Tag Archives: press release

UCSC Bioinformatics Group announces free OpenHelix tutorial suite for ENCODE.

Online tutorial suite teaches how to access ENCODE (ENCyclopedia of DNA Elements) data in the UCSC Genome Browser.

Quote startThe ENCODE project and data are crucial to ongoing genomics research and have already changed our understanding of the organization and function of the genome.Quote end

Bellevue, WA (PRWEB) November 9, 2010

An online tutorial suite is now available that teaches users how to access the ENCODE data in the UCSC Genome Browser. The online tutorial, created by OpenHelix in conjunction with the UCSC Bioinformatics Group can be viewed for free at http://www.openhelix.com/encode

The ENCODE Project, (ENCyclopedia of DNA Elements), is an international consortium of researchers who are moving beyond the basic information of the reference genome sequence. Researchers are using the newest sequencing technologies and numerous strategies to generate data to learn as much as possible about variations, genes, non-coding transcripts, regulatory elements, and genome structure and more, in extensive detail across the entire genome.

The ENCODE project is coordinated by the NHGRI. The UCSC Genome Browser is the designated Data Coordination Center (DCC) , for the ENCODE project, and the official ENCODE data repository.

“The ENCODE project and data are crucial to ongoing genomics research and have already changed our understanding of the organization and function of the genome,” said Kate Rosenbloom, the ENCODE technical project manager at UCSC. “New data are continually submitted to the Data Coordination Center before appearing in the literature. To maximize the impact on the broader biomedical community it is important to bring people up to speed quickly and efficiently on how to navigate the data. The OpenHelix tutorial suite will contribute greatly to our outreach and usability efforts for ENCODE.”

The online narrated tutorial, which runs in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders. The approximately 60 minute tutorial examines aspects of the ENCODE project and data types, and explores ways for you to access and learn about the ENCODE data available within the UCSC Genome Browser. Combined with the OpenHelix tutorials on the search and display features of the UCSC Genome Browser, the ENCODE data will enable researchers to access cutting-edge data, including pre-publication information.

The tutorial can be used by new users to introduce them to ENCODE, for previous users to view new features and functionality, or simply as a reference tool to understand specific features.
In addition to the tutorial, users can also access useful training materials including the animated PowerPoint slides used as a basis for the tutorial, suggested script for the slides, slide handouts, and exercises. This can save a tremendous amount time and effort for teachers and professors to create classroom content.

In addition to the ENCODE tutorial suite, OpenHelix offers over 90 tutorial suites on some of the most powerful and popular bioinformatics and genomics tools available on the web. Some of the tutorials suites are freely available through support from the resource providers. The whole catalog of tutorials suites is available through a subscription. Users can view the tutorials and download the free materials at openhelix.com.

About UCSC Bioinformatics Group
The UCSC Bioinformatics Group is part of the Center for Biomolecular Science and Engineering (CBSE) at the University of California, Santa Cruz. Director and HHMI investigator David Haussler leads a team of scientists, engineers and students in the study and comparative analysis of mammalian and model organism genomes. Research Scientist Jim Kent heads up the engineering team that develops and maintains the UCSC Genome Browser(http://genome.ucsc.edu). The UCSC Bioinformatics Group continues to uphold its original mission to provide free, unrestricted public access to genome data on the Web.

About OpenHelix
OpenHelix, LLC, (http://www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

The University of Toronto Announces Free OpenHelix Tutorial and Training Materials for GeneMANIA, a Gene Function Prediction Tool

Quote startThe OpenHelix tutorial suite is sure to help current and new users to get up to speed on our site and its new features, and therefore get their results more quickly to support their research.Quote end

Bellevue, WA (PRWEB) August 11, 2010

The creators of GeneMANIA have contracted with OpenHelix to provide comprehensive online training for the gene function prediction tool (http://genemania.org ).

GeneMANIA is a free public resource that offers a simple, intuitive web interface that shows the relationships between genes in a list and analyzes and extends the list to include other related genes. The web interface is backed by powerful analysis software and a large data warehouse containing extensive amounts of existing functional genomics data, and also includes Cytoscape Web, a web based advanced visualization tool to enable browsing of query results and creation of publication-ready figures.

