Category Archives: OpenHelix News

UCSC Intro

Free Webinars: World Tour of Resources and UCSC Genome Browser

OpenHelix will be presenting two webinars: World Tour of Genomics Resources, May 21st at 1:00 EDT, and Introduction to the UCSC Genome Browser, June 17th at 1:00 EDT.

World Tour of Genomics Resources Webinar World Tour of Genomics Resources

This world tour of genomic resources will discuss the number and breadth of publicly available bioscience resources available to researchers. It will include a tour of example resources, organized by categories such as algorithms and analysis tools, expression resources, genome browsers (both eukaryotic and prokaryotic/microbial), literature and text mining resources, and resources focused on nucleotides, proteins, pathways, disease and variation.

Introduction to the UCSC Genome Browser

We will cover the topics needed to effectively use this powerful, free, publicly-accessible tool, including basic functionality of the Genome Browser searching and BLAT use. Only basic knowledge of genomics and biology concepts are required. This will be an introduction on how to use the Browser so no programming skills are required.

For more information and to register, visit http://openhelix.com/webinars.cgi.

 

OpenHelix Unveils New Online Training Site, Subscriber Services

OpenHelix, a division of Bio-IT World, the provider of online and onsite training on some of the most popular and powerful open-access bioinformatics resources, announced the release of a new and enhanced website, as well as expanded subscriber services for both academic and commercial research institutions.

OpenHelix.com currently offers over 100 tutorial suites on popular and powerful bioinformatics and genomics tools, and the new redesigned website enhanced the offerings with an updated modern design, more concise and accurate navigation, integration of the Bioinformatics and Genomics Blog, easier access to popular OpenHelix tutorial suites, and quick access to Video Tips of the Week.

“Learning to use the latest bioinformatics tools is critical to genomics research, and with the enhanced platform OpenHelix now offers, our current and future subscribers will greatly benefit from training from this instrumental service. We anticipate OpenHelix will expand the number of tutorial suites and product offerings in 2016” said Phillips Kuhl, President of Cambridge Healthtech Institute.

“In addition to the value of over 100 tutorial suites, our subscribers gain insight and value from the content in the OpenHelix blog,” said Mary Mangan, Ph.D., Director of Product and Content at OpenHelix “Not only have we been able to utilize that content, especially from the Video Tips of the Week, but we have been able to integrate the content into the new website through our more robust search functionalities.”

Subscriptions to OpenHelix are available to both commercial and academic customers, and a subscription to OpenHelix encourages faster and more effective research by enabling the efficient use of publicly available tools to access biological data.

“We are excited about the re-launch of OpenHelix.com,” said Scott Lathe, General Manager, OpenHelix, “It is one example of how Bio-IT World is bringing the infrastructure, resources, and market reach needed to further grow our tutorials, subscriptions, and product offerings.”

About OpenHelix (www.openhelix.com)

OpenHelix, a division of Bio-IT World, was founded in 2003 to provide training on what was then a fledgling but quickly growing market of open access web based bioinformatics resources. OpenHelix has provided training and outreach services for many providers of resources, such as the UCSC Genome Browser, OMIM, and the Protein Data Bank (RSCB PDB). OpenHelix received a $1.2 million grant in 2007 to create a search engine for bioinformatics resources and to expand its tutorials suites. In 2009, it launched the subscription service to over 100 tutorial suites.

About Bio-IT World (www.Bio-ITWorld.com)

Bio-IT World provides outstanding coverage of cutting-edge trends and technologies that impact the management and analysis of life sciences data, including next-generation sequencing, drug discovery, predictive and systems biology, informatics tools, clinical trials, and personalized medicine. Through a variety of sources including Bio-ITWorld.com, Weekly Update Newsletter and the Bio-IT World News Bulletins, Bio-IT World is a leading source of news and opinion on technology and strategic innovation in the life sciences, including drug discovery and development.

About Cambridge Healthtech Institute (www.chicorporate.com)

Cambridge Healthtech Institute (CHI), founded in 1992, is the industry leader in providing superior-quality scientific information to eminent researchers and business experts from top pharmaceutical, biotech, and academic organizations. Delivering an assortment of resources such as events, reports, publications and eNewsletters, CHI’s portfolio of products include Cambridge Healthtech Institute Conferences, Barnett Educational Services, Insight Pharma Reports, Cambridge Marketing Consultants, Cambridge Meeting Planners, Knowledge Foundation and Cambridge Healthtech Media Group, which includes Bio-IT World and Clinical Informatics News.

