Search Results for "standalone"
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Showing 25 open source projects for "standalone"
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biblioAssist
python3 version of bibus
python3 version of bibus https://sourceforge.net/projects/bibus-biblio/ It is nothing more than "it works on Debian testing (bookworm) AMD64. " -
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...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! ...
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genppi
GENPPI: standalone software for creating protein interaction networks
Our software GENPPI is efficient because, for example, it creates interaction networks from the central genome of 50 species/lineages of Corynebacterium, with an average size of 2200 genes, in less than 40 minutes, on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships between species and obtained in Average Nucleotide Identity (ANI) analyzes. Also, It allows the user to define how he intends to explore the... -
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ANDTool
Analysis Nuclei DAB (AND) Tool
...The tool requires as input the original RGB images, and the FastRed, FastBlue, DAB channel, easily obtained using the Fiji function: "ImageJ" -> "Image" -> "Colour Deconvolution" -> "FastRed FastBlue DAB" Then, the tool first segment the nuclei using the FastBlue channel and the DAB channel, and then computes statistics by subdividing the sample in three regions according to the FastRed channel: a dark-red ROI, a light-pink ROI and a white ROI. ANDTool is written in MATLAB (The MathWorks, Inc., Massachusetts, USA) and the source code and standalone versions are here available for download. USER MANUAL: see the specific PDF available in the Files section. REQUIREMENTS: MATLAB R2017b and Image Processing Toolbox 10.1 or later versions. MAIN CONTACT: Filippo Piccinini (E-mail: filippo.piccinini85@gmail.com) -
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An alignment-free standalone tool with interactive graphical user interface for DNA sequence comparison and analysis
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PsPM
A matlab suite for Psycho-Physiological Modelling
...It includes linear convolution models and non-linear models for SCR, and allows for modelling of other signals, too. A flexible import interface and many utilities make this software a standalone tool. IMPORTANT: As of 04.11.2019, the official code repository for PsPM has been moved to https://github.com/bachlab/PsPM . In order to check the latest releases, discussion and bug reports, please refer to our new repository. Although this website will maintained to provide further releases, there will be no active development on the SVN repository. ... -
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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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Meraculous-2D
Eukaryotic Genome Assembler
...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. Manuscripts in submission: https://arxiv.org/abs/1703.09852 https://arxiv.org/abs/1608 -
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CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
...To meet the needs of different CRISPR system with specific and efficient sgRNA design, CRISPR-offinder was developed. Given an input FASTA file of the target sites and queries the reference genome as well as a CRISPR system with a defined spacer length and PAM sequence, this standalone tool will identify putative sites and assign a predicted activity based on support vector machine model which conducted by sgRNA Scorer 2.0. In addition, sgRNAs with minimal off-target activity were predicted by Cas-OFFinder, and score with Off-Target Cutting Frequency Determination (CFD). -
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F-Tracker3D
A software tool for tracking fluorescent cells in 3D
F-Tracker3D is acronym of "fluorescent cell tracker in three-dimensions". It is a software tool designed to track fluorescent cells using time-lapse z-stacks of images acquired with a confocal or light-sheet microscope. First, each single cell is tracked in 2D by using the maximum intensity projections of the z-stacks and CellTracker, the free open source software available at: www.celltracker.website. Then, the 3D track of each cell is obtained analysing the z-stacks and looking for the... -
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runjags
The 'runjags' R package and standalone JAGS extension module
This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A... -
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Combenefit
Synergy analyses of drug and other other agent combinations
Combenefit software is a standalone application for Windows that performs surface analyses of drug and other agent combinations to identify synergy. Please cite as: "Di Veroli,G.Y. et al. (2016) Combenefit: an interactive platform for the analysis and visualization of drug combinations. Bioinformatics." (http://bioinformatics.oxfordjournals.org/content/early/2016/05/27/bioinformatics.btw230.abstract) Current version (2.021): https://sourceforge.net/projects/combenefit/files/Combenefit%202.02%20WIN_64%20%28PREFERRED%29/ Older version for 32-bit os: https://sourceforge.net/projects/combenefit/files/WIN_32/ Quick user's guide: https://sourceforge.net/projects/combenefit/files/Combenefit_v2.02_quick_guide_v1.03.pdf/download Examples: https://sourceforge.net/projects/combenefit/files/Examples/ Template file: https://sourceforge.net/projects/combenefit/files/REPLICATE_TEMPLATE.xls/download -
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PanCoreGen1
A comprehensive tool to profile, detect & annotate microbial genomes.
PanCoreGen is a Windows-based standalone tool offering 4-in-1 functionalities – (i) pan-/core-genomic profiles across the entire sample set; (ii) similar profiles within user-defined strain-groups; (iii) annotations of user-provided draft genomes; and (iv) detection of unidentified genes in annotated genomes. -
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Drug Extraction
Drug name extraction
...accuracy: 95.25%; precision: 85.70%; recall: 76.20%; FB1: 80.67 Using GATE Corpus Benchmark: Strict: P: 0.65 R: 0.73 F1: 0.69 Lenient: P: 0.74 R: 0.84 F1: 0.78 The details of how to reproduce evaluation, see README. To use standalone version for tagging download DrugExtractionStandalone.tar.gz from Files. -
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xAffect
Sensor Middleware
...xAffect can be used as a flexible, customizable middleware between physiological sensors and applications which require online feature computation (e.g. biofeedback or affective computing). Moreover, it can also be used as a standalone application for data acquisition and visualization. -
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ConoSorter
A Large-scale Cone Snail Transcriptome/Proteome Analysis Program
ConoSorter is a high-throughput standalone program that implements regular expressions and profile Hidden Markov Models (pHMMs) for large-scale identification and classification of precursor conopeptides into gene superfamilies and classes based on the ER signal, pro-, and mature conopeptide regions generated from raw next-generation transcriptomic or proteomic data. -
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PPSeq: Parallel NGS Analysis
Parallel Processing for Next-Generation Sequencing (NGS) Analysis
...However, along with its rapid development, the data magnitude and analysis complexity for NGS far exceed the capacity and capability of traditional small-scale computing facilities, such as multithreading algorithms on standalone workstations. To address this issue, here we present a solution using the ever-increasing supply of processing power by massive parallel processing (MPP) systems. -
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eFECTIV performs shape outline analysis based on Elliptical Fourier transforms. The software includes a graphical user interface and several options to assist the user during the analysis
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clinicalStudyTracker
Clinical study tracker tracks case study members through activities.
Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports. -
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BIL++ is a set of standalone C++ packages for data processing in Bioinformatics (Graph mining, Bayesian networks, Genetic algorithm, Discretization, Gene expression data analysis, Hypothesis testing).
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splitsmb is a standalone application for calculating topological convergence diagnostics on MrBayes tree-output files (unrooted only at this point). It calculates the average- and maximum standard deviations of partition frequencies between runs.
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SISSIz is a program for randomizing multiple sequence alignments preserving dinucleotide content. It can be used as a control strategy for comparative noncoding RNA gene prediction programs and as a standalone RNA gene finder.
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aln2dist is a standalone program that uses a multiple sequence alignment to calculate a set of distance matrices and a set of distance restraints (lower and upper bounds). Also require the pdb structure files of homologous proteins to be used as models.
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RmscopII is a Tcl/Tk script responsible to redirect protein structure files (PDB files) or RasMol scripts to multiple RasMol sessions. It can be used as a web browser helper application or as a standalone program.
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gbwget is a command line/screen oriented tool to search in nucleotide or protein databases and to view or retrieve database entries. It can easily integrated into the EMBOSS seqence analysis Suite can also be used standalone.
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