Get to know Galaxy

I’m deeply immersed in a new project right now, so my blogging has been light of late.  But in lieu of that–you can check out a new paper on Galaxy that’s just come out!  We were approached by the Current Protocols in Molecular Biology team last year because they saw the need for works that were aimed at the folks who aren’t already in bioinformatics.  So we crafted a couple of papers designed to be useful for people who are doing benchwork and need to accomplish things with bioinformatics tools, but don’t need to be experts or coders.

The Galaxy paper has now been published, and you can check it out here: (subscription required)

Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists

Current Protocols in Molecular Biology, UNIT 19.10 DOI: 10.1002/0471142727.mb1910s89

I think it is very effective at step-by-step guidance on some tasks that scientists are likely to need, if I do say so myself as one of the authors .  There are also accompanying screen casts for additional assistance.   You can also see our free tutorial sponsored by the Galaxy team for an overview and orientation of Galaxy as well.

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Once experimentalists realize the range of problems Galaxy could solve for them–without writing code–they are very excited.  We’ve seen it in the workshops we’ve done.  It really offers a lot of utility.

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[Note: If you didn't see our other paper with a similar aim for end users, you can check that out in this post: Our Current Protocols paper on the UCSC Genome Browser is out! ]

(this Post content was reproduced from: http://blog.openhelix.eu/?p=3521#comments, Via The OpenHelix Blog.)

VISTA, genome comparison resource

The VISTA comparative genome analysis resource updated their interface a few months ago. Additionally, they’ve added VISTA-Point (which replaces and greatly extends VISTA text browser) which, as the site says, allows the user to:

Access complete data and visual presentation of pairwise and multiple alignments of whole genome assemblies.

The homepage has undergone a very nice redesign. Much of the underlying VISTA browser and other tools functionality and use is similar (though updated of course). We understand also that there will be upcoming updates to some tools and the addition of others. Look for that here .

Also, we’ve updated our tutorial to reflect the new site and functions. As before, this tutorial is free to users and sponsored by VISTA. Check it out.

(this Post content was reproduced from: http://blog.openhelix.eu/?p=3550#comments, Via The OpenHelix Blog.)

Tip of the Week: PhyloWidget

Got phylogeny? So, you’ve created a phylogeny using some software and would like to draw the tree from the Newick formatted file* you exported. Of course there is no shortage of tree drawing programs out there (or phylogeny generating ones either). We found another one recently; a web-based, API-usable, opensource tree drawing tool that is quite intuitive and functional. It’s called PhyloWidget. The paper describing PhyloWidget is here and you can find some very nicely done step-by-step instructions here. I’ve done a quick 4 minute tutorial here to give you a quick overview. If it looks like something you could use, you might want to delve into it right away, or check out their ‘walk through.’ Happy climbing.

*Here’s the file I use in the tip: ((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700, seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201, weasel:18.87953):2.09460):3.87382,dog:25.46154);

(this Post content was reproduced from: http://blog.openhelix.eu/?p=3507#comments, Via The OpenHelix Blog.)

Tip of the Week: WebGBrowse, now v2.0

From the GBrowse mailing list this week comes word of the new version of WebGBrowse.  I talked about WebGBrowse in the past as a very handy tool for creating a GBrowse visualization of data that you may have.  Using WebGBrowse permits you to upload, view, and interact with the data without the overhead of installing a local copy of GBrowse and having to maintain that.  This short Tip of the Week demonstrates how easy it is to interact with this web-based, customizable, implementation of GBrowse.

The full announcement can be found here, but briefly here were the highlights for me:

- The users will now have a choice of GBrowse display between versions

1.7 and 2.0.

- The display from one version can be migrated to the other by simple

button clicks. This helps the users to compare their data display between the two versions without much hassle. It also helps the WebGBrowse users in upgrading/migrating their existing GBrowse displays to version 2.0 seamlessly.

This would be great for a smaller project team that can’t maintain their own local copy of GBrowse, or as a way to pilot the project before committing to the whole thing.  I also think this could be a very handy teaching tool for instructors who want to get students up to speed on some of the foundations of genome browser display without too much overhead.

(this Post content was reproduced from: http://blog.openhelix.eu/?p=3463#comments, Via The OpenHelix Blog.)

