Genomics Resource Training

Video Tip of the Week: MetaboAnalyst 2.0

OpenHelix — Tue, 28 Aug 2012 08:43:34 -0700

MetaboAnalyst 2.0 is a web-based resource that allows high-throughput metabolomic data analysis from a user-friendly interface. For more information of this tool, please see our blog post at http://blog.openhelix.eu/?p=13481

Genomics Resource Training

Getting leads from Big Data

OpenHelix — Mon, 20 Aug 2012 10:18:40 -0700

This video illustrates a search of the ICGC, International Cancer Genome Consortium, for a gene lost in tumor samples. For more details see the blog post: http://blog.openhelix.eu/?p=13404

Genomics Resource Training

Tip of the Week: Browsing Butterflies with GBrowse and Ensembl

OpenHelix — Tue, 14 Aug 2012 08:10:31 -0700

Community genome browsers are important tools to supplement publications. For more details and links visit http://blog.openhelix.eu/?p=12182 .

Genomics Resource Training

Video Tip of the Week: Microbiome Resources From JGI

OpenHelix — Tue, 31 Jul 2012 07:30:07 -0700

For more information about this resource, see our blog post at URL http://blog.openhelix.eu/?p=13147. We visit both IMG/M (IMG with Microbiome Samples) (briefly) and the Integrated Microbial Genomes-Human Microbiome Project, or IMG/HMP in today’s tip.

Genomics Resource Training

Tip of the Week: Galaxy Tool Shed

OpenHelix — Wed, 18 Jul 2012 10:09:58 -0700

Today's tip of the week is on the Galaxy Toolshed, to find more read the blog post and tip at: http://blog.openhelix.eu/?p=12988

Genomics Resource Training

Video Tip of the Week: ScienceSeeker for science blogging

OpenHelix — Fri, 06 Jul 2012 11:59:59 -0700

Learn how you can join the ScienceSeeker blog network to communicate about science, including special ways to highlight posts you've done on peer-reviewed publications. More details here: http://blog.openhelix.eu/?p=12676

Genomics Resource Training

Tip of the Week: ChromoHub

OpenHelix — Wed, 04 Jul 2012 03:33:10 -0700

Today's tip of the week is on Chromohub, an annotated phylogeny of chromatin mediated signaling genes. For more information, check out our blog post at http://blog.openhelix.eu/?p=12671

Genomics Resource Training

Video Tip of the Week: The PSI SBKB's New Content Hubs

OpenHelix — Tue, 26 Jun 2012 07:50:34 -0700

For more information about this resource, see our blog post at URL: http://blog.openhelix.com/?p=12634 In the tip I will feature the newly organized content hubs over at the Protein Structure Initiative's Structural Biology Knowledgebase, or PSI SBKB. These scientific hubs, organized by content, make it easy for users to access specific content offered by both the SBKB and the PSI as a whole.

Genomics Resource Training

Video Tip of the Week: Publications track in UCSC Genome Browser

OpenHelix — Tue, 19 Jun 2012 07:50:12 -0700

An important new track in the UCSC Genome Browser provides text mining results from the literature to annotate genomic regions. For more details see http://blog.openhelix.eu/?p=12420 .

Genomics Resource Training

Tip of the Week: Visualizing Galaxy

OpenHelix — Tue, 12 Jun 2012 13:09:49 -0700

A tip of the week introducing visualizing genomic data using Galaxy's visualization tool. For more information, check out the blog post at http://blog.openhelix.eu/?p=12439

Genomics Resource Training

Video Tip of the Week: FancyGene for quick accurate diagrams

OpenHelix — Tue, 05 Jun 2012 06:57:42 -0700

Create accurate and effective diagrams of genes of interest with FancyGene: http://blog.openhelix.eu/?p=12264

Genomics Resource Training

Tip of the Week: BioProject

OpenHelix — Tue, 24 Apr 2012 22:08:15 -0700

A quick intro to BioProject. For more information see http://blog.openhelix.eu/?p=11931

Genomics Resource Training

Video Tip of the Week – The Cell: An Image Library

OpenHelix — Tue, 17 Apr 2012 08:31:40 -0700

For more information about this resource, se our post at URL http://blog.openhelix.com/?p=11799. For my video tip this week I decided to check out the images available from "The Cell: an Image Library", which is brought to you by the The American Society for Cell Biology (ASCB). The library contains thousands of images, time series and groups of images, videos and animations of cells in a variety of organisms.

