Bioinformatics and Lab Informatics Resources
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Bioinformatics and Lab Informatics Resources
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Run an analysis using Data Cruncher · The CGC Knowledge Center

Run an analysis using Data Cruncher · The CGC Knowledge Center | Bioinformatics and Lab Informatics Resources | Scoop.it
Documentation for the Seven Bridges Cancer Genomics Cloud (CGC) which supports researchers working with The Cancer Genome Atlas data.
Sandrine Palcy's insight:
"Data Cruncher allows you to enter and execute Python, R or Julia code to perform further analyses on your data on the CGC. This page will explain how you can access Data Cruncher from a project on the CGC, set up an analysis and execute code within the analysis. To be able to run the analysis, you need execute permissions in the project."
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Structural Bioinformatics Library

Structural Bioinformatics Library | Bioinformatics and Lab Informatics Resources | Scoop.it

"Structural Bioinformatics Library" is a Template C++/Python API for solving structural biologic problems.

Sandrine Palcy's insight:
"The Structural Bioinformatics Library (SBL) is a generic C++ / Python library, providing models and algorithms for structural bioinformatics, so as to foster our understanding of the relationship between the structure and the function of macro-molecules and their complexes. Its design accommodates various molecular geometric models coding the physical and chemical properties of macro-molecular structures, and the variety of operations undertaken on these models."
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DNAdigest: Empowering efficient access and sharing of Data.

DNAdigest: Empowering efficient access and sharing of Data. | Bioinformatics and Lab Informatics Resources | Scoop.it
We do everything for the benefit of patients. We are a non-profit organisation empowering efficient access and sharing of genomics data.
Sandrine Palcy's insight:
"DNAdigest is a charity working to promote efficient sharing of human genomic data to improve the outcome of genomic research and diagnostics for the benefit of patients. Repositive, a social enterprise spin-out of DNAdigest, is building an online platform that indexes genomic data stored in repositories and thus enables researchers to search for and access a range of human genomic data sources through a single, easy-to-use interface, free of charge."  http://dx.doi.org/10.1371/journal.pbio.1002418
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Sandrine Palcy's curator insight, April 18, 2016 10:55 AM
"DNAdigest is a charity working to promote efficient sharing of human genomic data to improve the outcome of genomic research and diagnostics for the benefit of patients. Repositive, a social enterprise spin-out of DNAdigest, is building an online platform that indexes genomic data stored in repositories and thus enables researchers to search for and access a range of human genomic data sources through a single, easy-to-use interface, free of charge."  http://dx.doi.org/10.1371/journal.pbio.1002418 ;
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SAMSON Connect |

SAMSON Connect | | Bioinformatics and Lab Informatics Resources | Scoop.it
"SAMSON - Software for adaptative modeling and simulation for nanosystems"
Sandrine Palcy's insight:
"SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON's generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means "Software for Adaptive Modeling and Simulation Of Nanosystems"."
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Bio.tools : A portal to bioinformatics resources world-wide

Bio.tools : A portal to bioinformatics resources world-wide | Bioinformatics and Lab Informatics Resources | Scoop.it

The Tools & Data Services Registry provides essential scientific and technical information about analytical tools and data services for bioinformatics. The registry is provided by a community effort coordinated by the Danish node of ELIXIR - the European infrastructure for biological information.

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Sandrine Palcy's curator insight, March 2, 2016 5:21 AM
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A workflow for omic data analysis - OMICtools

A workflow for omic data analysis - OMICtools | Bioinformatics and Lab Informatics Resources | Scoop.it
OMICtools is a workflow for genomic, transcriptomic, proteomic, and metabolomic data analysis. All tools have been classified by omic technologies ( NGS, microarray, PCR, MS, NMR ), applications and analytical steps.
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The Cloud of the French Institute of Bioinformatics | IFB

The Cloud of the French Institute of Bioinformatics | IFB | Bioinformatics and Lab Informatics Resources | Scoop.it

The IFB cloud must not only provide hardware resources but must also facilitate the access to the hundreds of databases used in biology and the use of the great many software tools available to analyze experimental data produced by the life sciences community.

Sandrine Palcy's insight:

IFB provides trainins sessions for end-users and developers. More information at http://www.france-bioinformatique.fr/en/node/1439

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artich.io

artich.io | Bioinformatics and Lab Informatics Resources | Scoop.it

artichio is a modern tool designed to ease scientific collaboration and promote Open Science & Open Data in life sciences research.

Sandrine Palcy's insight:

Coming soon...