“GeneMANIA will soon be updated to include significantly increased functionality,” according to Gary Bader and Quaid Morris, assistant professors in the Donnelly Centre (http://tdccbr.med.utoronto.ca/) and co-principal investigators for GeneMANIA. “OpenHelix based their tutorial on our development site, and even provided user feedback on our new features that resulted in improvements to our system. OpenHelix had very strong understanding of the GeneMANIA interface, which then translated into a powerful learning resource. The OpenHelix tutorial suite is sure to help current and new users to get up to speed on our site and its new features, and therefore get their results more quickly to support their research.”

The new training initiatives include a free online tutorial suite on GeneMANIA. The online narrated tutorial (http://www.openhelix.com/genemania ), which runs in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders. The approximately 60 minute tutorial highlights and explains the features and functionality needed to start using GeneMANIA effectively. The tutorial can be used by new users to introduce them to GeneMANIA, for previous users to view new features and functionality, or simply as a reference tool to understand specific features.

In addition to the tutorial, GeneMANIA users can also access useful training materials including the animated PowerPoint slides used as a basis for the tutorial, a suggested script for the slides, slide handouts, and exercises. This can save a tremendous amount time and effort for teachers and professors to create classroom content.

“GeneMANIA is an innovative, hypothesis generating tool that can be used to extend a given gene list to find related genes sharing similar functions,” said OpenHelix founder and President Dr. Mary Mangan. “OpenHelix is excited to contribute to furthering the field of gene function prediction by assisting researchers in effectively and efficiently using such a critical tool.”

Users can view the tutorials and download the free materials at www.openhelix.com .

In addition to the GeneMANIA tutorial suite, OpenHelix offers over 90 tutorial suites on some of the most powerful and popular bioinformatics and genomics tools available on the web. Some of the tutorials suites are freely available through support from the resource providers. The whole catalog of tutorials suites is available through a subscription. Users can view the tutorials and download the free materials at www.openhelix.com .

About GeneMANIA
GeneMANIA (www.genemania.org ) is a free web-based prediction tool that finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets.

GeneMANIA is actively developed at the University of Toronto, in the Donnelly Centre for Cellular and Biomolecular Research, in the labs of Gary Bader and Quaid Morris, with input from an independent scientific advisory board. GeneMANIA development is funded by Genome Canada, through the Ontario Genomics Institute (2007-OGI-TD-05).

About OpenHelix
OpenHelix, LLC, (www.openhelix.com ) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

Updated Online Tutorials for NCBI resources including an NCBI Overview and PubMed and the Gene Expression Omnibus tutorials

Comprehensive tutorials on the publicly available NCBI resources enable researchers to quickly and effectively use these invaluable resources.

Seattle, WA (PRWEB) June 8, 2010 – OpenHelix today announced the availability of three updated tutorials on NCBI resources.

The National Center for Biotechnology Information, NCBI, is home to many of the most commonly used publicly available databases and tools in molecular biology today. They house such popular and widely used databases as GenBank, PubMed, GEO, Entrez Gene, Entrez Protein, and more. NCBI also produces, maintains and updates a variety of tools, like the large family of BLAST sequence similarity searching tools and the Entrez search and retrieval tools. In addition, they provide an extensive variety of services for education, news dissemination and different types of data submission. This tutorial presents a broad overview of NCBI’s databases, tools, educational resources and data submission protocols. In addition to an update on this overview, OpenHelix has updated both it’s PubMed and GEO tutorials. PubMed is the premiere search engine for biomedical literature. More than 18 million citations from life science journals can be searched through this free service. The Gene Expression Omnibus, or GEO, is a valuable resource designed to store high-throughput gene expression and molecular abundance data. These three tutorials, in conjunction with the many other OpenHelix up-to-date tutorials on NCBI resources such as BLAST, Entrez, dbSNP, MMDB, Viral resoruces, MapViewer and others will give you a set of training resources to help be efficient and effective at accessing and analyzing genome data.

