Tools services

Name of service Description ELIXIR Node
Atomic Charge Calculator

Atomic Charge Calculator - web application using the Electronegativity Equalization Method.

ELIXIR Czech Republic
bio.tools

Web portal for tools registry and discovery, incorporating tool benchmarking and service monitoring information and the use of EDAM for precise scientific tool description. 

ELIXIR Denmark
BioXSD / GTrack

The BioXSD / GTrack ecosystem is an infrastructure of generic state-of-the-art data formats for integrative bioinformatics, with focus on genomics and epigenomics, sequence and structure bioinformatics, and other applications. 

ELIXIR Norway
CAMEO

Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. 

ELIXIR Switzerland
CAVER 3.0

Tool for analysis of molecular channels in proteins. CAVER Analyst allows interactive visualization of the channels and cavities in protein structures.

ELIXIR Czech Republic
ClustVis

ClustVis is a web tool for visualizing clustering of multivariate data. This web tool allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps.

ELIXIR Estonia
Consulting/Expertise

Expertise on very diverse subjects of data processing, analysis and curation as well as connections to existing infrastructure RI's like EUDAT. This expertise can be made available to research projects and organisations.  

ELIXIR Netherlands
CSC Chipster

Chipster is a user-friendly analysis software for high-throughput data. It contains hundreds of analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. 

ELIXIR Finland
Decryptor

System for identification of alterations using protein mass spectrometry.

ELIXIR Czech Republic
DNATCO

Web interface for assignment and analysis of DNA conformers.

ELIXIR Czech Republic
ExPASy

SIB's resource portal with access to all major tools and databases provided by different SIB groups and external partners. Specific query features allow interacting with many resources at the same time. 

ELIXIR Switzerland
FAIRsharing

An information and educational resource of inter-related data standards, databases and policies. 

ELIXIR UK
g:Profiler

g:Profiler is a bioinformatics toolkit for characterising and manipulating gene lists of high-throughput genomic data.

ELIXIR Estonia
GnpIS

GnpIS is an interoperable Information System for plant and pest genomics. It is a powerful multispecies centralized information system with seven linked relational databases. 

ELIXIR France
GraphWeb

GraphWeb is a public web server for graph-based analysis of biological networks.

ELIXIR Estonia
HAMAP

HAMAP is a system for the classification and functional annotation of protein sequences. It consists of a collection of expert curated family profiles for protein classification and associated rules for protein annotation. 

ELIXIR Switzerland
HotSpot Wizard

Web server for identification of hot spots in protein engineering.

ELIXIR Czech Republic
IMGT

An integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) of human and other vertebrate species. 

ELIXIR France
InterMine

A database framework widely used to support model organism databases. 

ELIXIR UK
IreSite

Non-coding genome sequences and genetic network tools. The IRESite presents experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions.

ELIXIR Czech Republic
IS Finder

International Reference Center for Prokaryotic Insertion Sequences (IS) is a public database and a research tool that provides a list of insertion sequences (IS) isolated from bacteria and archae.

ELIXIR France
ISMARA

Models genome-wide expression data in terms of genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample- dependent activities, and their genome-wide targets. 

ELIXIR Switzerland
KEGGAnim

KEGGanim is a tool for visualizing data in the context of biological pathways. KEGGanim produces animations or static images of KEGG pathways by overlaying high-throughput data over handdrawn KEGG pathway maps.

ELIXIR Estonia
Marine Metagenomics Portal (MMP)

Freely accessible microbial genomics and metagenomics reference databases that include MarRef, MarDB, and MarCat. The MMP also includes a search engine that you can use to query all three databases at once.

ELIXIR Norway
MEM

MEM is a web-based multi experiment gene expression query and visualization tool. It gathers thousands of publicly available gene expression data sets from ArrayExpress database.

ELIXIR Estonia
META-pipe

The META-pipe pipeline for annotation and analysis of marine metagenomics samples provides insight into phylogenetic diversity and metabolic and functional potential of environmental communities.

ELIXIR Norway
Metadyn View

Interactive viewer of metadynamics results.

ELIXIR Czech Republic
MicroScope

MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. 

ELIXIR France
MOLE

Toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in (bio)macromolecular structures, e.g., proteins, RNA, DNA and biomacromolecular assemblies.

ELIXIR Czech Republic
MOLEonline

Web interface providing a direct access to MOLE 2.0 functionality and enabling on-line and easy-to-use interactive channel analysis.

ELIXIR Czech Republic

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