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Electronic Lab Notebook - eLabJournal

Web-based Digital Lab Notebook

eLabJournal is web-based Laboratory Information Management System (LIMS) developed and operated by Bio-ITech. It facilitates GLP-compliant data management in life science research laboratories and assists in full workflow automation, by providing data management solutions to laboratories.

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BioJS - An open source library of JavaScript components to represent biological data

BioJS - An open source library of JavaScript components to represent biological data | Bioinformatics and Lab Informatics Resources | Scoop.it
Sandrine Palcy's insight:

"BioJavaScript (BioJS) is a free, accessible software library that develops visualisation tools for different types of biological data. Data visualisation allows researchers to present their data to communicate key scientific hypotheses and concepts to a wider audience. Helping us to understand complex biological systems in relation to improving plant, animal and human health." (More at

http://www.technologynetworks.com/Informatics/news.aspx?id=182546 )

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Sandrine Palcy's curator insight, September 23, 2015 5:51 AM

 

"BioJavaScript (BioJS) is a free, accessible software library that develops visualisation tools for different types of biological data. Data visualisation allows researchers to present their data to communicate key scientific hypotheses and concepts to a wider audience. Helping us to understand complex biological systems in relation to improving plant, animal and human health." (More at http://www.technologynetworks.com/Informatics/news.aspx?id=182546)

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MolMeth

MolMeth | Bioinformatics and Lab Informatics Resources | Scoop.it

The Molecular Methods database (MolMeth) is a database to collect laboratory protocols and standard procedures applicable in molecular biology and life science.

The database has financially been supported by the Swedish biobanking infrastructure (www.BBMRI.se) and the EU FP7 project Affionomics (www.affinomics.org) in order to promote harmonization of laboratory techniques in biobanking as well as provide a repository for protocols commonly used to analyze samples.

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BD2K Home Page | NIH: ADDS Portal

BD2K is a trans-NIH initiative established to enable biomedical research as a digital research enterprise, to facilitate discovery and support new knowledge, and to maximize community engagement.
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Its purpose is to support the development of new approaches and tools to accelerate the use of metadata in biomedical research.

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Training portal | GOBLET

Training portal | GOBLET | Bioinformatics and Lab Informatics Resources | Scoop.it

GOBLET, the Global Organisation for Bioinformatics Learning, Education and Training

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Sandrine Palcy's curator insight, April 16, 2015 5:48 AM

The Training Portal allows you to browse course pages and training materials, and to download content of interest.

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EMBL-ABR Best Practice workshop series: the data life-cycle - EMBL-ABR

EMBL-ABR Best Practice workshop series: the data life-cycle - EMBL-ABR | Bioinformatics and Lab Informatics Resources | Scoop.it

24-28 October 2016 - This series of five workshops will cover the best practice data life-cycle for researchers

Sandrine Palcy's insight:
This series of five workshops will cover the best practice data life-cycle for researchers working with plants, animals, non-model, microbial and medically relevant genomes. It aims to provide insights into the different phases of the data life-cycle and map what is present or missing in Australia for the specific biological domains in terms of open data and FAIR principles.
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NCBO BioPortal

NCBO BioPortal | Bioinformatics and Lab Informatics Resources | Scoop.it



BioPortal, the world’s most comprehensive repository of biomedical ontologies.

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Last Release: 4.27 (May 2016) - 515 ontologies
The National Center for Biomedical Ontology is one of the National Centers for Biomedical Computing supported by the NHGRI, the NHLBI, and the NIH Common Fund
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Sandrine Palcy's curator insight, May 18, 2016 10:16 AM
Last Release: 4.27 (May 2016) - 515 ontologies
The National Center for Biomedical Ontology is one of the National Centers for Biomedical Computing supported by the NHGRI, the NHLBI, and the NIH Common Fund
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Stemformatics - Dataset Search