The tutorial suites, available through an annual OpenHelix subscription, contain an online, narrated, multimedia tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. The scripts, handouts and other materials can also be used as a reference or for training others.

These tutorials will teach users:

NCBI Overview

*to understand the basic structure of NCBI and its different types of resources
*to navigate NCBI to find the databases and analysis tools you need
*what types of educational resources are available at NCBI
*basic data submission procedures and background information
*how to search the entire NCBI site, as well as just the subset of Entrez databases

PubMed

*basic, advanced, and Boolean search methods
*additional searching methods like the Entrez Global query and the MeSH query
*tips to understand the visual cues and displays
*to use My NCBI to customize your results and save searches which can be run and emailed regularly

Gene Expression Omnibus (GEO)

*efficient ways to query GEO for specific genes or experimental designs
*how to navigate through GEO output displays to find the specific information you want
*how to navigate GEO’s complex data architecture to search GEO by specific record types

To find out more about these and over 85 other tutorial suites visit the OpenHelix Catalog and OpenHelix. Or visit the OpenHelix Blog for up-to-date information on genomics and genomics resources.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

Washington University Subscribes to OpenHelix Training Portal

Researchers, faculty, students and staff at Washington University can now efficiently and effectively learn to use bioinformatics and genomics resources with the extensive tutorial suite catalog from OpenHelix.

Bellevue, WA (PRWEB) April 26, 2010 — Bernard Becker Medical Library at Washington University School of Medicine has purchased a subscription to OpenHelix (www.openhelix.com) giving faculty, students and staff access to over 90 tutorial suites on bioinformatics and genomic resources.

With OpenHelix tutorials, Becker Library offers the Washington University community a quick and effective way to learn about the most powerful and popular genomics and bioinformatics databases and resources. These tutorials cover many types of resources including protein databases, bioinformatics analysis tools, model organism databases, SNP databases, comparative genomics, pathway and interaction resources and much more. “We’re thrilled that we are able to provide such a fantastic suite of resources to our research community,” said Kristi Holmes, PhD bioinformaticist at Becker Medical Library. “These tutorials are the perfect compliment to the instruction and consultation services offered by our Bioinformatics@Becker program.”

These tutorials are the perfect compliment to the instruction and consultation services offered by our Bioinformatics@Becker program

The online narrated tutorials, which run in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders. The approximately 60 minute tutorials highlight and explain the features and functionality needed to start using the resources effectively. The tutorial can be used by new users to introduce them to a resource, or by previous users to view new features and functionality, or simply as a reference tool to understand specific features.

In addition to the tutorial, users also have access to useful training materials including the animated PowerPoint slides used as a basis for the tutorial, suggested script for the slides, slide handouts, and exercises. This can save a tremendous amount of time and effort for teachers and professors creating classroom content.

“It is difficult, and certainly cost prohibitive, for university Libraries to create and provide training on the many critical genomic resources available,” said Scott Lathe, Chief Executive Officer of OpenHelix. “With an OpenHelix subscription, Washington University provides an efficient and effective training solution for their researchers.”

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

The Protein Structure Initiative announces free OpenHelix tutorial and training materials for the Structural Genomics Knowledgebase (SGKB)

Free tutorial and training materials available for the Structural Genomics Knowledgebase bionformatics resource

Working with OpenHelix to provide online training materials and increased visibility is an effective way to add to our efforts

Bellevue, WA (PRWEB) March 18, 2010 — The Structural Genomics Knowledgebase(SGKB), a one-stop shop for information about proteins hosted at Rutgers University, has partnered with OpenHelixTM to provide free comprehensive training and outreach programs for its online protein “portal” located at http://kb.psi-structuralgenomics.org.

The SGKB is a free, comprehensive resource produced through a collaboration between the National Institutes of Health’s Protein Structure Initiative and Nature Publishing Group. The PSI SGKB contains genetic, structural, functional and experimental information about proteins that is easily accessible through a variety of reports and displays. The portal also includes links to many additional resources.