Tip of the Week: iceLogo for conserved sequence display

I’ve always been a fan of clever graphical displays that convey key data points.  They can be so effective when done well.  And from way back when I was first exposed to the logo-style histogram displays for conserved promoter sequences they’ve always struck me as particularly suited to this method.  Usually for ease-of-use I’ve gone to WebLogo.  It’s easy, and quick to use.  But recently I learned of another tool that provides the logos and has a bit more to it.  The iceLogo tool seems to be a useful option for these now as well, particularly suited to protein motif display.

A brief correspondence in a recent issue of Nature Methods introduced me to iceLogo.  When I first tried it out, I had to download it and run it locally (and you can still do that).  But there is also a web interface for this tool now, and that will be the focus of my tip of the week.

You can enter a set of sequences as a multiple sequence alignment, then you can choose the reference set of everything in Swiss-Prot or set your own background, and then visualize the sequence data with conserved positions in a couple of ways. You can see the larger letter sizes using several logo styles, or you can access a heat-map style display.  You can download the images (although I often just screen shot things like this).  I wish it had a clear button to easily swap out my items of interest, but that’s not a huge problem really. In this tip of the week movie I run their sample sequence to show you how it displays the data.

Their manual (PDF) goes in to the detail on the statistics and the theory.  The Nature Methods paper is quite short–there real meat is in the manual.  And there’s actually a neat feature to the manual PDF: you can click on Figure 1.4 to directly load up that example in the web interface and change it around if you want.

Check out iceLogo if you want to explore these types of visualizations for your data. Visit the iceLogo web interface here.

Just a final note: there is also a SOAP server that you could access with other tools as a web service that might be handy if you are setting up analysis pipelines in various situations.

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Colaert, N., Helsens, K., Martens, L., Vandekerckhove, J., & Gevaert, K. (2009). Improved visualization of protein consensus sequences by iceLogo Nature Methods, 6 (11), 786-787 DOI: 10.1038/nmeth1109-786

(this Post content was reproduced from: http://blog.openhelix.eu/?p=3329#comments, Via The OpenHelix Blog.)

Tip of the Week: PSI SGKB’s Monthly Structural Genomics Update (Edited)

In today’s tip I’d like to show you the monthly Structural Genomics Update from the Protein Structure Initiative  Structural Genomics Knowledgebase or PSI SGKB. Some of you may not be aware of the PSI SGKB, but it is a resource related to the RCSB PDB resource, which is very well known. We are currently creating a tutorial that will feature the whole knowledgebase & we will be sure to let you know when that is available. Today I want to feature their monthly Structural Genomics Update, which provides a great collection of articles and features related to structural genomics and protein biology as a whole. The Update is produced by Nature Publishing Group in collaboration with the Protein Structure Initiative.

I cannot begin to cover the full functionality of the SGKB in this tip, so go over there & explore it, watch for our tutorial to come out, maybe even add an SGKB widget (Trey talked about it here) to your web site!  Also, feel free to let me know what your favorite part of the PSI SGKB is, when you get a chance. Enjoy the tip!

EDIT: If you tried to watch this tip yesterday & had trouble, it was not on your end. Apparently there was some glitch part way through during my upload (thanks for the heads up, Greg!). I’ve reloaded the movie file & it plays through now, so please try it again – this is a great resource that should not be missed!

(source URL, Via The OpenHelix Blog.)

Tip of the Week: Year of Tips, part deux

As Trey posted last week in part I, we’ve been doing tips-of-the-week for two years now. We have completed over 100 little tidbit introductions to various resources*.  At the end of the year we are doing a summary post to collect them all.  If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

I’ve got the second half of this year to summarize–July through December 2009. Check them out!

July 2009

7/1  UCSC wiki annotations UCSC has created a way for anyone to add annotations to their genes of interest using a wiki.

7/8  CellMiner from NCI A relational database for cancer cell line data.

7/15  ENCODE data at UCSC The Data Coordination Center, or DCC, for the human ENCODE data is introduced, with guidance on how to access ENCODE data in the UCSC Genome Browser.

7/22  It’s a duplicate Check out Deja Vu, a program to assess scientific abstracts for similarity, including duplication or possible plagiarism events.

