The OpenHelix Blog

Recently when I was adding videos to our SciVee collection, I noticed that there was a set of new videos about BindingDB. This database has been around for a long time, and I was surprised to realize that we hadn’t covered it yet. And it certainly only grows more important to understand proteins and their binding partners–whether they are other proteins or chemical compounds that can be important effectors of health and disease.

For a decade now this database has been curated and maintained to provide access to information from publications that is often not easily accessible. As their homepage says today:

BindingDB contains 832,773 binding data, for 5,765 protein targets and 362,123 small molecules.

That’s a lot of information available to you to investigate that they have collected. You can start with a protein of interest, or a compound, or a paper, and find related information from those points. There are various other tools and entry points as well.

In addition, it is integrated with many other key resources, including PDB and UniProt, MMDB and KEGG, and more. ChEMBL links offer handy links to compounds.

You can see from their “News” that they are actively maintaining this site, and are developing new tools to offer users ways to interact with the data. But the newest feature seems to be their videos–I’ll let them show you more about how to use their site.

BindingDB: Find and view all data for a target of interest

They offer several other quick tips on ways to interact–starting with an article and obtaining the data, and more. You can access them from the end of the video in the “Related” links, or explore their SciVee set. They are also found on the homepage of BindingDB right now. So check them out if you need protein binding data. They may have what you seek.

Quick link:

BindingDB site: http://bindingdb.org/

Reference:

Liu, T., Lin, Y., Wen, X., Jorissen, R.N. & Gilson, M.K. (2007). BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities, Nucleic Acids Research, 35 (Database), D198. DOI: 10.1093/nar/gkl999

Welcome to our Friday feature link collection: 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…

• RT @Dr_Bik: Cool visualization w/dragging ability RT @moorejh: Integrative multi-species prediction http://t.co/vZC0QgLU #bioinformatics #genomics [Mary]
• From NCBI News: “The Netblast client (blastcl3) that has provided batch search access to the NCBI Web BLAST service will be discontinued in the near future. The BLAST+ applications replace and improve upon the functions provided by blastcl3. Blastcl3 users should switch to BLAST+ as soon as possible… ” More information is available here. [Jennifer]
• Super Science Shoes AWAY!! (can you say weekend project?) RT @DrRubidium featuring @Seelix! -> Make your own superhero heels and walk a mile in Wonder Woman’s shoes http://on.io9.com/JGT2UP via @io9 [Jennifer]
• RT @GenomeWeb: From CDC’s genomics group: three-tiered list of genomic tests, organized by level of evidence for utility and validity: http://t.co/R9d46Li6 [Mary]
• More new genome-related tools from NCBI, again announced in their News: “The Genome Remapping Service (Remap) and the Variation Reporter are related tools that find locations on current and past genome builds…The Variation Reporter… takes a set of locations in a human genome assembly and identifies known human variations (NCBI Reference SNPs) at those positions. This service is particularly helpful for identifying experimentally or clinically determined variants. ” [Jennifer]
• BioGPS is  nice tool. RT @andrewsu: SuLabBlog: BioGPS retrospective – the four year anniversary http://t.co/QasGAbAg [Mary]
• Fascinating case of genetics, interventions, and law. RT @_Genethics: Reading a grounded and interesting piece on knotty genomic issues @canlawmag Legal lag in medical advances http://t.co/xzrJHu5V [Mary]
• Very, cool – adding it to our updated tutorial now! RT @NCBI: PubMed’s new Filter Sidebar is now available – ex: http://t.co/3LiWNJc6 , Info: http://t.co/p76e0915 & YouTube Video: http://t.co/tH1ViFZc [Jennifer]
• “an interactive resource for global biodiversity analysis ” RT @AgroBioDiverse: Map of Life goes live http://t.co/x8MSN89A [Mary]

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This question was raised a couple of days ago, and generated quite an interesting discussion and some interesting resources:

Question: database of essential genes

I was searching for the list of essential genes in human. I found the http://www.essentialgene.org/ which has 118 genes for human in its database. However, I am sure that the number of essential genes in human is much more that 118. Does anyone knows another database of essential genes? Also if you know any for organisms other than human, I would b e happy to hear about. thanks.