Genomics Resource Training

Video Tip of the Week: A 3D Worm!

OpenHelix — Fri, 06 Apr 2012 07:02:22 -0700

Explore the OpenWorm Browser, a 3D representation of C. elegans. For more details and links visit: http://blog.openhelix.eu/?p=11669

Genomics Resource Training

Tip of the Week: TFBS using Mapper

OpenHelix — Wed, 21 Mar 2012 07:53:35 -0700

An intro to Mapper, a database of transcription factor binding sites. For more information, check the blog at http://blog.openhelix.eu/?p=11517

Genomics Resource Training

Video Tip of the Week: New Genetic Testing Registry (GTR) Resource

OpenHelix — Tue, 13 Mar 2012 10:16:57 -0700

For more information, see our blog post at http://blog.openhelix.eu/?p=11439. In this movie we compare the new GTR resource from NCBI to other clinical resources that you may already be using, to answer why you may want to use the GTR.

Genomics Resource Training

Video tip of the week: Highlights [heh] of the Cannabis browser

OpenHelix — Tue, 06 Mar 2012 13:51:31 -0800

An introduction to the Cannabis genome browser. For the paper and links, visit http://blog.openhelix.eu/?p=11320 .

Genomics Resource Training

Tip of the Week: eGIFT, extracting gene information from text

OpenHelix — Tue, 28 Feb 2012 21:32:42 -0800

This week's tip is on eGIFT, a tool that allows you to extract information from text. For more information, check out the post at http://blog.openhelix.eu/wp-admin/post.php?post=11293

Genomics Resource Training

Video Tip of the Week: OMIA, Online Mendelian Inheritance in Animals

OpenHelix — Tue, 14 Feb 2012 06:53:28 -0800

The OMIA database specializes in traits of animals that are not typical laboratory animals. For more details and links visit http://blog.openhelix.eu/?p=11073

Genomics Resource Training

Tip of the Week: SNPxGE2, SNP-coexpression associations

OpenHelix — Wed, 08 Feb 2012 08:58:29 -0800

This tip of the week introduces SNPxGE2, a SNP-coexpression association database. See more here:http://blog.openhelix.eu/?p=11050

Genomics Resource Training

Video Tip of the Week: SNPeffect 4.0

OpenHelix — Tue, 31 Jan 2012 12:15:06 -0800

This quick tip explores the new version of SNPeffect. For more information and links see http://blog.openhelix.eu/?p=10257

Genomics Resource Training

Video tip of the week: OpenHelix App on SciVerse to Extend Research

OpenHelix — Fri, 13 Jan 2012 13:01:37 -0800

See our blog post at URL http://blog.openhelix.com/?p=10810 for more information on this resource. In today’s tip I will introduce you to another one of our efforts to “extend research” by showing you a glimpse of an OpenHelix app that we designed for the SciVerse platform from Elsevier. This app scans a ScienceDirect journal article for any database names or URLs that we train on, and then displays a list of such resources in the window of the app.

Genomics Resource Training

Tip of the Week: eggNOG, orthologous genes

OpenHelix — Tue, 20 Dec 2011 22:47:07 -0800

A 5 minute tip on eggNOG, database of orthologous genes. Check out our blog post for more information: http://blog.openhelix.eu/?p=10634

Genomics Resource Training

Video Tip of the Week: Big Changes to NCBI's Genome Resources

OpenHelix — Tue, 13 Dec 2011 10:34:56 -0800

For more information about this resource see our blog post at URL http://blog.openhelix.eu/?p=10546. My video will focus on the "completely redesigned Genome site", which was recently rolled out and announced in the most recent NCBI newsletter.