7/29 VirusMINT The Molecular Interaction Database that we love added a component for Virus protein interactions.

August 2009

8/5  Genomic Encyclopedia of Bacteria & Archaea (GEBA) This piece on the strategy of choosing new genomes to sequence was introduced in August.  If this is of interest to you, also check out the recent publication about this project that we talked about here.

8/12  NCBI’s New BioSystems Resource Wherein NCBI takes on the storage and representation of biological network data.

8/19  PLAN2L for Arabidopsis literature A helpful tool for literature searching for Arabidopsis.

8/26  Acytelome, String and a new database An introduction to the Phosida database, for phosphorylation and acetylation information.

September 2009

9/2 A mouse for all reasons Learn about the knockoutmouse.org site, which provides information and reagents for generating knockout mice.

9/9  TARGeT A resource for identifying transposable elements and genes relationships from sequence submissions.

9/16  The National Center for Biomedical Ontology This central repository for Ontologies can be really helpful for bioinformatics software project developers.

9/23  JBrowse, a game changer? A look at a new strategy in genome browsing software.

9/30  Finding the right genomics resource This is a quick introduction to OpenHelix’s own new interface for searching for training movies and materials!

October 2009

10/7  NCBI Makeover! The overhaul of the NCBI interface–with a walk through memory lane at some of it’s previous incarnations–is provided.

10/14  Getting flanking sequence A quick look at how to use Galaxy to obtain adjacent sequences, which is a question we are asked frequently in training situations.

10/21  SwissVar, a New Genotype-phenotype Resource from SIB Explore ‘a portal to Swiss-Prot diseases and variants.’

10/28  Sol Genomics Network Do you like tomatoes, eggplants, potatoes, peppers, and other members of the Solanaceae? If so, check out this resource.

November 2009

11/4  CHOP CNV database If you are curious about copy-number variations, be sure to explore the collection at CHOP.

11/11  GeVo and Genome Comparison A nifty tool for genomic comparisons.

11/18  FABLE, text mining for literature on human genes A literature mining resource to improve you searching.

11/25  Got tips for us? We opened the floor for suggestions of tools to look at as we celebrated the Thanksgiving holiday.  We’ll still take suggestions–we love to explore new resources!

December 2009

12/2  RCSB PDB Comparison Tool Compare sequences for structural similarities with this handy widget.

12/9  GRAIL for prioritizing SNPs Use a list of SNPs to identify associated genes, and then sweep the literature for leads on the processes that might be involved.

12/16  GenomePad Check out this very cool iPhone app for exploring the UCSC Genome Browser.

12/23  Tip of the Week: Year (2nd!) of Tips for the first half of the year’s summary of tips.

*for the vast majority of resources we introduce in our tips, we have no financial relationship with the provider or developer. The ones we do are listed here.

(source URL, Via The OpenHelix Blog.)

Tip of the Week: Year (2nd!) of Tips

If you’ve been following this blog, you’ll know that every Wednesday, come rain, shine or travel, we post a tip of the week. 98% of the time that’s a short 3-5 minute screencast of some genomics database or resource we like or an aspect of one we think you might find useful*. We’ve been doing this for just over 2 years now, with over 100 tips. That’s a lot of screencasting! At the end of last year we recapped that year’s tips in two posts, the first half of the year, and the second half. We are going to do that this year to over these last two weeks of the year. Today I’ll list the tips we posted during the first half of the year, next week Mary will list the second half of the year’s worth. The list for January through June is below the fold:

Jan 7: BioData Mining OpenAccess Journal about the journal “BioData Mining”

Jan 14: Genomic Data Resources about our article on the state of genomic resources and Scitable.

