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AI-generated apps that pass security review
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Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.
PHLIP is a MATLAB centric academic software application for quantification of biofilm structure from confocal laser scanning microscopy (CLSM) data, intended for automated processing and statistical analysis of large data sets produced by CLSM.
The CHIP Cluster Generator attempts to create spatio-temporal cluster data in an automated fashion to help evaluate epidemic detection software. The spatio-temporal data will then be used to determine robustness of spatial detection algorithms.
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 dataanalysis environment R
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BLASTgres is a set of modules that can be added to PostgreSQL for data management of biological sequences. It extends PostgreSQL with datatypes for sequence information and middleware for dynamic access to sequence analysis tools & services like BLAST.
BACMan is a Microsoft Access based application designed for the management and analysis of hybridization data related to the high throughput screening of large insert genomic libraries associated with physical mapping projects.
To develop a software package for time series manipulation and cycles analysis. Cycles means repeated occurrences at nearly equal time intervals in any time series data. See http://www.cyclesresearchinstitute.org/ for a site about cycles.
This is a lightweight database system to support bioinformatics data mining. See BMC Bioinformatics. 2005 Mar 24; 6(1): 72 for the first publication. It supports large-scale data mining and data mining tools.
openSputnik is a robust distributed platform for massive scale precalculation of genetic and genomic data using contemporary bioinformatics methods. Annotated DNA, RNA and protein sequences are stored as binary objects in a variery of relational database
Python library to convert networks from/to many different formats, like the ones used in Pajek, Cytoscape and other popular graph formats like GML. It also includes support to integrate experimental data to the netowork.
Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.
MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic
BioCSharp is an open-source project designed to provide a bioinformatics .NET framework for processing biological data. It will include objects for manipulating sequences, file parsers, DAS, database access and analysis and statistical routines.
TAS (Transcription Analysis System) is a multi-tier framework for running parameterized SQL queries. Users can analyze new data or new combinations of data with a few clicks in a GUI. Potentially complex/repetitive database interaction is all automated
GATA is a graphic alignment tool for comparative sequence analysis. It makes use of BLAST to graphically align two DNA sequences, creating box- line- box representations of window scored local alignments. GATA also displays extensive GFF gene annotation.
A Java software for 3D visualization of graphs/networks. It implements many graph layout algorithms (such as force-directed methods), graph generators (such as scale-free networks) and graph modifiers. Most functions can be accessed through its GUI.
Rana, Restriction Analysis Libraries.
Rana is written in Python and provides a set of libraries and scripts to work with restriction enzymes and ADN. The aim is to ease the development of molecular biology software for research or education purposes.
TM4 is a suite of applications for managing and analyzing microarray data. TM4 provides data storage and tracking, image analysis, normalization, data filtering, clustering and statistical analysis capabilities. Includes MADAM, Spotfinder, MIDAS, and MeV.
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.