Cambridge Healthtech Institute Announces the Acquisition of OpenHelix

Cambridge Healthtech Institute (CHI) announced the purchase of Washington–based OpenHelix, the provider of online and onsite training on some of the most popular and powerful open-access bioinformatics resources on the web.

“Knowing how to use the latest bioinformatics tools is critical to genomics research, which will only grow in importance,” said Phillips Kuhl, President of Cambridge Healthtech Institute “With an over ten year track record of developing and presenting training on open access bioinformatics databases and programs, OpenHelix is an instrumental service to researchers and a key addition to CHI’s family of conference and training products.”

OpenHelix will join the Cambridge Healthtech Institute as a division of Bio-IT World, a leading source of news and opinion on technology and strategic innovation in the life sciences, including drug discovery and development. “OpenHelix brings Bio-IT World an extensive and solid audience in the academic research community, as well as the opportunity to extend to our existing audience a valuable training product line,” said Lisa Scimemi, Publisher of Bio-IT World, “training that many of our readers need for themselves or their staff or students but may not be aware of.”

“We are proud of the success we have had in the past, with some of the top universities and medical schools subscribing to OpenHelix,” said Scott Lathe, CEO of OpenHelix “Working with Bio-IT World will bring us the infrastructure, resources, and market reach we need to further grow our tutorials, subscriptions, and product offerings.”

As part of the acquisition, Scott Lathe, CEO and co-founder of OpenHelix will become General Manager of the OpenHelix unit and Mary Mangan, President and co-founder of OpenHelix will become Director, Product and Content of the OpenHelix unit.

About Bio-IT World (www.Bio-ITWorld.com)
Bio-IT World provides outstanding coverage of cutting-edge trends and technologies that impact the management and analysis of life sciences data, including next-generation sequencing, drug discovery, predictive and systems biology, informatics tools, clinical trials, and personalized medicine. Through a variety of sources including, Bio-ITWorld.com, Weekly Update Newsletter and the Bio-IT World News Bulletins, Bio-IT World is a leading source of news and opinion on technology and strategic innovation in the life sciences, including drug discovery and development.

About Cambridge Healttech Institute (www.chicorporate.com)
Cambridge Healthtech Institute (CHI), founded in 1992, is the industry leader in providing superior-quality scientific information to eminent researchers and business experts from top pharmaceutical, biotech, and academic organizations. Delivering an assortment of resources such as events, reports, publications and eNewsletters, CHI’s portfolio of products include Cambridge Healthtech Institute Conferences, Barnett Educational Services, Insight Pharma Reports, Cambridge Marketing Consultants, Cambridge Meeting Planners, Knowledge Foundation and Cambridge Healthtech Media Group, which includes Bio-IT World and Clinical Informatics News.

About OpenHelix (www.openhelix.com)
OpenHelix, a Washington State company, was founded in 2003 to provide training on what was then a fledgling but quickly growing market of open access web based bioinformatics resources. OpenHelix has provided training and outreach services for many providers of resources, such as the UCSC Genome Browser, OMIM, and the Protein Data Bank (RSCB PDB). OpenHelix received a $1.2 million grant in 2007 to create a search engine for bioinformatics resources and to expand its tutorials suites. In 2009, it launched the subscription service to over 100 tutorial suites.

Heartbleed security issues, we’re ok

We’ve been tracking the concerns about the Heartbleed security issues, as has everyone with an internet login anywhere. And the actual depth of the issue continues to be discussed and disputed. Also XKCD:

Most people who read our blog, or access the free materials, haven’t had to register anyway so there wasn’t an issue with those. But we have checked with our development team to see if we were affected by the security flaw for our registered users.

We are told that we are unaffected by this vulnerability on our registration-accessible pages. So although it is always wise to change passwords from time-to-time, we won’t be requiring that for our registered users. Feel free to do so though if you want to. Let us know if you have any problems with that.

A fix was implemented for the Google Wallet checkout feature that some people might have used, and it’s already in place.

Safe travels around the ‘tubz.

Free “Introduction to GenoCAD” Webinar presented March 27th.

The Peccoud Lab, based at Virginia Bioinformatics Institute at Virginia Tech, is sponsoring a free webinar on GenoCAD, presented by OpenHelix on Thursday, March 27th, at 18:00 p.m. UTC/2:00 p.m. ET/11:00 a.m. PT.

GenoCAD is a Computer-Assisted Design application for synthetic biology projects, which was developed by the Peccoud Lab at Virginia Tech and supported by the National Science Foundation under Grant No. EF-0850100. The GenoCAD website enables researchers to generate libraries of parts that can be used and re-used to generate unlimited designs supporting bench biologists in molecular biology construction efforts. Grammars that specify the order of elements provide a consistent yet flexible framework for creating construct designs. In this introductory tutorial, the foundations of the GenoCAD system are explored, and basic functionality of the software is demonstrated with hands-on tasks.

