Tag Archives: training

Scivee group

I’ve mentioned this before, but as I am trying to get this weeks tip ready, I thought I’d remind our readers that we have a community over at Scivee (youtube for science :): Genomics Resource Training. We post all our tips there now and we add videos from other users that train users about genomics resources. We have about 2-3 dozen videos in our community now. Come on over and join!

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.

SciVee and OpenHelix

Visit Genomics Resource Training Community If you haven’t noticed, we’ve started adding our tips of the week to SciVee and using the embed to embed them here. This allows you to view the video and share it on your web site or with friends. We’ve also created a “community” over at SciVee we’ve called “Genome Resource Training” where we will be gathering all these video tutorial tips along with any other video tutorials we find over at SciVee that train or introduce researchers on some of the huge amount of resources out there (click the “SciVee” icon above to visit the community). We’ve got about 8 tips over there now and another 8 or so videos from other sources. This community will only grow! So, come check it out, join SciVee and join our community! Of course you will _always_ find our tips here and much more on this blog, so keep us in your feeds and bookmarks and don’t forget to get some in-depth training with our tutorials! We are looking forward to a longterm and expanding work with SciVee.

We also now have a Facebook page, where we will be posting these tips weekly with an occasional ‘general-interest’ genomics link or two. So, please.. follow us there if you are on Facebook and ‘share with friends!

Friday SNPpets

Welcome to our Friday feature link dump: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Education at NCBI

I’d like to point out the new NCBI Education page. There is a lot there that you might want to check out. NCBI will be, starting this fall, offering a series of two-day training courses they are calling Discovery Workshops. Two years ago they ended the NCBI Field Guide workshops, so this seems to be a welcome change.

There are also webinars. Our research suggests that webinars are not particularly popular, so I’m curious how these turn out. There are also ‘how-to’ guides, documentation, community, teacher resources. It’s quite a nice site with lots of things to check out.

I’d also like to point out the “recommended links” section. There are lots of links to additional educational resources like the Cold Spring Harbor’s Dolan DNA Learning Center and much more. And, incidentally :), a link to our own free tutorials which was very nice to see. You might want to check those out, we have over 10 including PDB, SGKB, UCSC Genome Browser, Galaxy, several model organism databases, and more.

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.

Genomics resource training scholarship, sponsored by Gramene and OpenHelix

Just thought our readers might like a heads up. I quote from a recent press release:

Cold Spring Harbor Laboratory, Oregon State University and Cornell University, creators of the Gramene Resource for Comparative Plant Genomics, partner with OpenHelix to offer online training on genomic resources to encourage diversity in science.

The Resource for Comparative Grass Genomics, Gramene, sponsors a Gramene tutorial with us, which is thus free to users. Additionally, Gramene is also sponsoring a program, partially funded by NSF,  to open all OpenHelix tutorials to educational institutions serving underrepresented populations. This will give all students, faculty and staff at the institution unlimited access to a wealth of tutorials in our catalog including training on NCBI’s PubMed, Entrez, PlantGDB and over 90 other tutorials on genomic resources. This would be a great opportunity for students and researchers at the applying institution to train on genomics resources!

If you belong to a qualifying institution and would like to apply for this program, please find more information here and send us your application! The deadline for application is June 30th, 2010.

(tweeted here)

Gramene Announces Scholarships for Groups Underrepresented in Science to Learn How to Use Bioinformatics and Genomics Resources

Cold Spring Harbor Laboratory, Oregon State University and Cornell University, creators of the Gramene Resource for Comparative Plant Genomics, partner with OpenHelix to offer online training on genomic resources to encourage diversity in science.

Bellevue, WA (PRWEB) April 22, 2010 — The creators of the Gramene Resource for Comparative Grass Genomics and OpenHelixannounce the availability of scholarships to colleges and universities serving underrepresented minorities for full access to over 85 online tutorial suites on bioinformatics and genomics resources. The program is partially funded by the National Science Foundation (NSF).

