Search Results for "sarahhlynn.7"

We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this...

GUI front-end for the OMSSA proteomics search engine. 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/omssagui/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124

BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions: (1) sequencing quality assessment, (2) sequence cleaning, (3) sequence read mapping, (4) methylation quantification, (4) sample comparisons based on methylation profile, (5) identification of DMRs (differentially methylated regions), (6) annotation of DMRs, (7) functional analysis of differentially methylated genes, (8) generation of input files for visualization, and (9) support for advanced sequencing technologies such as TAB-seq, OxBS-seq, MAP-it, and NOMe-seq.

NOTE: Code commits are FROZEN on SourceForge: New code is now at <http://github.com/Xastir/Xastir>. Real-time tracking & messaging of stations via radio/internet APRS data streams, w/125 map formats supported. Linux/FreeBSD/Solaris/MacOSX/Windows in any of 7 languages. Can also be used for mobile mapping w/GPS. MAILING LISTS ARE AT: PROJECT->WEB SITE.

Metro is a CLI tool that computes possible paths between two stations. It is written in Perl and available under the BSD license.

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.

A database of linguistic annotation of medical text (from MEDLINE), including corpora used with ABGene, BioCreative I and II, and the MedPost training corpus.

APoDIx is a Portable Bio-Database Index system. It retrieves biological database information from the website of Oxford Journals, save them in a local position, and provides a viewer for display and search the information.

The goal of the GeneText project is the development of a software package that will enable users to dynamically generate an information summary page from multiple sources given a search term. Fields of interest are biology, genetics and bioinformatics.

OpenBRR is an initiative to create an open and standard framework for software assessment process. We strive to provide the industry standard framework in the open source world, and also the trusted data source to aid software assessment process.

The Scenario Data Selector is a Perl script that serves up scenario data on the web. Users can browse data and choose to show by value or as growth rates or indices. Data can be shown by region or indicator - the script takes care of regional aggrega

gnufe is a perlqt program that provides a front-end to gnuplot, the powerful plotting system. It is designed to work on a lot of data files, and should be fast to use via lots of keyboard shortcuts.

A collection of many different perl-scripts doing math-stuff, including date and time scripts.

FreeNorm is a cross-tabulation web application adapted from SurveyComplete's real-time reporting system. Currently it can run tabs on extremely large datasets, export to Excel, read ASCII data, and understand table definitions in the UNCLE tab language.

blaSTOR is a Microsoft Access database used to BLAST, store and analyze multiple nucleotide and protein sequences. It has an easy-to-use graphical interface that allows users to perform BLAST operations and organize their data quickly and effectively.

LavaRnd is a random number generator that converts a digitized chaotic source (such as a lens capped web camera) into cryptographically strong random numbers. LavaRnd comes with both an APIs (currently C and Perl) as well as a number of demos.

An attempt at developing an Artificial Inteligence software, based on the notion that inteligence is a set of conditional choices (in programming terms, it means a whole lot of if statements).

See Matt Wright for PERL CGI scripts. Upgrade to Oracle8i if you need MD4/5 or binary operations for PL/SQL.

A collection of Perl modules and programs for bioinformatics. Design intention is to make most common, straight-forward tasks in computational biology as simple, and portable, as possible.

Leo is a project to provide an architecture for defining XML specifications of grammars for different natural language parsing systems and tools for using that architecture to permit sharing of grammar resources across different systems.

Featurama, superceding ProbePicker, is a bioinformatics program used to generate short probes from large datasets for use in DNA microarray experiments. A new project, BioSap, will extend the functionality of featurama.

LibGPIB is a library of C++ classes which can be used to program various GPIB controllers and instruments including GPIB-ENET, GPIB-232-CT-A, and the NI488-GPIB cards.

The dream of Leibniz. A project devoted to realising the lingua characteristica and calculus ratiocinator using XML technologies where appropriate. Includes (at this stage mainly consists of) research in philosophy and logic.