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PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.
Io (ISREC ontologizer) is a program to classify high-throughput genomics data (e.g. microarray results) in the Gene Ontology. Io includes a statistical estimation of the significance of data in the GO nodes and reannotation files for Affymetrix chips.
Fully managed relational database service for MySQL, PostgreSQL, and SQL Server
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Cloud SQL manages your databases so you don't have to, so your business can run without disruption. It automates all your backups, replication, patches, encryption, and storage capacity increases to give your applications the reliability, scalability, and security they need.
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
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.
Web-based Electronic Data Capture (EDC) software for clinical trials. Uses XML-based data store based on CDISC ODM standard for clinical data interchange.
ReadSeq is a program and library for conversion of biosequence data from one format to another, useful in various bioinformatics programs and services. It is written in Java, though an earlier version in C remains available.
TM4 is a suite of applications for managing and analyzing microarray data. TM4 provides datastorage and tracking, image analysis, normalization, data filtering, clustering and statistical analysis capabilities. Includes MADAM, Spotfinder, MIDAS, and MeV.
Maple Tree is a Java based visualization tool used by researchers in the biological sciences to visualize and graphically browse the results of analyses of gene expression data collected from microarray experiments.
An Evolution Simulator of Single Cells in a Pond. This shows a crosssection of
water with sun shining from above. A single cell is dropped in and has various genes. The cells multipy and evolve. See Files above for download and screenshot.
Annotated Gel Markup Language is a simple markup language that is being proposed to markup data obtained by 2D gel electrophorosis.The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases.
GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work
Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.
A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).
This tool integrates and enhances publicly available genome data from different sources into a local database. Using a web browser, scientists may view and query the data, keep persistent notes, and schedule batch services (such as BLAST) from NIH.
...You can write your Envolvable Code with it;
You can make your computer write program itself;
You can run program without compiling time;
You can manage source as data
OmniGene is a set of reausable components that have been packaged into frameworks. These frameworks are used to produce domain specific services for common bioinformatics tasks including: visualization, database access, and pipeline building.