Search Results for "arch linux gui"
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Showing 90 open source projects for "arch linux gui"
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STRIKER-GUI
Refine the spectral library to enhance its completeness and coverage.
STRIKER is a tool for correcting spectra with missing or incorrect adduct annotations. It also enables efficient construction of an HMDB-based spectral library and extraction of sublibraries from large spectral libraries. -
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering,... -
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miRge3
Comprehensive analysis of small RNA sequencing data
An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User... -
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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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Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. HBAT 2 is migrated from PERL to Python. Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal... -
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Cylindrical Alignment App
Arranges alignments in a rotating cylinder
The Cylindrical Alignment App is the successor to Cylindrical BLAST Viewer. Similarly, it arranges search or other comparisons, against their "axis". Searches can be made by Basic Local Alignment Search Tool, ClustalW, or Gene Machine to name a few. This version does not require downloading or installing Java3D, and has more modern GUI features. -
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Toxtree: Toxic Hazard Estimation
Toxicity prediction for chemical compounds
A GUI application which estimates toxic hazard of chemical compounds. The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation and Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Skin sensitisation reactivity domain -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated... -
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KimBlast
Blast+ the easy way
KimBlast GUI formats and indexes Fasta databases for Blast, performs Blast searches and analyzes results. Python 3.x version. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/kimblast3/code/ci/default/tree/README.md -
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VMS Draw
user-friendly access to the latest computational spectroscopy tools
VMS Draw provides general utilities (e.g. normalization, conversion, and other manipulations of several spectra at the same time) and a flexible graphical user interface (GUI) for an easy use by non-specialists which allows a seamless flow of information between experimentally and theoretically oriented researchers. Finally, it permits effective interactions with other electronic structure codes [e.g., nuclear magnetic resonance (NMR), microwave] even if Gaussian 16 offers the widest set... -
DAT Freight and Analytics - DATDAT Freight & Analytics operates DAT One, North America’s largest truckload freight marketplace; DAT iQ, the industry’s leading freight data analytics service; and Trucker Tools, the leader in load visibility. Shippers, transportation brokers, carriers, news organizations, and industry analysts rely on DAT for market trends and data insights, informed by nearly 700,000 daily load posts and a database exceeding $1 trillion in freight market transactions. Founded in 1978, DAT is a business unit of Roper Technologies (Nasdaq: ROP), a constituent of the Nasdaq 100, S&P 500, and Fortune 1000. Headquartered in Beaverton, Ore., DAT continues to set the standard for innovation in the trucking and logistics industry.
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SMTracker (v1.5, v2.0)
A tool for analysis and visualization of single-molecule tracking data
SMTracker v2.0 is a MATLAB-based graphical user interface (GUI) for automatically quantifying, visualising and managing SMT data via five interactive panels, allowing the user to interactively explore tracking data from several conditions, movies and cells on a track-by- track basis. Diffusion parameters and motion behaviour is analysed by several methods: a) by a Gaussian mixture model ,or b) by using the cumulative probability distribution of square displacements, c) Mean-Squared... -
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CBMPy
PySCeS Constraint Based Modelling
PySCeS CBMPy is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. CBMPy supports the latest standards for encoding CBM models encoding, SBML L3 FBC, COBRA as well as MIRIAM compliant RDF and custom annotations. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently... -
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NOVA
Analysis and visualization of complexome profiling data.
NOVA is a program designed to analysis complexome profiling data (Heide et al., 2012). A graphical user interface (GUI) provides various visualization tools, such as heat maps and 2D plots. 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... -
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FastaTools
Performs several operations to Fasta protein databases
FastaTools performs several operations to Fasta protein databases. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/fastatools/code/ci/default/tree/README.md Or you can download the Documentation an Tutorial PDF file in the Files section: https://sourceforge.net/projects/fastatools.lp-csic-uab.p/files/FastaTools%20Documentation%20and%20Tutorials.pdf - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M.,... -
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An alignment-free standalone tool with interactive graphical user interface for DNA sequence comparison and analysis
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DrawGlycan-SNFG
Renders glycans and glycopeptides with frag. info using SNFG format
DrawGlycan-SNFG is a simple and robust drawing tool for displaying glycans and glycopeptides from IUPAC-condensed format text inputs. It also supports the depiction of glycan and glycopeptide fragmentation. The program is available in the form of web (link below) and standalone GUI applications. Program source code is also provided.. The web and GUI apps do not require any additional software to run. To install the GUI version, simply download and run the installer for PC or Mac. To install in Linux, follow in-package instructions or visit the VirtualGlycome.org FAQ page. The source code can be edited and run using MATLAB2014b or later. ... -
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RELEASE NOTE: Get raxmlGUI 2.0 at the NEW PROJECT LOCATION: https://antonellilab.github.io/raxmlGUI/ raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI:...
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OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS and GC/FID systems and vendors. Its functionality and algorithms can be extended using a flexible plugin approach, based on Eclipse RCP.
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BioSeq
A simple GUI for some of the biological sequence analysis.
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JSiteDescriptor
Binding site descriptor generation for SVM based classification.
A set of java programs that extract coordinate and chemical information from PDB files. The binding site regions are extracted using grid based scheme. For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too). -
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DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.
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Open-source Python software library and GUI desktop environment for direct bioinformatic analysis of mass-spectrometry data through powerful scripting tools and interfaces to many machine data formats, database search engines, and peptide data formats. For a copy of the source code, check out our Github repositories: mzDesktop: https://github.com/MaxAlex/mzDesktop multiplierz: https://github.com/MaxAlex/multiplierz
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The increasing demand of next-generation sequencing (NGS) studies has remarked the necessity of integrated and reliable pipelines to analyse deep-sequencing experiments in an efficient way. We present RUbioSeq+, a stand-alone and multiplatform application for the integrated analysis of NGS data. More specifically, our software implements pipelines for the analysis of single nucleotide and copy-number variation, bisulfite-seq and ChIP-seq experiments using well-established tools to perform...
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CoverageAnalyzer
RNA modification detection by RT signatures in deep sequencing data
Combination of reverse transcription (RT) and deep sequencing has emerged as a powerful instrument for detection of RNA modifications, a field that has seen a recent surge in activity because of its importance in gene regulation. 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.... -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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LGTmate
Lateral Gene Transfer utility
LGTmate is a simple and powerful bioinformatic software tool to identify lateral gene transfer events and contaminants in Eukaryotic proteomes. It is available as a GUI or command-line application, with no dependencies and no installation required.