Stemformatics - Dataset Search | Bioinformatics and Lab Informatics Resources | Scoop.it
Datasets from 294 public studies with 4774 human and 1616 mouse samples
Sandrine Palcy's insight:
"Stemformatics is a collaboration between the stem cell and bioinformatics community."
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Sandrine Palcy's curator insight, April 15, 2016 10:48 AM
"Stemformatics is not a substitute for good collaboration between bioinformaticians and stem cell biologists. We think of it as a stepping stone towards that collaboration."
Samuel Viana's curator insight, April 15, 2016 12:53 PM
As células tronco (em inglês, "stem cells") são muito importantes em biologia do desenvolvimento e na medicina restituitiva uma vez que são capazes de se diferenciar em qualquer tipo de célula no organismo. Num futuro não muito distante, seria possível produzir qualquer tipo de órgão em laboratório o que evitaria o eterno problema de encontrar um dador compatível aquando dos transplantes.
Este portal pretende ser uma porta de entrada para muitos estudos na área, integrando diversas bases de dados provenientes de estudos em feitos em humanos e ratos.
Won Gi Yoo's curator insight, August 31, 2016 5:40 AM
"Stemformatics is a collaboration between the stem cell and bioinformatics community."
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All 2.3 Million Species Are Mapped into a Single Circle of Life

All 2.3 Million Species Are Mapped into a Single Circle of Life | Bioinformatics and Lab Informatics Resources | Scoop.it
Lineages of all known species on Earth are finally pieced together
Sandrine Palcy's insight:
"Researchers from a dozen institutions recently completed a three-year effort to combine tens of thousands of trees into one diagram, most readable as a circle " (Database OpenTreeOfLife.org -http://www.opentreeoflife.org/)
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Sandrine Palcy's curator insight, March 9, 2016 6:41 AM
"Researchers from a dozen institutions recently completed a three-year effort to combine tens of thousands of trees into one diagram, most readable as a circle " (Database OpenTreeOfLife.org -http://www.opentreeoflife.org/)
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PyMOL | www.pymol.org

PyMOL | www.pymol.org | Bioinformatics and Lab Informatics Resources | Scoop.it

PyMOL is a user-sponsored molecular visualization system on an open-source foundation.

Sandrine Palcy's insight:
The researchers used PyMOL to design the protein standard, creating a synthetic gene that they expressed in a PET33b vector - See more at: http://acceleratingscience.com/proteomics/indigestion-relief-with-digestif/#sthash.gikY3gAl.dpuf
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Interactive Modeling of Biological Networks

Interactive Modeling of Biological Networks | Bioinformatics and Lab Informatics Resources | Scoop.it
Explore and simulate a variety of existing models. Build and analyze your own models.
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PLAST | Parallel Local Sequence Alignment Search Tool

PLAST | Parallel Local Sequence Alignment Search Tool | Bioinformatics and Lab Informatics Resources | Scoop.it

PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.

Sandrine Palcy's insight:

PLAST is an open source project.

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T-BIOINFO: a Bioinformatics Big Data Analysis Platform

T-BIOINFO: a Bioinformatics Big Data Analysis Platform | Bioinformatics and Lab Informatics Resources | Scoop.it

 

T-BioInfo platform is a flexible and user-friendly bioinformatics distributed computational system. It is meant to provide an intuitive and user -friendly interface for building pipelines (chains) of bioinformatics algorithms for the analysis of big data: NG genomics and transcriptomics sequencing, mass-spectroscopy proteomics/metabolomics, as well as phenotypic visual information and knowledge databases.

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Rescooped by Sandrine Palcy from From Data to Knowledge in the Translational medicine
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MetaRNA-Seq – An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies | RNA-Seq Blog

MetaRNA-Seq – An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies | RNA-Seq Blog | Bioinformatics and Lab Informatics Resources | Scoop.it
The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control) to very

Via DEXSTR, a Translational Science Company
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The NDEx Project |

The NDEx Project | | Bioinformatics and Lab Informatics Resources | Scoop.it

The NDEx Project provides an open-source framework where scientists and organizations can share, store, manipulate, and publish biological network knowledge.

The NDEx Project maintains a free, public website; alternatively, users can also decide to run their own copies of the NDEx Server software in cases where the stored networks must be kept in a highly secure environment (such as for HIPAA compliance) or where high application load is incompatible with a shared public resource.

The NDEx Project is a joint effort of the Cytoscape Consortium and the Ideker Lab at the UC San Diego School of Medicine.

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SIGNOR

SIGNOR | Bioinformatics and Lab Informatics Resources | Scoop.it

SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow.

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myExperiment

myExperiment | Bioinformatics and Lab Informatics Resources | Scoop.it

myExperiment is a collaborative environment where scientists can safely publish their workflows and in silico experiments, share them with groups and find those of others.

Sandrine Palcy's insight:

De Roure, D., Goble, C. and Stevens, R. (2009): The Design and Realisation of the myExperiment Virtual Research Environment for Social Sharing of Workflows. Future Generation Computer Systems 25, pp. 561-567. doi:10.1016/j.future.2008.06.010

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