“An ongoing goal for Gramene, our institutions, and the NSF, has been to provide opportunities for advancement and training to underrepresented groups in science,” said Dr. Doreen Ware, of Cold Spring Harbor Laboratory and Principal Investigator of Gramene, “So we are excited to be able to offer individual and institution scholarships to an extensive and valuable catalog of online training on genomics resources.”

…we are excited to be able to offer individual and institution scholarships to an extensive and valuable catalog of online training on genomics resources.

Recipients will have access to the OpenHelix catalog of tutorial suites on a wide range of bioinformatics and genomics resources, including Gramene, PlantGDB, NCBI tools such as Entrez Gene, BLAST and PubMed and many more. A full catalog of tutorial suites is available at http://www.openhelix.com/cgi/tutorials.cgi.

Each tutorial suite includes a 45-60 minute, online, self-run, narrated introductory tutorial on how to use a specific resource. The tutorial suite also includes PowerPoint slides, slide handouts and exercises which can be used as reference material or to build classroom content.

“The study of genomics has affected just about every area of life sciences, so learning how to access and interpret genomic data is critical to research success,” said Scott Lathe, Chief Executive Officer of OpenHelix, “With the convenience and broad accessibility of online training, we hope these scholarships will help in leveling access to this important training and further the potential and ongoing careers of the recipients.”

Institutions can apply for a scholarship for access to the tutorials at http://www.openhelix.com/cgi/scholarships.cgi. The scholarships are available to to minority serving colleges and universities. Underrepresented in science means those racial and ethnic populations that are underrepresented in biology research relative to their numbers in the general population. Individual scholarships are available to U.S undergraduates, graduate students, post-doctoral students, faculty and staff. Application deadline is June 30, 2010 and a limited number of scholarships are available.

About Gramene
Extensive research over the past two decades has shown significant conservation of gene order within large segments of linkage groups in agriculturally important grasses such as rice, maize, sorghum, barley, oats, wheat, and rye. Grass genomes are substantially colinear at both large and short scales, opening the possibility of using syntenic relationships to rapidly isolate and characterize homologues in maize, wheat, barley and sorghum.

As an information resource, Gramene’s purpose is to provide added value to data sets available within the public sector to facilitate researchers’ ability to understand plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species.

Current work is being supported by the NSF Plant Genome Research Resource grant award #0703908.

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.

National Institutes of Health subscribes to OpenHelix training portal

NIH scientists and staff can now efficiently and effectively learn to use bioinformatics and genomics resources with the extensive tutorial suite catalog from OpenHelix.

Bellevue, WA (PRWEB) April 19, 2010 — The National Institutes of Health Library (www.nihlibrary.nih.gov) has purchased a subscription toOpenHelix (www.openhelix.com) giving NIH scientists and staff access to over 90 tutorial suites on bioinformatics and genomic resources.

With OpenHelix tutorials, NIH now offers their employees 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.

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 research institutions themselves to create and provide training on the many critical genomic resources available.” said Scott Lathe, Chief Executive Officer of OpenHelix, “NIH uses the OpenHelix subscription to provide an efficient and effective training solution for their researchers.”

About the National Institutes of Health
Composed of 27 Institutes and Centers, the NIH provides leadership and financial support to researchers in every state and throughout the world.

For more than a century, the National Institutes of Health has played an important role in improving the health of the nation. The NIH traces its roots to 1887 with the creation of the Laboratory of Hygiene at the Marine Hospital in Staten Island, NY.

NIH is the steward of medical and behavioral research for the Nation. Its mission is science in pursuit of fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to extend healthy life and reduce the burdens of illness and disability.

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.

Pointing us out at Genome.gov :)

ohonnhgripageNHGRI recently pointed out our new set of tutorials on model organism databases (funded mainly by NHGRI :) on their home page, genome.gov. Always nice to be recognized :D.

And it gives me the opportunity to again point out that we do indeed have seven publicly available tutorials and training materials (slides, exercises, etc) on model organism databases including SGD, RGD, MGI, WormBase, FlyBase and ZFIN… and a seventh on GBrowse, a generic genome browser used by some of these and other genome databases.

Check them out (and fill out the new poll to the left :D.