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.

Genomics Resource Training

Tip of the Week: Synteny and DotPlots at VISTA

OpenHelix — Tue, 26 Apr 2011 23:08:44 -0700

A quick tip introducing how to access the dot plot and synteny information of VISTA. CHeck out the blog post for more information: http://blog.openhelix.eu/?p=8185

Genomics Resource Training

Tip of the Week: LAMHDI for animal models

OpenHelix — Sun, 17 Apr 2011 10:48:23 -0700

Searching for animal model sources is made easy with the LAMHDI database. http://blog.openhelix.com/?p=7897 for additional details and links.

Genomics Resource Training

Tip of the week: VirusMINT

OpenHelix — Fri, 08 Apr 2011 08:30:34 -0700

For more information about this resource, see our blog post at URL http://blog.openhelix.eu/?p=7790. VirusMINT shows interactions BETWEEN human and viral proteins on the same interaction map.

Genomics Resource Training

Tip of the Week: MetaPhOrs, orthology & paralogy prediction

OpenHelix — Tue, 29 Mar 2011 22:05:52 -0700

A tip of the week on MetaPhOrs, a orthology and paralogy prediction database. For more information see the write up at: http://blog.openhelix.eu/?p=7707

Genomics Resource Training

Tip of the Week: ORegAnno for regulatory annotation

OpenHelix — Tue, 22 Mar 2011 07:50:15 -0700

Literature-curated annotation of regulatory elements + visualize them with UCSC Genome Browser. http://blog.openhelix.eu/?p=7567 for links and references.

Genomics Resource Training

Tip of the Week: Encyclopedia of Life

OpenHelix — Wed, 16 Mar 2011 09:36:54 -0700

A brief reintroduction to the Encyclopedia of Life. See http://blog.openhelix.eu/?p=7491 for more information about EoL and other life tree databases.

Genomics Resource Training

Tip of the Week: DAnCER for disease-annotated epigenetics data

OpenHelix — Tue, 01 Mar 2011 10:25:37 -0800

DAnCER allows exploration of chromatin modifications and disease relationships; see http://blog.openhelix.eu/?p=7245 for links and references.

Genomics Resource Training

Tip of the Week: Melina II for promoter analysis

OpenHelix — Tue, 15 Feb 2011 12:12:51 -0800

Melina II is a handy interface for motif discovery. For details and references see our blog at http://blog.openhelix.eu/?p=7124 .

Genomics Resource Training

Tip of the Week: SIFT: Sorting Intolerant (SNPs) From Tolerant

OpenHelix — Wed, 09 Feb 2011 11:44:05 -0800

Today's Tip of the Week is a quick intro to SIFT, find more information at: http://blog.openhelix.eu/?p=7098

Genomics Resource Training

Tip of the Week: RCSB PDB Data Distribution Summaries

OpenHelix — Tue, 01 Feb 2011 10:43:57 -0800

For more information about this resource please see our blog post at URL http://blog.openhelix.eu/?p=6978. In today's tip I will feature the data distribution summaries and their drill down features which you can see from many RCSB PDB searches.

Genomics Resource Training

Tip of the Week: iRefWeb + protein interaction curation

OpenHelix — Wed, 26 Jan 2011 05:08:00 -0800

See our post at http://blog.openhelix.eu/?p=6896 for links and references for iRefWeb.

Genomics Resource Training

Tip of the Week: PolyPhen

OpenHelix — Tue, 18 Jan 2011 21:31:02 -0800

This week's tip is on PolyPhen, a predictor of nonsynonymous SNP impacts on protein functions. For more information about PolyPhen and SNP functional prediction see the blog post: http://blog.openhelix.eu/?p=6867

Genomics Resource Training

Tip of the Week: Twitter in Bioinformatics

OpenHelix — Thu, 06 Jan 2011 14:03:37 -0800

A quick view of my strategy for using Twitter to get useful information in this field. http://blog.openhelix.eu/?p=6591 See my blog post for additional details.

Genomics Resource Training

Tip of the Week: SKIPPY predicting variants w/ splicing affects

OpenHelix — Tue, 04 Jan 2011 12:39:00 -0800

For more information about this resource see our blog post at URL http://blog.openhelix.eu/?p=6658. This tip features the NHGRI reosurce named SKIPPY which predicts whether an exonic variant is likely to effect splicing by changing exonic splicing regulatory sequences (ESRs).

Genomics Resource Training

Tip of the Week: RepTar, miRNA database

OpenHelix — Tue, 14 Dec 2010 22:31:31 -0800

Today's tip of the week is on RepTar. To learn more about this tip, the database and other miRNA databases, visit the blog post on RepTar

Genomics Resource Training

Tip of the Week: BioGPS for expression data and more

OpenHelix — Tue, 07 Dec 2010 07:27:35 -0800

This tip introduces BioGPS, a gene annotation portal that enables searching and visualization of integrated data on genes and regions with great customization features. For more details see http://blog.openhelix.eu/?p=6261 .

Genomics Resource Training

Tip of the Week: NCBI's FLink

OpenHelix — Mon, 22 Nov 2010 11:03:50 -0800

For more information about this resource see our blog post at URL http://blog.openhelix.eu/?p=6208. Here I'll introduce you to FLink, or Frequency weighted Links, NCBI's tool for linking items from one of their databases to a weighted list of associated items in another of their databases.

Genomics Resource Training

Tip of the Week: Canonical gene information

OpenHelix — Wed, 10 Nov 2010 09:48:22 -0800

Today's tip of the week is how to get canonical gene information using the UCSC Genome and Table Browsers. For more information see the blog post

Genomics Resource Training

Tip of the Week: iTol

OpenHelix — Tue, 26 Oct 2010 20:11:25 -0700

Our latest weekly tip on the Interactive Tree of Life, iTOL. You can find out more at our blog