide a flexible infrastructure for managing patient and assay data from clinical studies. It uses a plugin system for study-specific web forms and arbitrarily complex test classifiers, and supports XML import/export.
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PIVOT
PIVOT is a simple yet flexible visualization data tool
PIVOT is a simple yet flexible visualization tool based on Circos (Krzywinski et al., 2009), which offers a fast and aesthetical visualization of data and information. The Protein Interaction Visualization and Observation Tool (PIVOT) was developed specifically for the visualization of protein interaction. It is difficult to spot the proteins that have an interaction when given a large list of proteins but with PIVOT, it is easy to identify the them at a glance. PIVOT displays an image... -
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CySBGN
Cytoscape plug-in that enables handling SBGN maps
CySBGN adds support to Cytoscape to import, export, visualize and analyse System Biology Graphical Notation (SBGN) maps. -
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Xi Spectrum Viewer
Mass Spectrum Viewer Tool
...It comprises 3 parts: (1) the core Spectrum Viewer displays peptide-spectrum matches and implements zooming, mouse-over peaks to highlight matching parts of peptide, mouse-over parts of peptide to highlight matching peaks, export SVG, and API; (2) the Auxiliary Annotator matches peptide to spectrum for given parameters and prepares the data for the Viewer; (3) these reside on a web page that provides the user control over peptides, spectra and other parameters e.g. linker mass. -
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JFinisher
JFinisher is software for alignment, editing and manipulation DNA seqs
...It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and ability to export results in the standard formats of the area. -
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A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