–pegahtv

The discussion includes more biology than some of them do, and ways to think about approaching the study of essential genes in humans. Check it out.

There is none.

Ok, so that is the simple answer. The complicated answer is this: my ideal genome browser iPad app would have the flexibility to go from a mass market browser to look at an individual’s genomic variants in a genomic context with information about the research, genes, etc presented in such a manner so that any thoughtful person or doctor could understand, to a full fledged UCSC genome browser type research tool.

So, that’s not feasible. Instead, I’m going to look at three genome browsers for the iPad, two for research, one for the mass market. The former are GeneWall by Bioskoop and Wowser by the Children’s Hospital of Philadelphia, the latter is MyGenome by Illumina (links take you to iTunes app store).

The iPad and other touch tablets are perfect research assistants and the day is fast approaching, if it’s not already here, where most researchers will have one on the lab bench for entering and accessing data.

So what am I looking for in a iPad genome browser?
Navigable: it should have a very intuitive, iPad native navigation. I should be able to pinch and swipe my way through the genome with finely controlled ease.
Comprehensive: I should be able to access my genome of choice, past assemblies, and a huge range of annotations.
Flexible: I should be able to upload my own annotations with ease.

Why not just go to the UCSC Genome Browser? You could, but it fails the first test. It’s definitely usable, but many features available on a computer are not available on the iPad and navigation is obviously not iPad native.

GeneWall works nicely on the first criteria, but zooming in and out takes several (sometimes many) pinches of the fingers. There is no simple way to zoom in and out or walk the chromosome in a more fine tuned manner. On the second, though it comes with a single genome (human) with only a few annotation tracks so it’s not very comprehensive to start, you can easily add annotation tracks downloaded as bed files. So it has some flexibility. The pathway search and gene list function are nice too. A quick YouTube intro here.

Wowser is somewhat different in that it is an iPad interface to the UCSC Genome Browser. It works natively with the iPad and so is easy to navigate. Zooming and walking was intuitive. On a few different wireless networks it was slow to load, but not excruciatingly so. It is quite comprehensive, including the latest human reference sequence and many, but not all, of the UCSC tracks. The tracks are simple to hide or add in. Future updates are said to be including other genomes and more tracks. I could not find a way to add your own custom tracks or data, so on flexibility GeneWall wins out.

Both apps are great, if not quite “there” yet. I think either would be useful if you are looking at the human genome for research.

MyGenome is a different beast. From Illumina, it’s audience is not the researcher but the medical professional and patient. It’s a beautiful app with a nice interface. Easily navigable, it was simple to get to the information wanted. There is a lot of information there, but it is still quite limited. I took several variations that effect propensity for prostate cancer and other diseases and was unable to find information on them either because the variation is listed but no information, of variation was in an intergenic region which seemingly isn’t included. A user can not yet upload their own data,or other annotations, which is understandable since by Illumina’s own account this is only the beginning. Currently it’s a great educational tool (though I was a hung for more gene information), in the future it will be a good way to browse your own data.

So the bottom line for all three of these are that they are useful as they stand and for their stated purpose, but I’m looking forward to the future of browsing genome data like I was on an Avatar set . It’s coming.

As we have in the past, we are offering free webinars in the coming weeks on the UCSC Genome Browser and Advanced discovery using the Table Browser and custom tracks. These have been quite popular in the past, so sign up soon!

The Intro to the Genome Browser webinar will be Thursday, May 17th at 10am Pacific time (1pm ET). Check here for your time zone.

The Table Browser and custom tracks webinar will be Thursday, May 24th at 10am Pacific time (1pm ET). Check here for your time zone.