In “Introduction to GenoCAD” webinar, participants will learn:

  • the basic aspects of the site usage with an orientation and overview
  • the organizational features of libraries and their component parts
  • to use a grammar to create customized designs of expression constructs
  • to run a simple simulation to investigate the behavior of synthetic systems

The webinar will held Thursday, March 27th, 18:00 p.m. UTC/2:00 p.m. ET/11:00 a.m. PT (for local time zones, check here: http://bit.ly/GenoCADintro). Register at http://www.openhelix.com/cgi/webinars.cgi.

Seminar Summary:

What: “Introduction GenoCAD” sponsored by the Peccoud Lab at Virginia Bioinformatics Institute at Virginia Tech presented by OpenHelix, LLC.

When: Thursday, March 27th, 18:00 p.m. UTC/2:00 p.m. ET/11:00 a.m. PT

Who:  Anyone interested in learning about GenoCAD.

OpenHelix Bioinformatics Tutorial Suites Now Available on Mobile Devices.

OpenHelix announced today of its launch of bioinformatics and genomics tutorial suites that can now run in browsers of mobile devices including those running iOS, Android, and Windows mobile operating systems as well on desktop browsers.  Over 100 tutorials introduce researchers, teachers, and students to biomedical resources that are freely available on the web.

“Learning how to use resources that are critical to biomedical research is a high priority,” said Scott Lathe, CEO of OpenHelix “but it is sometimes difficult to find the time.  With our tutorials now available on mobile devices, users now have more options to view tutorials at a time convenient for them. We have had many Librarians who subscribe to OpenHelix ask for this functionality”

The online narrated tutorials run in just about any browser and can be navigated in a number of ways. The tutorial highlights and explains the features and functionality needed to start using a resource effectively and efficiently. The tutorial can be used by new users to introduce them to resources, by previous users to view new features and functionality, or simply as a reference tool to understand specific features.

In addition to the tutorials, users can also access useful training and teaching 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.

Some of the tutorials are free as the resource provider sponsors their availability (for a list of free tutorials visit www.openhelix.com/free). The other tutorial suites are available through individual purchase, a single subscription or through an institutional subscription. (To see if your institution subscribes, email information@openhelix.com).  A full list of tutorials can be viewed at www.openhelix.com/catalog.

About OpenHelix

OpenHelix, LLC, (www.openhelix.com) provides a bioinformatics and genomics search and training website, giving researchers one place to find and learn how to use resources and databases on the web.  Researchers and institutions can save time, budget and staff resources by leveraging a subscription to over 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

Virginia Bioinformatics Institute announces an OpenHelix tutorial suite on GenoCAD.

The Peccoud Lab, based at Virginia Bioinformatics Institute at Virginia Tech, has partnered with OpenHelixTM to provide a tutorial suite on their GenoCAD application.

GenoCAD is a Computer-Assisted Design application for synthetic biology projects, which was developed by the Peccoud Lab at Virginia Tech and supported by the National Science Foundation under Grant No. EF-0850100. The GenoCAD website enables researchers to generate libraries of parts that can be used and re-used to generate unlimited designs supporting bench biologists in molecular biology construction efforts. Grammars that specify the order of elements provide a consistent yet flexible framework for creating construct designs. In this introductory tutorial, the foundations of the GenoCAD system are explored, and basic functionality of the software is demonstrated with hands-on tasks.

The “Introduction to GenoCAD” narrated tutorial is available online; it can be run in just about any web 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 GenoCAD effectively.

Viewers will learn:

  • the basic aspects of the site usage with an orientation and overview
  • the organizational features of libraries and their component parts
  • to use a grammar to create customized designs of expression constructs
  • to run a simple simulation to investigate the behavior of synthetic systems

The tutorial can be used by new users to introduce them to the resource, 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 can also access useful training and teaching 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 planning classroom content.

Users can view the tutorial and download the materials at www.openhelix.com/genocad.

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.  Researchers and institutions can save time, budget and staff resources by leveraging a subscription to over 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

About Virginia Bioinformatics Institute
Established in 2000, Virginia Bioinformatics Institute is one of seven acclaimed research institutes designed to support Virginia Tech’s research mission. Our emphasis on informatics of complex interacting systems scales from the microbiome to the entire globe, helping to solve challenges posed to human health, security, and sustainability. Headquartered on the Blacksburg, Virginia campus, the institute occupies 154,600 square feet in research facilities, including state-of-the-art core laboratory and high performance computing facilities, as well as research offices in the Virginia Tech Research Center in Arlington, Virginia.

