Search Results for "one-wire" - Page 2

...Publication: ScreenSifter: analysis and visualization of RNAi screening data Pankaj Kumar, Germaine Goh, Sarawut Wongphayak, Dimitri Moreau and Frédéric Bard BMC Bioinformatics. 2013 Oct 3;14(1):290. http://www.biomedcentral.com/1471-2105/14/290/abstract

...It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of SNPs differs from the ancestral allele, it may be better explained as a mutation or sequencing error. But if a series of SNP alleles differ from the ancestral pattern, then it may be more likely that an HRE has occurred, particularly if the allele pattern matches that from another part of the tree better than that of the ancestral node.

These are Python scripts plus C/C++ programs for automating the reference free genomic analysis described in: Kua C-S, Ruan J, Harting J, Ye C-X, Helmus MR, et al. (2012) Reference-Free Comparative Genomics of 174 Chloroplasts. PLoS One 7(11). http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048995 Analytical concept conceived by CHCannon and CSKua. Original script written in Mathematica by CHCannon.

...In order to perform the analysis, one also need the DEDA computation core program. Please email a request to me, entitled: 'Request for DEDA computation core', if you wish to have a copy.

...An unlikely-to-be-the-most-parsimonious tree is printed upon completion in basic Newick tree format. As all parts of the program are the original work of a beginner programmer, this may represent one of the worst approaches to solving the phylogenetic problem. I have clearly avoided object-oriented programming. Nevertheless, I distribute this imagining it might someday be slightly educational or at least provide a laugh at the pathetic attempt it makes to reinvent the wheel

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...

Febrl (Freely Extensible Biomedical Record Linkage) does data standardisation (segmentation and cleaning) and probabilistic record linkage ("fuzzy" matching) of one or more files or data sources which do not share a unique record key or identifier.

GUI program to perform multiple searches on proteins for specific groups of amino acids in specific protein regions and to be able to filter by signalp scores. I hope to add lots of new functionality including the ability to create local database

Naimath (syn. blessing) is a project to create tools for diagnosis, management of clinical cases in the form of Rule based Medical Expert System integrating Interactive Health education, Semantified EMR, and serve as a learning tool for students. Website seen at www.naimath.com

A collection of corpus and access routines for developing biological literature analysis systems.

SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.

At the outset, the goal of this program is to provide a suite of tools to aid in the back-translation of amino acid sequences in a manner that provides useful information for synthetic gene design.

A collection of python classes for computational ecology and evolutionary biology.

Inter University Multi-Modal Imaging

This project implements an algorithm for segmenting protein sequences into smaller meaningful blocks. The method is based on the pure statistical approach and it uses an analogy between proteins and natural language.

This project is started out of the idea to simulate simple creatures like game of live. The goal is to build up an multi processor/host environment to simulate the building of simple live in given world environments.

This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.

MIVF - Medical Imaging and Visualization Factory, is a framework for medical applications. It supplies a platform, in which image processing and 3D visualization algorithms can be employed as reusable components (functional modules or plugins).

Integration of results from multiple homology searches

pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use. Please see our new project page and wiki at http://code.google.com/p/pygr.

a cross-platform framework and environment for haplotype analysis with a special focus on human and medical genetics in python/wxpython

MetaPepSeq is metaserver for protein identification in Mass Spectrometry Experiments. It helps joining the power of Mascot and de novo sequencing algorithms by merging together into one tool.

Random Genome Sequence Downloader.

BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.

RStatServer is a system for quickly developing and deploying web applications that integrate statistical computations and graphics. It is built using the Zope web application develeopment system and the open-source statistical data analysis environment R