You can register here for the UCSC Genome Browser Intro and register separately here for the Table Browser and custom tracks webinar. You’ll need to register at OpenHelix if you haven’t already. It’s free and you’ll get no emails from us unless you opt in to our most excellent newsletter  or ask to be notified of future webinars :D. Registration and attendance are free.

We have several months of free webinars planned including on ENCODE, Galaxy, PDB  and others. Keep tabs with us here or on the webinars page (or though email notification) to be notified when those free webinars are coming.

Welcome to our Friday feature link collection: 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…

• RT @bffo: good read! RT @GenomeRef: GRC: Updating the Human Reference Assembly, part 1 http://t.co/fnwg6itO #genomics #bioinformatics [Mary]
• From GeneomeWeb: “Janelia Farm’s Newest Addition to HMMER“. You can kick the tires on the new jackhmmr resource, which does an iterative search versus a protein sequence database, here. [Jennifer]
• Bioimage informatics is the new category of submission in the journal Bioinformatics, in recognition of the growing number of papers and data being published in this area. HT Matthew Dublin of GenomeWeb [Jennifer]
• RT @natalieclairoux: RT @GaiaTek: #bioinformatics declining? http://t.co/Vht3YD1F My Pubmed trends disagree (using #rstats ggplot) 1/2 http://t.co/F0vbzUHu [Mary]
• RT @mike_schatz: Solving the genomic jigsaw puzzle http://t.co/nDWWKmen [Mary]
• Another post on big data: Cloud Moves in on Bioscience Plus a new resources from Broad: GenomeSpace-beta  HT:Bio SmartBrief [Jennifer]
• From BioTechniques, interesting article: “NCBI Heads to the Cloud” [Jennifer]
• RT @marinkazitnik: ‘Ome,’ the Sound of the Scientific Universe Expanding http://t.co/Rd8oomRh [Mary]

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This question was raised in the last month, and there was some discussion–but there’s been a big change in the options since, and I wanted to highlight that so people know:

Question: Is OMIM no longer available as structured data?

One of our project used to query OMIM data as XML through NCBI’s efetch utility, as described here for example:

[?]What is the best way to interact programmatically with OMIM?[?]

However, it seems the service has stopped functioning a few months ago. It now simply returns the following error:

Database: omim – is not supported

I can find no mention of an update to the API on NCBI’s website or anywhere else. At the same time, the pages accessible directly on OMIM’s website offer no link to structured data (XML or otherwise) and the downloadable file, while using some specific format to delimit fields, is still far from the flexibility of the former XML files (for example, it is impossible to retrieve metadata for each reference).

Is there currently any way to regain access to OMIM data in a structured, parsable format (XML…)?

There was a lot of discussion about the changes since OMIM at NCBI moved away from to its new spot at OMIM.org, but just this week I spotted a tweet from OMIM which directly answers the access issue now:

OMIM API is now open, see omim.org/api and omim.org/help/api #OmimOrg

— omim.org (@OmimOrg) April 30, 2012

I’ve you’ve been waiting for the OMIM API access, check it out at the Help page.

The UCSC Genome Browser has been providing access to reference genomes and associated annotation data for many years now. If you go to the “archives” page you can see the old genomes all the way back to 2003. Check it out–you can find the teeny (but colorful) look at the human assembly from April 2003–and the rather small selection of tracks that were present then. Really–go have a quick look–and realize how much more we have now.

There are new species and new assemblies of the genomes over time, of course. New and updated annotation tracks. New types of tracks–the super-tracks are so loaded with detail and incredibly useful–but are a new concept to grasp. Sometimes tracks get split out–like we’ve seen with the dbSNPs set that now is show as 4 sets instead of the 1 we used to get. Sometimes tracks come back from the past–like the new “Old UCSC Genes” track that just re-appeared on the current human assembly. The paper from the NAR database issue (below) provides a lot of recent highlights.

We’ve been providing training on how to use the features of this browser for many years too. But it certainly has changed over time. We are on version 20 of the intro slides at this point!

