Tag Archives: OpenHelix

OH Launches Genomics Search and Learn Portal

OpenHelix today announced the launch of the new www.openhelix.com web site, a first-of-its kind portal that assists researchers in conducting breakthrough research.  The portal directs scientists to the most relevant publicly available bioinformatics and genomics resources on the web, and then gives them immediate access to tutorials, training materials, and useful tips and information developed by OpenHelix.

“There are now thousands of databases and analysis tools for the researcher to use when doing biological research,” said Scott Lathe, CEO of OpenHelix, “The first problem researchers have is just finding the most relevant tool.  There are catalogs of resources on the web, but they are cumbersome to use and using a keyword search on them more often than not delivers irrelevant results. The OpenHelix portal solves this problem”

The OpenHelix portal searches a highly relevant, curated database of genomics and biological resources, OpenHelix tutorials and training materials, and tips and information on the resources on the OpenHelix blog.  The portal delivers a list of relevant resources for the user using a proprietary relevancy system developed by OpenHelix scientists. Once a user finds the most relevant resources in the results, they can immediately go to training on the resource.

Searching for the most relevant resource is free to all users.  Some of the tutorial suites are also free, as they are sponsored by the resources themselves, such as the UCSC Genome Browser.

“The second, and possibly most significant problem a researcher faces is learning how to use these often complex and changing resources”, explained Lathe “Since OpenHelix has multiple trainers all having PhDs in biological sciences, intimate knowledge of the resources, and having years of experience with on-site and online training, we have a unique ability to provide the solution to this problem.”

With an OpenHelix individual or institution subscription, users can access the complete catalog of OpenHelix tutorial suites, over 80 currently, in categories including pathways, expression, variation, literature and general databases. These tutorials are continuously updated each month with new tutorials added frequently. (For a complete catalog, go to http://www.openhelix.com/cgi/tutorials.cgi)

With a subscription, scientists quickly learn how to use the tools they need when they need them. 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 30-60 minute tutorials highlight and explain all the features and functionality needed to start using the resource effectively. The tutorials are used to introduce a new resource, to view new features and functionality, or simply as a reference tool to refresh a users knowledge on a resource.

In addition to the tutorials, subscribers also receive 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.

The new portal was partially funded by NHGRI grant 3R44HG004531.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix 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.  More efficient use of the most relevant resources means quicker and more effective research.

Tip of the Week: Finding the right genomics resource

ohsearch_thumbOpenHelix just opened our new web site. We will still be offering the tutorials we’ve always offered (80 and growing!), but now we have a new search engine and database of many more resources. And it’s publicly available and free.

There are now thousands of databases and analysis tools for the researcher to use when doing research in biology and genomics. The first problem the researcher has is just finding those resources, finding the right one. In another step toward helping that happen, we’ve put together a highly relevant, curated database of genomics and biological resources available to the researcher and a search engine to find them based the context of the keyword found at the resource site, tutorials and even our blogs posts that mention the database. You will find that your searches will lead you to resources relevant to your needs. Today’s tip introduces this new search.

We strongly believe this is the best method available now for the researcher not only to find relevant resources, but to find training on how to use those resources. And check back, our database of resources will be growing, as will our features.

Blog and Site are moving

We’ll be having a bigger announcement later, but we are moving!

The URL is the same: http://www.openhelix.com. Though we also now have http://www.openhelix.eu for our European users. They’ll both go to the same place of course! (though in the next couple days as our domain moves to the new servers, the first will be our old site, the latter will be our new one).

We have a new site and functionality! OpenHelix will now have a great new search engine (free and publicly available) to search through hundreds of genomics resources to find exactly what you are looking for. We believe this will be a great boon to finding your data. A large number of those (approaching 100 now) will have links to our tutorials for you to view and learn how to use those resources, some are sponsored and free to the user, others have reasonable subscription cost.

Our blog will have a new look and a new URLhttp://blog.openhelix.com. Of course, if you use http://www.openhelix.com/blog, you’ll be easily redirected.

We have lots of exciting plans for the search, for the site, for the blog and for our tutorials over the next few months and into the future, so keep an eye out! And please, if you find a feature you want or hit a snag, let us know!

New Online Tutorial for iHOP from OpenHelix

Comprehensive tutorial on the publicly available iHOP database enables researchers to quickly and effectively use this invaluable next-generation resource.

