Atera all-in-one platform IT management software with AI agents
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ChiBE (Chisio BioPAX Editor) is an open source pathway editor for biological pathways in BioPAX format. ChiBE converts BioPAX graphs into process diagrams where complexes and compartments are represented with compound nodes.
!!! For latest version, please see !!!
http://code.google.com/p/chibe
Visualize chromatographic properties for peptides from replicate, multi-site HPLC-MRM Mass Spectrometry experiments. RT Viewer was developed to easily visualize and troubleshoot chromatographic properties of a study across multiple laboratories.
Contextor is a light-weight simple-to-use Java based library to help developers and researchers working with the general concept of a resource; as examples, resources can be text resources, web resources, images and videos.
Generate secure, production-grade apps that connect to your business data. Not just prototypes, but tools your team can actually deploy.
Build internal software that meets enterprise security standards without waiting on engineering resources. Retool connects to your databases, APIs, and data sources while maintaining the permissions and controls you need. Create custom dashboards, admin tools, and workflows from natural language prompts—all deployed in your cloud with security baked in. Stop duct-taping operations together, start building in Retool.
TreeViewJ is a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches, and add names to nodes. Collection dates can be mapped onto a timeline, and sorted.
BorderFlow implements a general-purpose graph clustering algorithm. It maximizes the inner to outer flow ratio from the border of each cluster to the rest of the graph.
MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
Anna is lightweight Java framework to build pipeline systems of any kind.
It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.
EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
Trial Criteria Online Data Entry (trialCODE): a Java-based user interface that codifies eligibility requirements used to automate the screening of potential subjects to clinical trials. Used for caMATCH screening engine on BreastCancerTrials.org site.
The development and curation of a range of XML-based tools
for using Chemical Markup Language (CML), including
XSD XML Schemas for validation, datatyping and constraining CML
documents and XSLT Stylesheets for transforming, filtering and rendering.
A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.
GEM is a computational method for identification of transcription factor modulators, using expression datasets. The method tests if the correlation between factor and target gene depends on the expression of the modulator.
OpenClinica is a web-based electronic data capture platform for clinical research. See http://www.OpenClinica.org/ for downloads, documentation, and mailing lists.
The purpose of this project is to develop ontology-based tools for the study of animal behavior (ethology). The goal is not to produce a general ontology or editor, but comparative methods
and (behavior) data entry tools (ethontos and owlwatcher).
A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.