This week we are announcing availability of the re-recorded and updated movie, and companion slides and exercises. This focuses mostly on the current human assembly, and includes many of the same basic aspects of organization and function that new users need to understand about the browser. But it also touches on more recent aspects like super-tracks. In this tutorial we don’t cover the track hubs that are referenced in the paper–that’s covered in the recently updated Advanced tutorial with the custom tracks section. And additional details on super-tracks can be found in the ENCODE materials, which are undergoing updates and we’ll be releasing a new version of those materials soon.

As before, you can use the video to teach yourself about the browser features. Or you can use the slides in your lectures or computer labs (the “notes” section contains the things we say on each slide too). You can direct students to the materials too. The materials are all freely available as they are sponsored by the UCSC Genome Browser team.

Many thousands of people have used these movies, slides and exercises over the years to get better acquainted with the browser and tools. And as more data continues to flow in, the more efficient and effective you are with your time and your queries, the faster you’ll get to new discoveries that matter to your work.

Quick links:

UCSC Genome Browser: http://genome.ucsc.edu

Introductory materials: http://openhelix.com/ucsc

Advanced materials: http://openhelix.com/advucsc

Reference:

Dreszer, T., Karolchik, D., Zweig, A., Hinrichs, A., Raney, B., Kuhn, R., Meyer, L., Wong, M., Sloan, C., Rosenbloom, K., Roe, G., Rhead, B., Pohl, A., Malladi, V., Li, C., Learned, K., Kirkup, V., Hsu, F., Harte, R., Guruvadoo, L., Goldman, M., Giardine, B., Fujita, P., Diekhans, M., Cline, M., Clawson, H., Barber, G., Haussler, D., & James Kent, W. (2011). The UCSC Genome Browser database: extensions and updates 2011 Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr1055

Usually we don’t get too political on this blog. But we take a pretty clear stand on teaching evolution. And if anyone ever came to us and demanded that we “teach the controversy“, we’d laugh really hard and then move our company to a country that wasn’t completely insane. So my perspective on what happened with the revision of science curriculum and textbooks in Texas is probably not a surprise. And I’ll be describing my view of the new film The Revisionaries with that in mind.

++++++++++

For some people, the concept of “evolution” is something of an esoteric discussion. It doesn’t really impact most of their days. Here at OpenHelix, though, it’s sort of the foundation of what we do. At each workshop we do I stand in front of people and talk about the representation of “evolutionary relationships” that they can evaluate in the UCSC Genome Browser, or some other tool.

So when I was notified by NCSE that this new documentary film The Revisionaries, about the Texas SBOE (State Board of Education) process to review and revise the science textbooks to discredit evolution, was playing at the Boston Independent Film Festival, I wanted to see how that transpired.

I had been aware that the process had happened, and that it was being driven by that odd species of Young Earth Creationist (YEC) that you hear about if you live in Massachusetts, but rarely see in the wild. It was fascinating to learn about how the Texas process played out.

The film focuses largely on the guy who was chair of the board from the round of revisions that comprised the science pieces. Don McLeroy is a dentist and unabashed YEC. You see him in his office proselytizing to patients who can’t really talk back, ironically enough. And you see him steer the board into some dangerous and wrong conclusions about what students should be hearing in their science classes. You can seem him quickly degenerate into word salad when asked to explain concepts related to the material. At the same time they dismiss the testimony of anyone with actual expertise in science. It’s excruciating to see.

It’s something like watching the croquet scene in Alice’s Adventures in Wonderland. And a surprise in the film is that you discover that there is a Queen of Hearts on the board too:

I pictured to myself the Queen of Hearts as a sort of embodiment of ungovernable passion – a blind and aimless Fury.
–Lewis Carroll

She comes off as much more malign and scary than Don—but I don’t want to detail that much more, you should see that play out in full, it would be something of a spoiler to provide any more.