Jan 21: Visualizing GWAS with HapMap tools

Jan 28: Scitable Classrooms, building an online classroom with Nature Scitable

Feb 4: Model Organism Database tutorials, an introduction to 10 new free tutorials

Feb 11: from OSTI to a Plethora of Resources, an introduction to site to launch to lots of resources

Feb 18: Allergen Atlas

Feb 25: Converting Genome Coordinates, using Galaxy

Mar 4: Galaxy Intro, an introduction to the Galaxy analysis tool

Mar 11: International Stem Cell Registry

Mar 18: TDR Targets Database, datasets of drug targets in pathogens causing neglected diseases

Mar 25: Rice Kinase Database

Apr 1: My NCBI Database Search Filters

Apr 8: UCSC Cancer Genomics Browser

Apr 15: Current Protocol Tools, collection of utilities for bench work

Apr 22: Galaxy, the intro to the full one hour (free) tutorial on Galaxy

Apr 29: ViralZone at ExPASy, provides concise introduction to a virus as well as links to any variety of detailed information

May 6: Searching dbSNP for Human Variation

May 13: Sharing your analysis process, using Galaxy to share your workflow and analysis steps

May 20: Online Biomedical Textbooks

May 27: File Format Conversion, using ReadSeq

Jun 3: PhenX Toolkit for GWAS Penotype and Exposure Studies

Jun 10: DNAPlotter, a tool that will enable a circular graphical representation of the data

Jun 17: F-SNP, provides integrated SNP information from 16 tools and databases

Jun 24: Biodiversity Resources, an introduction to Bioversity International resources

*for the vast majority of resources we introduce in our tips, we  have no financial relationship with the provider or developer. The ones we do are listed here.

(source URL, Via The OpenHelix Blog.)

Tip of the Week: GenomePad

I discussed iPhone apps that would be useful for biology earlier this year and we’ve added one or two since. There is a new one now that I’m definitely putting on my iPhone, GenomePad. This is an iPhone app that creates an easy-to-use interface to the UCSC Genome Browser. Today’s tip is a quick introduction. Since I don’t have iPhone screencast capability, I’m going to quickly describe the basic functionality of the app below in a few screenshots. The GenomePad people also have a short video with an video introduction.

Opening GenomePad on your iPhone will bring you to this simple interface where you can do a search, view your bookmarks or past in a location. I’ll show here a simple search.

First you touch either the location box or the genome menus to start your search. Choose an assembly (I’ll chose human, 2006). The application gives you the iPhone ‘wheel’ interface, making the use easier than trying a web interface to UCSC:

Add the term or location using the iPhone text interface. I’ve added “clock.” Then touch “Search.”

You’ll get a list of records with your search term. The iPhone app automatically goes to landscape view for better viewing. I’ll tap the first link:

You’ll now be in the UCSC Genome Browser with the same web interface you have on your computer (see some comments below). For more information on how to use this interface, you can view the UCSC Genome Browser tutorial here. There is an icon that allows you to email results.

Below the graphic interface is the annotation track controls where you can add or change the track views.

An iPhone menu allows you to add and change the annotation view. Click “Done.”

The new track shows up. You can click on the annotation tracks to view details.

The details page shows up. You can browse back and forth to previous pages with these buttons.

The GenomePad is a great resource and I’m glad to see the app available (free btw!). It is an early iteration. The iPhone navigation interface makes searching easier and it has a few nice features that could be useful (like emailing yourself a location of interest to look at later). I would like to see something in the future where the genome viewer and details pages themselves are reconfigured to be more iPhone-friendly. Perhaps a simplified graphic with pull-up navigation menus. At the moment it is a iPhone skin on the web browser. Perhaps that is the kind of development that needs to be done by the UCSC team and beyond the scope of outside developers? I’m not sure, but it sure would be nice.

(source URL, Via The OpenHelix Blog.)

Tip of the Week: RCSB PDB Comparison Tool

In today’s tip I am going to feature a sequence and structure comparison tool brought to you by the RCSB Protein Data Bank, or PDB. The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data, and provides a variety of tools and resources to accessing these data.

I’m sure MANY of you are familiar with the RCSB PDB and rely on them to provide you access to protein structures. If you haven’t visited the RCSB PDB lately, you may be surprised to see how many features and functions they’ve updated and added. We are currently updating our tutorial on this great resource. When it is ready the tutorial will show you where to find many of these updates and how to use them. I’m sure we’ll announce the release of our updated materials, but for now I’m going to provide you with a RCSB PDB ‘teaser’ that I hope will entice you to into visiting and exploring the RCSB PDB, as well as watching for our updated tutorial.

And if after seeing this tip you think you might want to have an easy way to access this tool, you can add it to your own blog or lab homepage just by getting the widget code, as described in this post by Trey.  Enjoy this weeks tip!

(source URL, Via The OpenHelix Blog.)