ERGO

09 May 2024

Ergo, previously MAEviz, is an open-source project that helps reduce the time from discovery gap that exists between researchers, practitioners, and decision makers by integrating the latest research findings, most accurate data, and new methodologies into a single...

Trellis

09 May 2024

Trellis is an interactive web-based application for argumentation and decision-making. Using Trellis, users can come to individual and collaborative conclusions on virtually any topic, from scientific discourse to political and policy views to deciding which product...

RepeatExplorer

09 May 2024

RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next generation sequencing data from plant and animal genomes. It employs graph-based clustering (Novak et al. 2010) of sequence reads to identify repetitive...

Zenodo

09 May 2024

As CERN service, it is supported by European Commission, and powered by Invenio, digital repositories. It is a free and open-source software for the long-tail of science, enabling researchers to share and preserve any research outputs in any size, any format and from...

InterPro

09 May 2024

InterPro provides a functional analysis of proteins by classifying them into families and predicting domains and important sites. It combines protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual...

WINGS

09 May 2024

WINGS is a semantic workflow system that assists scientists with the design of computational experiments. A computational experiment specifies how selected datasets are to be processed by a series of software components in a particular configuration. Earth scientists...

Medicago truncatula genome database

09 May 2024

Medicago truncatula, a close relative of alfalfa, is a preeminent model for the study of the processes of nitrogen fixation, symbiosis, and legume genomics. The sequencing project was initiated with a generous grant from Samuel Roberts Noble Foundation (link is...

PRIDE

09 May 2024

PRIDE (The Proteomics Identifications Database) is a standards-compliant, public repository for proteomics data. It contains protein and peptide identifications and their associated supporting evidence.

Decryptor

09 May 2024

Analyses data from tandem mass spectrometry of human proteome for the presence of point alterations. Subsequently, decryptor deduces DNA/mRNA alterations whenever possible.

ARP/wARP 8.0

09 May 2024

ARP/wARP is a software project for automated protein model building and refinement. ARP/wARP combines pattern recognition-based interpretation of an electron density, its modelling as a hybrid model and a maximum likelihood parameter refinement with REFMAC.

GLASS (Global to Local Analysis of System Sustainability)

09 May 2024

Global to local analysis of systems sustainability to meet the Sustainability Development Goals on a changing planet with limited land and water resources.

INTERACTIVE PARALLELIZATION TOOL (IPT)

09 May 2024

Interactive Parallelization Tool (IPT) assists domain-­experts and students in efficiently parallelizing their existing C/C++ applications using any of the following parallel programming models: Message Passing Interface (MPI), OpenMP, CUDA, and hybrid programming....

bio.tools

09 May 2024

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

Multi Experiment Matrix (MEM)

09 May 2024

MEM is a web-based multi experiment gene expression query and visualization tool. It gathers several hundreds of publicly available gene expression data sets from ArrayExpress database. Different data sets feature different tissues, diseases and conditions. For...

SLATE and the Mobility of Capability

09 May 2024

SLATE (Services Layer at the Edge) is a new project that, when complete, will implement “cyberinfrastructure as code” by augmenting the canonical Science DMZ pattern with a generic, programmable, secure and trusted underlayment platform.

rPredictorDB

09 May 2024

rPredictorDB is a predictive database of secondary structures of individual RNAs and their formatted plots. The structures are generated by template-based prediction of RNA secondary structure with experimentally identified structures as templates. RNAs with large...

3DEM (3-D ELECTRON MICROSCOPY)

09 May 2024

A web-based research platform focused on developing and disseminating new technologies for enhanced resolution 3-dimensional electron microscopy.

ValidatorDB

09 May 2024

Database of validation results for ligands and non-standard residues in the Protein Data Bank.

Network for Computational Nanotechnology and nanoHUB

09 May 2024

The Network for Computational Nanotechnology (NCN) has a mission to connect theory, experiment, and computation in a way that will transform nanoscience into nanotechnology. While addressing challenges in the field, NCN researchers produce new algorithms, approaches,...

Chem Compute

09 May 2024

The Chem Compute website allows students to easily access state of the art computational software for free. Our hope is that this will enable faculty to incorporate computational chemistry into their undergraduate teaching and research curriculum without the hassle...

SILVA

09 May 2024

A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.

LIPID MAPS Lipidomics Gateway

09 May 2024

LIPID MAPS Lipidomics Gateway was created in 2003 via an NIH “Glue Grant” to provide access to lipid nomenclature, databases, tools, protocols, standards, tutorials, meetings, publications, and other resources and serving the international lipid research community. ...

Open OnDemand

09 May 2024

Open OnDemand is an NSF-funded open-source HPC portal based on OSC’s original OnDemand portal. The goal of Open OnDemand is to provide an easy way for system administrators to provide web access to their HPC resources, including, but not limited to: ...

GenePattern

09 May 2024

GenePattern is a powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to...

Pfam

09 May 2024

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pfam entries which...