There are some heroes of sanity. Kathy Miller of the Texas Freedom Network (TFN) clearly battles daily to keep religion and misinformation out of the public schools. Eugenie Scott (NCSE) and Ron Wetherington are shown carrying the flag of reality. But from the film you learn additional background of the Texas process and system that have really stacked the deck against them.

Although the film begins with the issues in 2009 on the science components, it turns later (and chillingly) to what happened next in 2010. I was unaware that the same group was focusing their attention to the Social Science and History curriculum. With the same strategies.  They were doing to history what they had done to science: using their influence and bafflegab to drop Jefferson from prominence, while elevating Aquinas and Calvin. They wanted to pump up the role of the social conservative movement during the Reagan era. And to strike hip-hop from the text and replace that with “country music”. I kid you not.

It’s hard to watch this film. Luckily I was with an audience that shared my horror at the anti-science sentiments that were flying around. And because it was a film festival showing we also were able to discuss the film with the director Scott Thurman to learn more. One attendee noted that in some ways Don comes off likeable—because at least he’s being honest about exactly who he is and what he believes. And the director tells us Don likes the film. It didn’t surprise me, because you also see him enjoying the radio attack ads against him during the re-election campaign which define him exactly how he sees himself—as a young earther trying to influence the textbooks. This doesn’t exactly gel with his claims that he’s not trying to influence the board with his own beliefs. But you can see how his brain works (such as it is).

More discussion with attendees after the film was hopeful. Textbook writers and publishers were in the group I was with, commiserating on the influences of special interest groups on education. It was noted that after learning about the Texas process some schools specifically avoid the texts approved there—which is a good side effect and may reduce their influence overall. A professor from Emerson College was hoping to bring this film to his communication students to show them about the influences on publishing. There were some good ideas: how the current technology should reduce the influence of big states like Texas and enable chapters to be swapped out to be better for other school districts. On the other hand—the publisher warned—this also enables teachers to swap out what they want more easily; be careful what we wish for here.

It was certainly a film you should see if you care about education, and science, even if it’s difficult to endure. Because this is not over. And it’s time that more people—especially science defenders–were paying attention to the down-ballot races, and school committees, and other types of community efforts like these. And don’t think they’ve stopped at science class—they are going after history and social studies now as well. Experts on those topics need to step up and join the fray.

One attendee noted that people who aren’t paying attention, aren’t voting, and aren’t participating in these types of things are just as responsible as Don for what happened. And I couldn’t agree more.

Trailer. Catch it if you can. Watch for local film festivals, maybe later on DVD.

Welcome to our Friday feature link collection: 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…

• Mmm hmm: RT @engagedethics: MT @BrianMBot: “everyone is all excited about ‘machine learning’ – need to remember human learning” #sagecon cc: @nwabr @nick_r_anderson [emphasis mine, Mary]
• RT @genetics_blog: GTF <–> GFF3 <–> BED <–> Genbank converter at Tubingen Galaxy instance #usegalaxy http://t.co/NuCYW812 [Mary]
• RT @ewanbirney: Yummy new Expression Atlas out from the EBI. Download/browse your favourite gene/part-of-body RNA-seq/Microarray. http://t.co/3NztqEbV [Mary]
• A very amusing read found through an indirect path: “Pathology in the Hundred Acre Wood: a neurodevelopmental perspective on A.A. Milne” Cited in several other papers – check out the list [Jennifer]
• Umm…yay? RT @iddux: Baby-poop paper accepted to Genome Biology. 1st time I turned shit into something good, as opposed to the other way around. [Mary]
• Yesterday the Office of Science and Technology Policy released a National Bioeconomy Blueprint as a 43 page PDF, you can see their press release here. [Jennifer]
• OMG!! Teh Toxins! But cool project, really. RT @uniprot: Find out more about animal toxins in the latest UniProt headline article, ‘Of serpents, humans and pain’  http://t.co/BSxcP1Pr [Mary]

And one last special item:

PhD The Movie is now available for streaming–check out the details here:

http://www.phdmovie.com/