Search Results for "two"
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Showing 39 open source projects for "two"
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Bowtie 2
A fast and sensitive gapped read aligner
...The tool builds compact FM-index-based reference indexes, keeping memory usage low even for large genomes like the human genome. Bowtie 2 outputs alignments in SAM format and includes companion utilities for building and inspecting indexes. It is widely used in bioinformatics pipelines for RNA-seq, DNA-seq, metagenomics, variant analysis, and other sequencing-based research tasks. Overall, Bowtie 2 remains a foundational command-line tool for high-throughput sequence alignment and reproducible computational biology workflows. -
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TVscript
Exploration of the removal of count variable transcripts.
> See TVscript wiki: https://sourceforge.net/p/tvscript/wiki/Home/ Related Software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: (See wiki) 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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Allelome.PRO
A pipeline to define allele-specific genomic features
Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here we present Allelome.PRO, an automated userfriendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analysed imprinted expression to give a complete picture of the “allelome” by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased biallelic or noninformative. ... -
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easy-dhpsf
GUI for fitting 3D single-molecule images using the double-helix PSF
This package of MATLAB routines with accompanying GUI allows scientific users to measure the 3D location of single molecules when using the double-helix point spread function (DH-PSF) widefield microscope. Version 2 also includes code that facilitates combining localization data from two spectral channels using a locally-weighted quadratic 3D registration function Features - Double-Gaussian estimator is calibrated via an axial scan of bright immobile fluorescent emitters (e.g. beads) - DH localization is performed through template matching and subsequent double Gaussian fitting - Tiff stacks of SM images are analyzed using template matching followed by double-Gaussian fitting to extract estimates of the molecule positions - Two spectral channels are registered by generating a locally-weighted quadratic mapping function from control point pairs -
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PF_HP
Prediction of proteinfolding in 2D HP model
Even in the simplified two dimensional HP-model (hydrophob/polar) the prediction of proteinfolding is NP complete. We implement a brute force algorithm with serial and parallel execution to solve short inputs of HP sequences (0-1 bitstrings). Selbst im vereinfachten zweidimensionalen HP-Modell (hydrophob/polar) ist die Proteinfaltung bereits NP-vollständig. -
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RElt
calculates overlap, kinetic integrals for numerical atomic orbitals.
...The implemented algorithm is described in my paper: "Numerical calculation of overlap and kinetic integrals in prolate spheroidal coordinates", International Journal of Quantum Chemistry, Volume 108, Issue 2, Year 2008, Pages 249–256 http://onlinelibrary.wiley.com/doi/10.1002/qua.21485/full -
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datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS... -
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This package includes a collection of MATLAB files which are designed to: 1. Given a calibration scan of the image of a point emitter with an engineered point spread function (PSF), 2. Perform a phase retrieval algorithm based on maximum likelihood estimation (MLE) of a phase aberration term which is added to the theoretical pupil function of the imaging system. 3. Use the phase-retrieved pupil function to perform single-emitter localization. Accompanying publication available here: https://doi.org/10.1364/OE.25.007945
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RAtom
solves nonlinear Kohn-Sham equation for the neutral atom.
...The implemented algorithm is described in the following papers: 1. Z. Romanowski, "Adaptive solver of a Kohn-Sham equation for an atom", Modelling Simul. Mater. Sci. Eng. vol. 17, 045001 (2009) 2. Z. Romanowski, "Application of h-adaptive, high order finite element method to solve radial Schrödinger equation", Molecular Physics, vol. 107, pp. 1339-1348 (2009). Further questions: romz@wp.pl -
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ISVASE
identification of sequence variant associated with splicing event
...Comparing with the existing software PVAAS, our method has several advantages such as stringent rule-depended filters and statistical filters in each step, detection sequence variants for known splicing events, identification sequence variants in two parts of splicing (junction) separately, detection junction shift events if providing known splicing annotation, evaluating splicing signal, comparing with known DNA mutation and/or RNA editing data, and short running time. -
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Toolkit for processing genetic data. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED, PED2RAW conversions; regions of homozygousity and other converters.
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MZmine 2
A framework for differential analysis of mass spectrometry data
MZmine 2 is a framework written in Java for differential analysis of mass spectrometry data. -
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openSEQ
NGS compute distro proloaded with pipeline analysis software
Forked Ubuntu 14.04 minimal install with XOrg and FluxBox desktop environment for web-based pipeline construction and job submission. HOWTO: 1) Set VM network settings to a bridged adapter type. 2) Load VM to client 3) From host: $ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure' --- passwd = 616287xx 5) or ssh into host with X forwarding, and type runme This will launch an X-session of Firefox on the client, which will then be forwarded to the host. The first homepage tab links to our pipeline constructer. ... -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
.... (2) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan 1;42(1):D756-63. (3) Cock PJ et al. Bioinformatics (2009) (4) Cokelaer et al, Bioinformatics (2013) -
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MDcons(Molecular Dynamics consensus)
Interpretation of Biomolecular MD simulations
...The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD. -
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PolySim
Polymer simulation utilites
Polymer simulation utilites for bead coarse-grained models of polymers. Includes 1) lattice monte carlo. Many kinds of lattices are supported. It shouldn't be a problem to implement any new specific one (discrete models) 2) off-lattice monte carlo and molecular dynamics (continuous models) Latter one is rebuild of earlier version of simpatico (http://gemini.cems.umn.edu/research/morse/code/simpatico/home.php) project. Input and output are based on PDB file format which is better to visualize with pymol. For specific non-pdb input/output of 2nd program there are convertation utils also available. ... -
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Project for develop force fields with using ab-initio calculations
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allink
Software for data analysis, image processing, simulations, solver.
Collection of utilities based on two basics classes: Matematica and VarData. Matematica) performs math operations on vectors and matrices for smoothing, interpolation, convolution, image processing... VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. -
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SPiM2Eclipse
Eclipse plugin for Stochastic Pi Machine
Stochastic Pi Machine (SPiM), created by Microsoft, is a programming language for modeling biological processes. Two tools are available from Microsoft for simulation. A web application Visual SPiM, and a destkop application SPiM Player. Both simulation tools require to be run on a Windows platform. Fortunately Microsoft has also released a command line version for Linux and Mac OS based on OCAML however this version will only output a CSV file for the simulation results. ... -
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TrajLab
MATLAB based programs for trajectory simulations of molecules
TrajLab (which stands for TRAJectory LABoratory) consists of two sets of MATLAB program packages. While subproject MolDynSim deals with generation of molecular trajectories (and other aspects of molecular simulation), subproject MetaStable is dedicated to the analysis of molecular trajectories by detecting metastable conformations (as well as other analysis techniques). Note that each of the two sub-projects has its own SVN repository, wiki, tracker, etc: Probably TrajLab is the first attempt for a general purpose molecular simulation package in MATLAB. ... -
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ScreeningAssistant 2 is a modular software dedicated to perform various simple and advanced chemoinformatics analysis around chemical libraries.
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The project devoted to develop LADY software. LADY is a abbreviation formed from LAttice DYnamics toolkit. The software is the semi-emperical program which aids to simulate the dynamical property of crystals within a selected potential function.
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This project is aimed at providing useful thermodynamic tools for biochemists, including formation energy estimation of virtually every biochemical compound and metabolic pathway analysis and profiling.