Seattle, WA,  August 10, 2009 — OpenHelix today announced the availability of a new tutorial suite for iHOP, or Information Hyperlinked Over Proteins. iHOP is a sophisticated, next generation text-mining database that provides comprehensive up-to-date information on specific genes and proteins by automatically scanning millions of PubMed abstracts each day. iHOP provides fast, accurate, comprehensive summary information on more than tens of thousands of genes, chemical compounds and Medical Subject Headings (or MeSH) terms. iHOP will selectively present only the information on genes and proteins you want. The control over the reliability and relevance of the retrieved information always remains in the hands of the user.

iHOP contains more than 15 million sentences and 80,000 different genes from over 1500 organisms and is updated daily. iHOP converts information derived from sentences in PubMed abstracts into one navigable resource using genes and proteins as hyperlinks. Superimposing this network of information on experimental interaction data makes simultaneous analysis of new and existing knowledge possible.

The iHOP tutorial suite, available for single purchase or through a low- priced yearly subscription to all OpenHelix tutorials, contains an online, narrated, multi-media tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. The iHop tutorial will teach users:

  • to understand the four main iHOP views
  • ways of filtering your searches to optimize results to your needs
  • how to use iHOP Gene Model to keep track of interesting sentences
  • how to download data from iHOP

With OpenHelix 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. To find out more about this and over 70 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 iHOP
iHOP was conceived and implemented by Robert Hoffmann and is maintained at the Computational Biology Center at Memorial Sloan Kettering Cancer Center headed by Chris Sander. iHOP is a free service from the academic domain, licenced under a Creative Commons Attribution-No Derivative Works 3.0 License.

About OpenHelix
OpenHelix, LLC, provides the genomics knowledge you need when you need it. OpenHelix currently 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.

New and Updated Online Tutorials for PROSITE, InterPro, IntAct and UniProt

Comprehensive tutorials on the publicly available PROSITE, InterPro, IntAct and UniProt databases enable researchers to quickly and effectively use these invaluable resources.

Seattle January 14, 2009 — OpenHelix today announced the availability of new tutorial suites on PROSITE, InterPro and IntAct, in addition to a newly updated tutorial on UniProt. PROSITE is a database that can be used to browse and search for information on protein domains, functional sites and families, InterPro is a database that integrates protein signature data from the major protein databases into a single comprehensive resource and IntAct is a protein interaction database with valuable tools that can be used to search for, analyze and graphically display protein interaction data from a wide variety of species. UniProt is a detailed curated knowledgebase about known proteins, with predictions and computational assignments for both characterized and uncharacterized proteins. These three new tutorials and an updated UniProt tutorial, in conjunction with the additional OpenHelix tutorials on MINT, PDB, Pfam, STRING, SMART, Entrez Protein, MMDB and many others, give the researcher an excellent set of training resources to assist in their protein research.

The tutorial suites, available for single purchase or through a low- priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides with full script, handouts
and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:

PROSITE

*how to access information on domains, functional sites and protein families in PROSITE
*to perform a quick and an advanced protein sequence scan
*to find patterns in protein sequences using PRATT
*to use MyDomains to create custom domain graphics

InterPro

  • to use both the basic and advanced search tools to find detailed information on entries in InterPro
  • how to understand and customize the display of your results
  • to use InterProScan to query novel protein sequences for information on domains and families

IntAct

  • how to perform basic and advanced searches to find protein interaction data
  • to effectively navigate and understand the various data views
  • to graphically display and manipulate a protein interaction network

UniProt

  • to perform text searches for relevant protein information
  • to search with sequences as a starting point
  • to understand the different types of UniProt records

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

About OpenHelix
OpenHelix, LLC, provides the genomics knowledge you need when you need it. OpenHelix currently 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.

Virtual Online NCBI Field Guide available from OpenHelix

Get a year access to over ten OpenHelix tutorials on NCBI bioinformatics and genomics resources.OpenHelix today announced it is offering a Virtual Field Guide on NCBI Resources, with a year subscription to over ten self-run, web based, narrated tutorials on NCBI bioinformatics and genomics resources.The Virtual NBCI Field Guide currently includes tutorials on dbSNP, Entrez Gene, Entrez Overview, GEO, Map Viewer, OMIM, and PubMed. Additional tutorials on BLAST, Entrez Protein, MMDB, and dbGaP will be added over the next three months. Subscribers to the Virtual NCBI Field Guide will have access to any and all of these tutorials and their updates for one year.

All tutorials are an introduction to the resources, explaining features, functionally and use for the beginning to intermediate user. The tutorials also include downloadable PowerPoint slides, handouts, and exercises for use as reference or for use in a classroom setting.

“NCBI provides many powerful and popular resources,” explained Scott Lathe, CEO of OpenHelix, “but with NCBI no longer offering onsite seminars, we are attempting to meet the urgent need for this training with a special subscription at a low price.”

