Category Archives: OpenHelix News

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. 

Dr. Warren Lathe receives Fellowship Award from the American Association for the Advancement of Science (AAAS)

OpenHelix (www.openhelix.com) announced today that its Chief Scientific Officer, Dr. Warren (Trey) Lathe will be taking a one year sabbatical to fulfill a Science and Technology  Policy fellowship at the National Science Foundation working with the Directorate of Computer and Information Science and Engineering.

The Science and Technology Policy fellowship is administered by the American Association for the Advancement of Science (AAAS) with the goal of having accomplished scientists and engineers participate in and contribute to the federal policymaking process.

“This is a fellowship that I have wanted to participate in for some time,” explained Dr. Warren (Trey) Lathe, “I’m excited to use my education, past education experience, and nearly ten years at OpenHelix to contribute to policy on computing and online education.”

The fellowships are highly competitive and use a peer-review selection process. Review is followed by individual interviews in Washington D.C. and conducted by selection committees comprised of professionals with expertise in the interface of science, technology and policy.

“Surely Trey will be missed for the year that he will be at the fellowship,” said Dr. Mary Mangan, OpenHelix President, “but luckily we have built a strong team that will assure continued success and growth at OpenHelix while giving Trey the year long opportunity to contribute to an extremely important policy area for the scientific community we serve.”

About OpenHelix, LLC.
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.

OpenHelix has its headquarters in Seattle, with offices in San Francisco and Boston. Further information can be found on www.openhelix.com or by calling 1-888-861-5051.

Free Webinars on how to use the UCSC Genome Browser

The UCSC Bioinformatics Group announces two free webinars on the UCSC Genome Browser (http://genome.ucsc.edu/). The webinars will be conducted by OpenHelix, the provider of training on 100s of free, publicly accessible bioinformatics and genomics resources.

The hour and 15 minute long webinars will cover the topics needed to effectively use this powerful, free, publicly-accessible tool. The first webinar, held Thursday, May 17 at 6:00 p.m. UTC/1:00 p.m. ET/10:00 a.m. PT (for local time zones: http://bit.ly/ucscintrowebinar), will be an introduction to the genome browser, designed for new users of the UCSC Genome Browser, and those who want to improve their skills at basic navigation and display.

In this webinar, you’ll learn:
• to perform basic text searches
• explore and understand display feature in a genomic region of interest
• customize displays to fit your needs
• use filters to highlight data you are interested in, such as displaying non-synonymous SNPs in red to stand out
• how to set up a view the way you want, and then save that as a “Session” to share with others

The second webinar, held Thursday, May 24, 6:00 p.m. UTC/1:00 p.m. ET/10:00 a.m. PT (for local time zones: http://bit.ly/tablebrowserwebinar), will cover advanced topics including creating Custom Tracks and using the Table Browser.

In this webinar, you’ll learn to:
• perform advanced searches of the UCSC genome databases
• export and download large quantities of targeted data
• create custom tracks resulting from your advanced searches
• create custom annotation tracks of your data to share with others

Seating is limited and registration is required. Register at www.openhelix.com/cgi/webinars.cgi. Download slides before the webinar for note taking at http://www.openhelix.com/ucsc.

Seminar Summary:
What: “Introduction to the UCSC Genome Browser” and “UCSC Genome Browser: Custom Tracks and Table Browser” free webinars sponsored by UCSC Bioinformatics Group and presented by OpenHelix, LLC.

When:
Introduction: Thursday, May 17, 6:00 p.m. UTC/1:00 p.m. ET/10:00 a.m. PT
Custom Tracks and Table Browser: Thursday, May 34, 6:00 p.m. UTC/1:00 p.m. ET/10:00 a.m. PT
Who: Anyone interested in learning how to use the UCSC Genome Browser. Requires knowledge of genomic/biological concepts. No programming skills required.

Cost: No cost.

Contact Information: Register at www.openhelix.com/cgi/webinars.cgi. You will receive an email with the URL for the webinar.

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), a research tool that integrates the work of hundreds of scientists worldwide into a graphical display of genome sequences and aligned annotations. The Genome Browser — originally developed to assist in the initial assembly of the human genome — now features a rich set of annotations on a multitude of mammalian and model organism genomes. The UCSC Bioinformatics Group continues to uphold its original mission to provide free, unrestricted public access to genome data on the Web.

About OpenHelix, LLC.
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.

OpenHelix has its headquarters in Seattle, with offices in San Francisco and Boston. Further information can be found on www.openhelix.com or by calling 1-888-861-5051.

Updated Tutorials on UCSC Genome Browser Now Available

University of California, Santa Cruz Bioinformatics Group and OpenHelix today announced the availability of free updated tutorial suites on the UCSC Genome Browser (http://genome.ucsc.edu/), a powerful and popular freely available web-based tool for mining genomic data.  The two updated tutorial suites include a general Introduction to the Genome Browser and an Introduction to Custom Tracks and the Table Browser.  Also available is an introduction to additional tools available, including Gene Sorter and VisiGene.

UCSC Genome Browser is a research tool that integrates the work of hundreds of scientists worldwide into a graphical display of genome sequences and aligned annotations. The Genome Browser — originally developed to assist in the initial assembly of the human genome — now features a rich set of annotations on a multitude of genomes. Increasingly it is crucial to master software tools like the UCSC Genome Browser and Table Browser, as “big data” biomedical research projects continue to generate volumes of data that are simply too large to include in traditional literature. That data resides in the databases—sometimes even long before publication of the project papers ensues.

The tutorial suites, created and maintained by OpenHelix (www.openhelix.com), include an online, narrated tutorial, which runs in just about any browser connected to the web and can be viewed from beginning to end or navigated using chapters and forward and backward sliders. The approximately 60 minute tutorials highlight and explain all the features and functionality needed to start using the Genome Browser and its tools effectively. The tutorial also includes a step-by-step movie which walks the user through an exercise using the tools of the Genome Browser. The tutorial can be used to learn how to use the Genome Browser, to view new features and functionality, or simply as a reference tool to refresh users’ memory.

Also included with each tutorial is a suite of training materials, including PowerPoint slides used as a basis for the tutorial, with a suggested script for the slides, slide handouts, and exercises. These materials can be used as reference for users or as a ready-made presentation for training others on the use of the Genome Browser.

The tutorial suites are used in many ways, including:

  • Researchers use the tutorial suites to learn how to use new or unfamiliar genomics resources they need as their work progresses.
  • Faculty and Staff use the tutorial suites to keep abreast of resources and technology, and as an excellent staff training and career development tool.
  • Faculty use the tutorial suites to save significant time in creating classroom content and to augment in-class learning.
  • Librarians and Bioinformaticians use the tutorial suites to provide their customers with basic resource training, allowing them to save their valuable time for more advanced user issues.

You can view the updated UCSC Genome Browser tutorials suites at www.openhelix.com/ucsc OpenHelix provides over 100 other tutorial suites on a number of genomic databases and resources through an individual, group, or institutional subscription. Further information can be found at www.openhelix.com.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

About UCSC Bioinformatics Group
The UCSC Bioinformatics Group is part of the Center for Biomolecular Science and Engineering (CBSE) at the Universityof 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), a research tool that integrates the work of hundreds of scientists worldwide into a graphical display of genome sequences and aligned annotations. The Genome Browser — originally developed to assist in the initial assembly of the human genome — now features a rich set of annotations on a multitude of mammalian and model organism genomes. The UCSC Bioinformatics Group continues to uphold its original mission to provide free, unrestricted public access to genome data on the Web.