Genomics Resource Training

Tip of the Week: Phosphida

OpenHelix — Tue, 29 Nov 2011 08:31:14 -0800

THis tip of the week is on Phosphida, a post translational modification database. For more information, see: http://blog.openhelix.eu/?p=10432

Genomics Resource Training

Video Tip of the Week: BioMart's new central portal

OpenHelix — Tue, 22 Nov 2011 07:18:17 -0800

BioMart has a new look, and new features. More details and links: http://blog.openhelix.eu/?p=10275

Genomics Resource Training

Tip of the Week: MapMi, mapping miRNA sequences

OpenHelix — Tue, 15 Nov 2011 10:27:15 -0800

Today's tip is on MapMi, a tool to map miRNA sequences to genomic sequences. See http://blog.openhelix.eu/?p=10282 for more information

Genomics Resource Training

Video Tip of the Week: The New Database of Genomic Variants – DGV2

OpenHelix — Tue, 08 Nov 2011 13:04:28 -0800

For more information about this resource, please see our blog post at URL http://blog.openhelix.eu/?p=10185. In today’s tip I will briefly introduce you to the beta version of the updated Database of Genomic Variants, or DGV.

Genomics Resource Training

Video tip of the week: Variation Data from Ensembl

OpenHelix — Tue, 25 Oct 2011 14:22:02 -0700

For more information about this resource see our blog post at URL http://blog.openhelix.eu/?p=10091. In today's tip I am going redo a movie originally done by Ensembl on SNP information in Ensembl, but I will use the updated Ensembl release 64.

Genomics Resource Training

Video Tip of the Week: Mitochondrial transcriptome GBrowser

OpenHelix — Thu, 13 Oct 2011 06:39:24 -0700

The data isn't in the papers anymore--it's in the browsers. Explore a nice example of next-gen sequencing data in a custom installation of GBrowse. References and more details: http://blog.openhelix.eu/?p=9830

Genomics Resource Training

Tip of the Week: UCSC Genome Browser Track Hubs

OpenHelix — Thu, 29 Sep 2011 12:51:36 -0700

This tip introduces a new feature at UCSC, Track Hubs. You can read more about it on the blog: http://blog.openhelix.eu/?p=9907

Genomics Resource Training

Tip of the Week: Getting flanking sequence of genomic locations

OpenHelix — Mon, 19 Sep 2011 21:51:31 -0700

This week's tip is on using Galaxy to get flanking sequence. See http://blog.openhelix.eu/?p=9808 for more information.

Genomics Resource Training

YeastMine: Editing Templates - HD

yeastgenome — Mon, 12 Sep 2011 12:57:54 -0700

Step-by-step instructions on how to edit YeastMine templates, from the Saccharomyces Genome Database (SGD).

Genomics Resource Training

Tip of the week: phiGENOME for bacteriophage genome exploration

OpenHelix — Mon, 12 Sep 2011 07:28:23 -0700

Investigate bacteriophage genomics and regulation with phiGENOME and phiSITE. Links and references available at http://blog.openhelix.eu/?p=9605 .

Genomics Resource Training

YeastMine: Saving Search Results as a List

yeastgenome — Fri, 09 Sep 2011 13:10:31 -0700

Describes how to save some or all of the search results from a YeastMine query into a list.

Genomics Resource Training

Tip of the Week: Plant comparative genomics with Plaza

OpenHelix — Wed, 07 Sep 2011 06:38:47 -0700

This week's tip is how to get gene family phylogenies from Plaza, a plant comparative genomics resources. More information here: http://blog.openhelix.eu/?p=9664

Genomics Resource Training

Tip of the Week: From UniProt to the PSI SBKB and Back Again

OpenHelix — Mon, 29 Aug 2011 13:52:47 -0700

For more information about these resources see our blog post at URL http://blog.openhelix.eu/?p=9579. In this tip I show you why & how you can move from a UniProt protein report to either an RCSB PDB structure page or to search results in the Structural Biology Knowledgebase that provide information on established protocols and available materials related to the protein of interest.