“Structural genomics is fast emerging as an essential tool in expanding our knowledge of the role of proteins in biology and in disease,” said OpenHelix founder and CSO Dr. Warren Lathe. “OpenHelix is excited to contribute to furthering this field by assisting researchers in effectively and efficiently using this powerful resource.”

The new training initiatives include a free online tutorial suite on how to use/search/find/etc. the SGKB.

The online narrated tutorial runs in just about any browser and can be navigated in a number of ways. In about 60 minutes, the tutorial highlights and explains the features and functionality needed to start using the SGKB effectively. The tutorial can be used by new users to introduce them to the protein portal, by previous users to view new features and functionality or simply as a reference tool to understand specific features.

In addition to the tutorial, SGKB users can also access useful training materials, including the animated PowerPoint slides used as a basis for the tutorial, suggested talking points for the slides, slide handouts and exercises. This can save a tremendous amount time and effort for educators looking to create classroom content.

Users can view the tutorials and download the free materials at http://www.openhelix.com/sgkb .

OpenHelix also has created a free Quick Reference Card for the SGKB. The Quick Reference card highlights search strategies, features and functionality. The cards can be ordered in packs of 30 from www.openhelix.com, and shipping is free within the United States.

“The SGKB sets itself apart by incorporating so many different types of biological data (genetic, structural, theoretical, functional, protocol, etc.) that is really is a ‘one-stop shop’ for a broad range of biological and biomedical fields. The challenge for training and outreach is to make this data accessible and understandable to scientists across different disciplines,” said Dr. Helen Berman, head of the SGKB. “Working with OpenHelix to provide online training materials and increased visibility is an effective way to add to our efforts.”

In addition to the SGKB tutorial suite, OpenHelix offers nearly 90 tutorial suites on some of the most powerful and popular bioinformatics and genomics tools available on the web. Some of the tutorial suites are freely available through support from the resource providers. The whole catalog of tutorial suites is available through a subscription. Users can view the tutorials and download the free materials atwww.openhelix.com.

About the PSI
The Protein Structure Initiative (PSI, http://www.nigms.nih.gov/Initiatives/PSI/), which is supported by the National Institutes of Health, is a federal, university and industry effort aimed at dramatically reducing the costs and lessening the time it takes to determine a three-dimensional protein structure. The long-range goal of the PSI is to make the three-dimensional atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences. The PSI strives to gain biological insights from new structures and to help the broad biomedical research community make use of PSI research findings.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

New and Updated Online Tutorials for GoMiner and XplorMed

Comprehensive tutorials on the publicly available GoMiner and XplorMed databases enable researchers to quickly and effectively use these invaluable resources

Seattle, WA (PRWEB) February 16, 2010 — OpenHelix today announced the availability of a new tutorial on GoMiner, and an updated tutorial suite on XplorMed.

GoMiner is a set of publicly available tools that can enable you to ascribe biological significance to large lists of genes by annotating them with their corresponding Gene Ontology, or GO, categories. XplorMed is a public web-based tool which allows you to access a text-mining algorithm that can improve upon standard PubMed searches by mining abstracts for word frequencies and combinations. These two tutorials, in conjunction with OpenHelix tutorials on PubMatrix, STRING. Gene Ontology and Textpresso, give you a set of training resources help you be efficient and effective at text and literature mining.

With these tutorials, researchers can quickly learn to effectively and efficiently use GoMiner and XplorMed.

The tutorial suites, available through an annual OpenHelix subscription, contain an online, narrated, multimedia tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. The scripts, handouts and other materials can also be used as a reference or for training others.

These tutorials will teach users:

GoMiner

*to use both the downloadable GUI and web-based High-Throughput GoMiner tools
*to understand and manipulate your GO annotated data
*to construct beautiful visuals to display and present your results clearly

XplorMed

*how to extract fascinating relationships among PubMed abstracts
*to use stored sets of abstracts to discover new information
*to start with identifiers of interest and collect relevant abstracts for further examination
To find out more about these and over 85 other tutorial suites visit the OpenHelix Catalog and OpenHelix. Or visit the OpenHelix Blog for up-to-date information on genomics and genomics resources.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.