OpenHelix announces an updated free tutorial and training materials for Online Mendelian Inheritance in Man (OMIM).

Online Mendelian Inheritance in Man® (OMIM), authored and edited at the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins, has collaborated with OpenHelix to provide an updated, revised and now free tutorial suite on the OMIM resource.

OMIM is a catalog of human genes and genetic conditions that helps researchers and clinicians understand the relationship between genes and genetic disease. OMIM is a foundational resource in genomics, and OMIM links and data are found at sites all around the bioinformatics sphere.  Knowledge of the full scope of OMIM’s data and resources provides access to the most comprehensive understanding of human phenotypes and disease. OMIM contains full text summaries of information from the scientific literature, and provides extensive links to the literature resources and other genomic resource tools as well.

The new tutorial reflects the many changes and enhancements to OMIM, including the new face it received during the move from NCBI to omim.org. New search functions enable more precise and relevant searches for different user communities, including clinical geneticists, genetic counselors, and basic researchers. In addition, OMIM now has more links to other relevant genetics and biomedical research resources around the world.

The online narrated tutorial runs in just about any browser and can be navigated in a number of ways. In just under 30 minutes, the tutorial highlights and explains the features and functionality needed to start using OMIM effectively. The tutorial can be used as an introduction to the catalog of human genes and genetic disorders, as a quick way 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 training and teaching materials, including the animated PowerPoint slides that serve 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 when creating classroom content.

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

About OMIM

OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily. The free-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. OMIM entries contain copious links to other genetics resources.

This database was initiated in the early 1960s by Dr. Victor A. McKusick as a catalog of mendelian traits and disorders, titled Mendelian Inheritance in Man (MIM). Twelve book editions of MIM were published between 1966 and 1998. The online version, OMIM, was created in 1985 by a collaboration between the National Library of Medicine and the William H. Welch Medical Library at Johns Hopkins. It was made generally available on the internet starting in 1987. In 1995, OMIM was developed for the World Wide Web by NCBI, the National Center for Biotechnology Information.  In 2010, Johns Hopkins Medicine created a new website OMIM.org.  OMIM is funded by a grant from the National Human Genome Research Institute (NHGRI).

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.  Researchers and institutions can save time, budget and staff resources by leveraging a subscription to over 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

Updated ENCODE tutorial and training materials from OpenHelix once again freely available.

OpenHelix and the UCSC Bioinformatics group have worked together to give everyone free access to the newly updated ENCODE tutorial until the end of February 2013.

The online tutorial suite 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/ENCODE2.  The tutorial has been updated to reflect the recent changes to the UCSC Genome Browser.

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 explores ways for you to access 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.

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. These resources are useful for teachers and professors to create classroom content.

In addition to the ENCODE tutorial suite, OpenHelix offers over 100 tutorial suites on other web-based bioinformatics and genomics tools as well.  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.

New Online Tutorial Suite and Quick Reference Card on How to Access ENCODE Data Now Available from OpenHelix.

Last week, dozens of papers were published by the ENCODE (ENCyclopedia of DNA Elements) project, capping a long effort of a worldwide consortia to build a comprehensive parts list of functional elements in the human genome. What can be lost in the press coverage and sometimes heated discussion of the results is the critical value of the ENCODE data to individual researchers, labs and smaller research projects working in a wide variety of fields.

However, to access and study the ENCODE data, researchers need to know how to do so within the UCSC Genome Browser. OpenHelix has released a new online tutorial suite 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/ENCODE2.

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.

Also available free (up to 30 cards shipped free in the U.S) is a Quick Reference Card (QRC). The QRC gives an overview of the site and many ways to access and view ENCODE data within the UCSC Genome Browser with screen shots and callouts of the various features and functions. You can order the card at www.openhelix.com/cgi/qrcOrder.cgi.

In addition to the tutorial and QRC, 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 100 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/free.

About OpenHelix
OpenHelix, LLC, provides the genomics knowledge you need when you need it. OpenHelix provides online self-run tutorials, web seminars, and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix also is contracted by resource providers to provide comprehensive, long-term training and outreach programs. Further information can be found on www.openhelix.com or by calling 1-888-861-5051.

EDIT: 10/12/12:  The OpenHelix contract for the ENCODE DCC at UCSC has ended and the DCC Center has now transitioned to a group at Stanford. The new DCC group has chosen to take in-house the training and outreach OpenHelix performed and chose not to fund the sponsorship of the tutorials. However, we have worked with the UCSC Bioinformatics group and the ENCODE tutorial is again freely available until February 2013.