Search Results for "research" - Page 8
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Showing 347 open source projects for "research"
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The igraph library
Library for creating and manipulating graphs
This is a library for creating and manipulating graphs with focus on speedy operations for large, sparse graphs. -
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Application to create 'electronic fluorescent pictographic' representations of gene expression patterns. Created at the Provart lab of the department of Cell & Systems Biology, University of Toronto.
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein... -
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GIIAF Microscopy Library
The GIIAF Microscopy Library, that uses customised OMERO software
This project incorporates a suite of tools that aim to allow researchers within Griffith's Imaging and Image Analysis Facility (GIIAF) to efficiently and effectively provide secure, centralised, web-accessible data storage, management and manipulation. The open-source Java-based OMERO software was customised to provide most of the features of this project. -
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SpiKeDeteKt
An automatic spike detection program to be used with new KlustaKwik
This is an automatic spike detection program which takes account of probe geometry and produces a .mask file to be used with the new masked version of KlustaKwik. We recommend you use Python 2.6 or 2.7, e.g. a free academic version can be obtained from Entthought Python. The input files for SpiKeDeteKt are: .dat (raw data file) .probe (probe file, described below - user constructed) parameters.py (optional - otherwise it uses defaultparameters.py) SpiKeDeteKt outputs... -
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The PyCogent project is moving to GitHub. When completed, you will find us at http://github.com/pycogent/pycogent/. You can find the PyCogent website at http://www.pycogent.org.
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Laboratory notebook using version control system and independent date-time stamping (as notarization), in order to ensure record accountability, auditing, and conforming to US FDA 21 CFR 21's rule on electronic records. Please kindly rate this application or drop me an email at [ mauriceling AT acm DOT org ] so that I can hear from you. Otherwise, I have no idea who the users are. Please kindly help.
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GUI for DEDA
GUI for DEmography Data Analysis
<This project has been completely rewrote and transformed into a new one: https://sourceforge.net/projects/deday/. 2013/06/26> The graphic user interface for DEDA (DEmography Data Analysis), a scientific software package fitting survivalship data to a number of distributions using maximum likelihood (ML) method. Currently, Weibull (2p), Gompertz and Gompertz-Makeham are supported. IMPORTANT NOTICE: Only the GUI is provided here. In order to perform the analysis, one also need the DEDA... -
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CoNIFER
Homepage for CoNIFER (Copy Number Inference From Exome Reads)
CoNIFER uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. -
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Prediction of MHC class I- and MHC class II-restricted T-cell epitopes. Prediction of proteasomal/immunoproteasomal processing of antigens. Prediction of peptide-TAP binding.
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Pysimony
A Pythonic Implementation of Parsimony Inference of Phylogeny
UPDATE: After some bug fixes, I've ditched Pysimony for Javamony: https://sourceforge.net/projects/javamony/ Given Python's beauty, I know that someday I will have to finish Pysimony. A student's first attempt at a phylogenetic inference program, written in the simplistic yet elegant Python. Pysimony reads a FASTA file (only ATGC accepted) specified as its only argument. Basic testing has shown that it is slow, inaccurate and most definitely inefficient. An... -
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u/sbmv2012
Taxonomy assignment of metazoans using a python based pipeline
The aim of this project is to create an automated pipeline for taxonomic assignment of DNA sequences obtained from environmental samples. We develop a series of python scripts to process the raw sequence data obtained from benthic environmental samples and to taxonomical assignment of these sequences and finally to integrate all data in a relational database. -
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Primer Design Tool
Design PCR primers
A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them. -
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brocc
BLAST Read and OTU Consensus Classifier
NOW HOSTED ON GITHUB: https://github.com/kylebittinger/brocc Old releases are kept here for archival purposes. -
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GemSIM is a software package for generating realistic simulated next-generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using appropriate empirical error models.
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pyBioImage
Biological Imaging Software suite
The pyBioImage is a python a python based biological imaging suite tailored to the problem of finding Germinal Center "spots" within multidimensional microscopy images as it is described in the research paper: "Software tool for 3D extraction of germinal centers", by David N. Olivieri, Merly Escalona and Jose Faro. -
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QUASR
Cross-platform NGS processing and analysis pipeline in Python
QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is... -
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Atlas2Cloud
Atlas2 Genome Analysis Pipeline on Amazon Web Services
This is the backend source code of the Atlas2-Cloud pipeline on Amazon which starts and terminates worker nodes, runs analysis and monitors worker instances. It is PRIMARILY meant to be used through Amazon Web Services (AWS) management console by looking for the public Atlas2-Cloud machine image. Alternatively, the code can also be used for running the pipeline from your computer. By installing this software on your computer you will be setting up your computer to act as the head node... -
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QDC (quick direct-method controlled) is an optimized exact implementation of the Gillespie's direct-method. It is designed for biochemical simulations when there is the need of dynamic parameters whose values can change during the simulation.
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CancerVaccine
In silico vaccination experiment to determine best vaccination schedul
This project is a simplified representation of the main immune system cells and their interactions. The aim is to simulate the effect of the introduction of a cancer vaccine cell which would stimulate the immune response against the tumor-associated antigen, and consequently against cancer cells themselves. In vivo vaccination experiments take very long to complete, so it would be useful to simulate these experiments such that the best schedule of vaccination is determined that would result... -
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cancer_dynamics
Cancer Dynamics web
Website that shows the dynamics of a tumor by solving a system of ordinary differential equations. The results are two kind of graph images, and a gif file, being all of them available for download as a compressed file.
