Tools developed and provided by ICTBioMed

ICTBioMed consortium groups partners with a long record of delivering informatics-based solutions for life sciences research.

The joint capacity of the consortium is reflected through the spectrum of informatics tools that have already been or could potentially be used in biomedical research. This tab contains a list of useful tools well-established in research communities or with potential for exploitation in cancer research.

Anvaya : A Workflow Environment for High Throughput Comparative Genomics

Anvaya is a software application, which provides a workflow environment for high throughput Comparative Genomics. It consists of an interface to Bioinformatics tools and databases, that are loosely coupled together in a coordinated system to execute a set of analyses tools in series or in parallel.

Genopipe

GENOPIPE is an automated pipeline for high-throughout comparative genomics, developed with a focus on the detection of orthologous groups, which serve as the seed for subsequent annotation and analysis. It also provides data on SNP, paralogs and probable protein coding regions missed by the gene prediction algorithms, hence serving as a reliable supplementary pipeline for prokaryotic genome annotation.

Mercury

Mercury provides telemedicine consultation for various fields of medicine. It facilitates safe (all patient data are encrypted) and comprehensive Electronic Medical Record (EMR). Extensive image processing features are also included in this Integrated Telemedicine Solution.

ROSETTA Protein Modelling Pipeline

The ROSETTA Protein Modelling Pipeline is a high throughput protein structure prediction platform delivered as a grid-based service.

Human Metabolic Atlas

Human Metabolic Atlas is one of the projects carried out in the group of Systems Biology at Chalmers.

Gaggle

The Gaggle is a framework for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data.

BioMet ToolBox


The BioMet ToolBox, is a web-based resource for analysis of high-throughput data, together with methods for flux analysis (fluxomics) and integration of transcriptome data exploiting the capabilites of metabolic networks described in genome scale models.

caBIG Tools

The caBIG® tools inventory includes over 40 software tools for biomedical research. They are based on open-source software and free. These tools allow researchers and clinicians to collaborate more effectively and support comprehensive studies.

Clepsydra

Clepsydra is a flexible and scalable system for aggregation, processing and provisioning of data from heterogeneous sources. It was designed and developed to be a basis for services focused on aggregation and enrichment of (meta)data describing on-line collections of cultural heritage digital objects. The first production deployment of this system is the PIONIER Network Digital Libraries Federation.

Vitrall

Vitrall is a distributed web based visualization system. In real-time visualization of a complex 3D content using remote servers users may watch the same content from different points of view simultaneously.

dArceo

dArceo is a system for long-term preservation of source data (e.g. master files), primarily focused on textual, graphical and audiovisual content. It makes migration of source data possible with respect to the OAIS model. Additionally, dArceo provides conversion and source data delivery functions, which may help both to build digital libraries and access source data by users.

Chimera - an Extensible Molecular Modeling System

Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.

QosCosGrid

The QosCosGrid middleware is an integrated system offering advanced job and resource management capabilities to deliver to end-users supercomputer-like performance and structure. By connecting many distributed computing resources together, it offers highly efficient mapping, execution and monitoring capabilities for variety of applications.

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