The Virtual NCBI Field Guide can be purchased for a single user, a lab, a department or for a company or institution. Subscription for one user for one year is only $199, with multiple user pricing as low as $15 per user per year.

For more information or to purchase, visit www.openhelix.com/FieldGuide.

OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix 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.

OpenHelix receives $1 million NIH grant for genomics training portal

January 21, 2008 (Seattle, WA) – Thanks to a $1 million grant, OpenHelix (www.openhelix.com) has been developing an innovative set of online tools for use by scientific researchers. The tools will greatly reduce the amount of time necessary to locate and use the vast genomics and bioinformatics resources available to scholars and scientists. Once relevant resources are located through an innovative search tool, researchers will learn how to use them with extensive tutorial suites. The SBIR (Small Business Innovation Research) grant was awarded by the National Human Genome Research Institute (Grant number 9R44HG004531).

Freely accessible genomics and bioinformatics resources

With numerous online databases and other genomics and bioinformatics resources available to scientists, the time spent identifying thebest resources and using them in an efficient manner has been a challenge for even the most well-staffed organization.Much data is underutilized due to a lack of awareness of its existence. When scholars and scientists do happen to locate needed information in an online resource, they then must figure out each resource’s unique navigation methods and each documentation style. Introductory training on many resources is either nonexistent or not sufficient to effectively teach users how to best use the site.

“The need for such a resource is clear in the bioinformatics area,” says Joan E. Brooks Ph.D., co-founder of Garbrook Knowledge Resources and former co-founder of Proteome, an online genomics information database company. “The OpenHelix solution will be a promising leap forward to assure the public investment in these resources is fully realized.”

Improving efficiency and effectiveness of research

While genomics resources and data continue to grow rapidly, scientists are at a disadvantage when trying to decide the best resource for them. The search and tutorial portal will enable faster completion of research projects, leading to an accelerated increase in the use and dissemination of scientific knowledge.“We are now looking at some very innovative ways to search a large number of resources, including semantic search using widely used and accepted ontologies” Warren Lathe, co-founder, OpenHelix Chief Scientific Officer and Principal Investigator on the grant said, “The science community will be very excited about the tools we are going to offer this year.”

The groundbreaking search function will provide various methods for locating and ranking genomics resources. As they use the OpenHelix online search for their projects, scientists and other researchers will use a ranking system within the search results to filter the list that pertains to their particular needs, something not previously available.The tutorials also include training material for use in the classroom setting, giving faculty ready-made, updated material to train students.By matching researchers quickly and efficiently with the resources that are most relevant to their needs and providing training so the researcher can effectively use the resource, the grant from the NHGRI will help fulfill the promise of research breakthroughs provided by the post-genomic era.

About OpenHelix

OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix currently 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. Headquartered in Washington State, OpenHelix also has offices in San Francisco, Boston and North Carolina. Further information can be found on www.openhelix.com or by calling 1-888-861-5051.

OpenHelix Announces Genomics Blog

January 14, 2008 (Seattle WA) OpenHelix today announced a new blog (www.openhelix.com/blog) exclusively focused on genomics and bioinformatics resources. The blog will be an instrumental, interactive forum for researchers to learn more about the rapidly changing and growing genomics databases and resources.The blog, authored by OpenHelix scientists with extensive experience with genomics and biology and industry expertise in databases and resources, will have daily postings about genomics resources, genomics news and research, and training tips on how to effectively find and use bioinformatics resources.

“Creating and maintaining this blog is one additional way that we provide our genomics expertise to the science community,” explained Warren Lathe, the Chief Technology Officer at OpenHelix, “With the addition of questions and answers, researcher comments, and guest posts from those in the industry, our goal is to provide a comprehensive information source about the invaluable genomics tools on the web.”

In addition to daily posts on relevant topics, the OpenHelix Blog on Genomics and Bioinformatics will include:

“Tip of the Week”: A short video outlining a tip on how to use a database to find something you need, some feature that you might not have noticed before, or introducing a new resource.

“What’s Your Problem?”: An “open office hours” open thread post every Thursday where you can ask questions about what database might have the data you need, how to find specific types of information from a resource, and more. With nearly immediate answers to your questions, you’ll have a virtual help desk on genomics and bioinformatics resources.

“Guest Post”: A periodic guest post from a scientist on an issue or topic that they feel is important to the community. Our guest posters will be people directly involved in developing and maintaining resources or genomics research.

“Free Tutorials”: You’ll find links to extensive tutorial suites on a number of genomics and bioinformatics resources. The suites include 40-60 minute narrated self-run tutorials, slide sets, hand-outs and exercises.

Visit the OpenHelix Blog at (www.openhelix.com/blog).

About OpenHelix

OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix currently 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.