Genomics Resource Training

Tip of the Week: DomainDraw for quick motif diagrams

OpenHelix — Tue, 23 Aug 2011 06:41:59 -0700

Use DomainDraw to create handy motif diagrams on proteins, with appropriate scale. See http://blog.openhelix.eu/?p=9459 for additional details and reference information.

Genomics Resource Training

Tip of the Week: CoGe, Comparative Evolution

OpenHelix — Tue, 16 Aug 2011 13:25:01 -0700

Todays tip is on the CoGe tool, SynMap and how to analyze genomic rearrangements. For more information visit the blog post: http://blog.openhelix.eu/?p=9450

Genomics Resource Training

Tip of the week: CompaGB for comparing genome browser software

OpenHelix — Tue, 09 Aug 2011 07:28:55 -0700

Select software for a project based on specific metrics. For details visit http://blog.openhelix.eu/?p=9189

Genomics Resource Training

Tip of the Week: SNPexp

OpenHelix — Mon, 01 Aug 2011 14:53:07 -0700

A quick introduction to a web-based tool that allows you to correlate SNPs in a region with gene expression levels. See http://blog.openhelix.eu/?p=9275 for more details.

Genomics Resource Training

Tip of the Week: PolySearch

OpenHelix — Wed, 13 Jul 2011 13:40:03 -0700

This tip is a quick introduction to PolySearch, for more information, see: http://blog.openhelix.eu/?p=9084

Genomics Resource Training

Tip of the Week: Gene Prioritization Portal

OpenHelix — Wed, 06 Jul 2011 06:17:30 -0700

Today's tip is a quick introduction to the Gene Prioritization Portal. To find more information, see: http://blog.openhelix.eu/?p=8988

Genomics Resource Training

Tip of the Week: Orphanet for Rare Disease information

OpenHelix — Mon, 27 Jun 2011 06:40:48 -0700

Explore Orphanet, a portal for rare disease and orphan drug information. Further details and links available here: http://blog.openhelix.eu/?p=8831

Genomics Resource Training

Tip of the Week: Update to NCBI's Cn3D Viewer

OpenHelix — Tue, 21 Jun 2011 10:24:09 -0700

For more information on this resource see our blog post at http://blog.openhelix.eu/?p=8838. In the tip I use the myosin VI structure summary page from NCBI's Molecular Modeling Database (MMDB) as my example of how to use the updated version of the Cn3D interactive 3D viewer from NCBI.

Genomics Resource Training

Tip of the Week: MutaDATABASE

OpenHelix — Tue, 14 Jun 2011 07:13:50 -0700

MutaDATABASE is a project to curate and organize human genomic variation of clinical significance. For references and links visit our blog post http://blog.openhelix.eu/?p=8688

Genomics Resource Training

Video demo on Human Epigenome Browser

Xin Zhou — Tue, 14 Jun 2011 06:22:57 -0700

The Human Epigenome Browser is an advanced web service that allows investigators to navigate and explore Roadmap Epigenomics project data set, and much more! This video clip briefly goes over main features of our web service. Visit the browser at http://vizhub.wustl.edu/. This video clip was made by Brett Maricque.

Genomics Resource Training

Tip of the Week: New and Improved OMIM®

OpenHelix — Tue, 31 May 2011 13:39:12 -0700

Explore the new interface for the venerable OMIM genetics resource; visit http://blog.openhelix.eu/?p=8539 for more details and references.

Genomics Resource Training

Tip of the Week: Allen Institute's Brain Explorer

OpenHelix — Tue, 17 May 2011 08:39:59 -0700

For more information about this resource see our blog post at URL http://blog.openhelix.eu/?p=8376. We show an overview of how researchers can use the Allen Institute's Brain Explorer to compare detailed gene expression data in two human brains, side-by-side.

Genomics Resource Training

YeastMine: Creating and Using Lists

yeastgenome — Fri, 13 May 2011 14:22:10 -0700

This tutorial covers how to create lists of genes and some of the list analysis options in SGD's data retrieval tool YeastMine.