Tag Archives: tutorials

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

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

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

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

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

These tutorials will teach users:

NCBI Overview

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

PubMed

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

Gene Expression Omnibus (GEO)

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

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

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

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!

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)

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.

RCSB PDB Teams with OpenHelix to Announce Free Tutorial and Training Materials

The Protein Data Bank (PDB) bioinformatics resource partners with OpenHelix to provide online tutorial suite, Quick Reference Cards, and other training and outreach programs.

Seattle, WA (PRWEB) April 13, 2010 — The Research Collaboratory for Structural Biology (RCSB) Protein Data Bank (PDB), has partnered with OpenHelixTM to provide comprehensive training and outreach programs for its free, web-based resource (www.pdb.org).

The RCSB PDB provides a variety of tools and resources to use to study biological macromolecules. The PDB is the single worldwide repository of experimentally-determined 3D biological structures of proteins, nucleic acids and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data, and presents basic and advanced search, display and visualization methods to access these data.

“RCSB PDB is a premier resource with a long history of providing researchers with excellent data and tools,” said OpenHelix founder and President Dr. Mary Mangan. “We are proud to be able to contribute to the effort to increase users’ access and understanding of these tools.”

The new training tools (at http://www.openhelix.com/pdb) include an online narrated tutorial that demonstrates: basic and advanced searches, how to generate reports, the different options for exploring individual structures, and many of the research and educational resources and tools available at the RCSB PDB. The approximately 60-minute tutorial, which runs in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders.

In addition to the tutorial, RCSB PDB users can 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.

OpenHelix also has created free Quick Reference Cards for the RCSB PDB. The Quick Reference Card highlights features found on the home page, as well as search strategies, features, and functionalities. The cards can be ordered at www.openhelix.com. Thirty cards can be ordered at a time and shipping is free within the United States.

“We are pleased to team with OpenHelix to offer these new training materials alongside their other great bioinformatics resource tutorials,” said Helen M. Berman, Director of the RCSB PDB. “The suite of materials can introduce new users to the RCSB PDB and serve as a quick reference for our experts.”

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

About the RCSB PDB
The RCSB Protein Data Bank (www.pdb.org), administered by the Research Collaboratory for Structural Bioinformatics (RCSB), supports scientific research and education worldwide by providing an essential resource of information about biomolecular structures. These molecules of life are found in all organisms, from bacteria and plants to animals and humans.

The RCSB PDB member institutions jointly manage the project: Rutgers, The State University of New Jersey and the San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego.

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.

Quick note: SGKB and PDB tutorials

We recently announced a free tutorial (sponsored by PSI) on the Structural Genomics Knowledgebase (SGKB). I thought it might be of interest to our readers. You can access the free tutorial (approx. a 1hr movie, slides, handouts and exercises) here.

We will also soon announce a free tutorial on the Protein Database (PDB), but you can already access it here.

For a full list of our free tutorials and training materials, click here (about a dozen), or view our other 80 or more tutorials on a wide range of topics by subscription.

University of Miami Adds Effective and Efficient Online Tutorial Suites to Bioinformatics Portal

University of Miami’s Center for Computational Science subscribes to OpenHelix tutorial suites for their online Bioinformatics Integrated Services (iBIS) portal.

Seattle WA (PRWEB) March 15, 2010 — The Center for Computational Science (CCS) at University of Miami (http://www.ccs.miami.edu/index.html) and OpenHelix (www.openhelix.com) announced the integration and availability of over 85 tutorial suites on bioinformatics and genomic resources to the Center’s Bioinformatics Integrated Services (iBIS) portal.

The iBIS portal (http://bio.ccs.miami.edu/ibis/), currently in phase one, offers a comprehensive list of genomic databases, protein structure databases, clinical genetics databases, as well as numerous software tools for the analysis of gene expression, regulation, signaling and metabolic pathways, genomics, proteomics, and systems biology. In addition, the portal allows access to a suite of tools and databases available to University of Miami faculty, staff, and students.

Once they find a resource, it is essential we provided them the training needed to effectively use it—and OpenHelix tutorials were the obvious choice.

With OpenHelix tutorials, iBIS offers a quick and effective way to learn about many of these powerful and popular databases and resources. The narrated tutorials run in just about any browser and show the user how to use the features and functionality of the resources.

“Our mission was to provide a comprehensive, user-friendly, and customizable interface for researchers to find the resource they need,” said Dr. Sawsan Khuri, Bioinformatics Senior Scientist at the Center, “but once they find a resource, it is essential we provided them the training needed to effectively use it—and OpenHelix tutorials were the obvious choice.”

The basic functionality of iBIS is available to all, however access to local software and databases and to the tutorials is limited to those at the University of Miami. Over 80 tutorials, including PowerPoint slides, slide handouts and exercises which can be used as reference material or to build classroom content, can be accessed by others through a subscription atwww.openhelix.com.

“It is difficult, and certainly cost prohibitive, for every university to create and provide training on the many critical genomic resources available” said Scott Lathe, Chief Executive Officer of OpenHelix, “the Center found a great solution to their training needs in licensing our content for integration into their portal. We’re certainly proud to be part of the iBIS platform.”

About the Center for Computational Science
The University of Miami Center for Computational Science (CCS) actively engages in interdisciplinary research to solve the complex scientific and technological problems of modern society. The CCS strives for excellence in research, teaching and service covering the fundamental, as well as, applied aspects of computational science.

Faculty and staff at the University of Miami Center for Computational Science (CCS) harness computing power, applied mathematics, and application sciences – such as physics, chemistry, biology, engineering, and earth sciences – to address the most pressing challenges of our generation. With programs in bioinformatics, physical sciences, chemoinformatics, data mining, and data visualization, the Center facilitates collaborative projects between departments and institutes. Engineers and scientists use the burgeoning field of computational science to manage huge volumes of data rapidly and economically to construct and test models of intricate phenomena.

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

New Online Tutorials for NCBI resources BioSystems and DCODE

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

Seattle, WA (PRWEB) February 23, 2010 — OpenHelix today announced the availability of new tutorials on BioSystems and DCODE.

The NCBI BioSystems database provides easy access to information about all the molecules that interact in a biological system, including genes and proteins, small molecules in a pathway, as well as the genes biomarkers and drugs associated with diseases. DCODE is a public NCBI suite of tools for genomic alignments, multiple and pairwise sequence alignments, identifying gene regulatory elements and conserved transcription binding sites and more. These two tutorials, in conjunction with OpenHelix tutorials on OMIM, PubMed, Entrez Gene, BLAST, GEO and several others, give you a set of training resources that help you become efficient and effective using NCBI resources.

These two tutorials, in conjunction with OpenHelix tutorials on OMIM, PubMed, Entrez Gene, BLAST, GEO and several others, give you a set of training resources that help you become efficient and effective using NCBI resources.

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

These tutorials will teach users:

BioSystems

*to perform basic searches and to understand your results
*to link out to a variety of related information in many different fields
*about Entrez tools that you can use to customize your searches and results*
*how to access and customize full-size pathway images
*some advanced searching techniques, including Boolean queries and batch searching

DCODE

*how to conduct whole genome alignments and identify ECRs
*how to create interactive conservation profiles and phylogenetic trees
*how to identify proximal and distant regulatory elements in desired sequences
*how to identify conserved transcription factor binding sites

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

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

New and Updated Online Tutorials for GoMiner and XplorMed

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

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

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

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

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

These tutorials will teach users:

GoMiner

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

XplorMed

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

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