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This is a topic that’s come up more than once in groups I’ve been associated with. A resource we used to like to use–or link to–has become unavailable or seems dead. So you look for answers–trying to contact them and see if it’s just as simple as their server being down. This has happened several times as we searched for tools–we have pinged the team responsible and they’ve rebooted for us. Sometimes they aren’t aware that it has gone down.

Other times you can’t get anyone to answer at all. Have they moved? Is this the wrong email address from their last paper? What can you do at this point?

You can post to help forums like BioStar, and I’ve seen this happen too. And then a bunch of people try the steps I mentioned above. You might be able to find someone with knowledge of the project though–so that can work.

But the best idea I’ve heard in a long time was to create obituaries for tools and resources that have become unavailable. Jeremy Leipzig wrote this some time ago:

One solution could be a obituary section to the web server issue, where sites are deemed dead, stale, or merely irrelevant by a panel of experts. Then corresponding authors could then indicate if they abandoned ship because of laziness, guilt, or simply out of spite.

Heh. I wonder how many will admit to spite. But the idea continued to be appealing to me–because I have wasted days looking for some tool that’s moved or dead. People ask us to help, and we try to find out. But it’s not always clear what’s happened.

So I decided to start a post on BioStars that could capture that information. At least that way people could Google for some information and possible not  have to spend days in the loop of looking around. And today I needed to add a resource that we didn’t realize was gone–GENSAT.

This was also noticed by Francis Ouellette–who might be able to help us get something more formal into NAR. He replied over there at the forum. Check out the idea and the discussion:

Forum: Bioinformatics tools and resources obituary section

If you find a resource that’s unavailable any more, help us out by adding it to the collection.  Or if you want just let me know here and I can post it over there. Provide as much detail as you can. Thanks! Oh, and I’m sorry for your loss…

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: Data visualization! http://t.co/BjWumyRG &  http://t.co/LOKFOuZC via .@joachimbaran [Mary]
• RT @DanforthCenter: Today’s blog post on Roots & Shoots features @NatureBiotech “Reference #genome sequence of the model plant Setaria,” http://t.co/FhzwQWj5 [Mary]
• Interesting GenomeWeb item: ELSI Panel Considers Public Understanding of Genomics at Biology of Genomes Meeting [Jennifer]
• Found via ScienceSeeker: good post on Map of Life, a project I’m interested in following. Like the idea. Hope execution is good. Visit at http://www.mappinglife.org/ [Mary]
• RT @BlueSEQ: Tweet archive of Biology of Genomes 2012 Conference #BoG12 http://t.co/1AbWhYX6 [Mary]
• Interesting…”Professor Says Big Data Is Just a “Fetish”” HT GenomeWeb [Jennifer]
• For the fun and for the ideas: “The evolutionary biology of the unicorn.” [Jennifer]
• RT @TCGAupdates: David Haussler of UCSC discusses CGHub: http://t.co/ICHwlOXy Check out CGHub here: https://t.co/UfcpLo2d [Mary]
• The current Nature Outlook is on Diabetes & is open access, available here. Older Outlooks can be browsed in their supplements archive. [Jennifer]
• RT @datacite New post on DataCite blog: New server for content negotiation in cooperation with CrossRef. Resolve DOI to metadata http://www.datacite.org/node/63 [Jennifer]

We’ll be having our May 17th webinar today, and we find there are questions to follow up afterwards that are often better handled in discussions on the blog.

If there are questions we didn’t have time to get to–or things we want to expand on with more detail–we can discuss them in this thread.

Or if you have other things you’ve been meaning to ask, let us know.

If you can’t make the webinar, the same material is covered in the training movie, slides, and exercises that are freely available, sponsored by the UCSC team: http://www.openhelix.com/ucsc

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 created 18 months ago, but new slides and comments have been added and is still an excellent resource for a course on NGS:

Question: I am preparing a course on NGS: any suggestion ?

The first answer (with 22 up votes!) is a treasure trove of material, along with some excellent resources from other answers. Want to learn more about analysis of NGS data?… here you go.

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]