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…
Wow: “rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old” RT @BiddleLab: Our new paper on subsurface fungi: http://t.co/bNXMjOJu
RT @DoctorZen: The power of pastiche: new critique of poster by @bioinformatics! http://t.co/E3vDs7jH New at Better Posters!
OMG–they do…. RT @legionella: @surt_lab – Good one! We’ve had a diminutive researcher doing gnomics in my lab for about 2 years now. http://t.co/k922p5TJ
For some great hashtag fun, check out the #DeNovoVol1Issue2 collection. These are proposed titles for the next volume of the journal that published the Sasquatch genome work.
BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community 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 items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.
This is an unusual item to highlight, it’s very much navel-gazing at BioStar, I know. But I thought it was interesting (and not just because I saw my name in it). It looks at the participation in the community over the years.
Users are represented by their names, and the small stars around them are the posts they create. These are color coded by the post type: red for questions, green and blue for answers and comments.
Starting May 2010 we focus on new user activity only. This means that we only show a user’s activity approximately within one month after they joined.
For January of 2011, 2012 and 2013 we show the activity by all users. For May 2011 and 2012 we show the moderator activity only.
The visualization is done via the code_swarm tool.
It’s also the kind of thing that’s useful to explore a type of visualization. It helps you to envision ways to think about visual representation of data sets, even if this particular data set isn’t something that will change the direction of your research. But it’s an engaging way to think about what “code swarm” might be able to do for other types of projects.
There’s much chatter right now, but nobody has actually read the paper. I am hoping a qualified science journalist takes a crack at it, because I’m unwilling to pay them (since they bought the journal) to see this thing.
EDIT to add things as they come along:
Dear denovojournal.com, my paper describes the midi-chlorian genome of Mace Windu. Why yes, I do want the Open Peer Review option!
We often like to highlight new resources in our tips of the week to show people about some new way to find, explore or analyze genomic data. But sometimes we also want to point out a new aspect of a resource we’ve seen before, or highlight some feature that people tell us they were wondering about. Lately I noticed a number of searches to our blog about viewing restriction enzymes in the UCSC Genome Browser. So I decided it was time to illustrate that.
In this week’s tip I point out where to find the restriction enzyme data track. The choices for the display of that data are shown. And we explore the track details page to learn more about the track source and properties. We’ll see that the track relies on REBASE, the restriction enzyme database from New England Biolabs, and we’ll see some of the display aspects that you should know about. I’ll show how to filter the REBASE data to show only one specific enzyme too.
This track has been around for a while, but I think a lot of people don’t realize it is there or how to use it. If you want more details about other features of the browser including some of the latest developments you should check out the recent publication from the UCSC team in the NAR database issue. There may be more tracks that you aren’t aware of yet that could help you to accomplish your research goals.
One of the other very exciting things in that paper was the note that they will be offering a way for people with assembly data that is not deposited at NCBI to use the browser and tools:
Many researchers have expressed interest in using the Genome Browser to visualize and analyse assemblies that are not deposited at NCBI. To assist such research, we intend to develop support for assembly data hubs, which will enable the genomics community to easily extend the Genome Browser to display genome assemblies that we are unable to integrate into our own database.
That’s a question we hear a lot at workshops lately: what’s the easiest way to use the UCSC genome browser for my genome of interest? This sounds like a terrific opportunity for that.
If you want a more complete exploration about the organization and visualization features of the UCSC Genome Browser, you should have a look at the full introductory tutorial: openhelix.com/ucsc . This tutorial is freely available because it is sponsored by the UCSC Genome Browser team. There’s a full video, slides, and exercises you can download and use to train yourself or others.
Meyer, L., Zweig, A., Hinrichs, A., Karolchik, D., Kuhn, R., Wong, M., Sloan, C., Rosenbloom, K., Roe, G., Rhead, B., Raney, B., Pohl, A., Malladi, V., Li, C., Lee, B., Learned, K., Kirkup, V., Hsu, F., Heitner, S., Harte, R., Haeussler, M., Guruvadoo, L., Goldman, M., Giardine, B., Fujita, P., Dreszer, T., Diekhans, M., Cline, M., Clawson, H., Barber, G., Haussler, D., & Kent, W. (2012). The UCSC Genome Browser database: extensions and updates 2013 Nucleic Acids Research, 41 (D1) DOI: 10.1093/nar/gks1048
Roberts, R., Vincze, T., Posfai, J., & Macelis, D. (2009). REBASE–a database for DNA restriction and modification: enzymes, genes and genomes Nucleic Acids Research, 38 (Database) DOI: 10.1093/nar/gkp874
I have just been made aware of the GMOD community survey that’s running right now, through March 1. The folks who support the GMOD tools and projects are interested in your experience with the tools, and the good features and the “needs improvement” sort of things about them.
They are also interested in hearing about what might be useful to include–areas they aren’t covering right now. And if there are strengths or gaps on other aspects of of the projects, such as training or support, that you may have encountered.
Here’s a bit more detail from the email I got:
We’re looking for feedback from users on what GMOD tools that they use, what they think works (and what doesn’t!), how they rate the support and training options available, and so on. The results will be used to help GMOD serve its user community better and to guide the future development of the GMOD project. As a bonus, everyone who completes the survey can enter a draw to win a genetic test from 23andMe.
So have a go at the survey yourself, and tell your colleagues. We all know how important it is for these projects to get feedback for future funding and support. And to drive the projects in the directions that we see as a need. Go! Help them out.
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 @bio_insilico: Nurses at forefront of genomics in health care – Science Codex: Nurses at forefront of genomi… http://t.co/C4Q8IT2v #biotech #genomics
RT @NIAIDBioIT: NIAID Bioinformatics is now in the Twitterverse! Follow us to stay up-to-date on bioinformatics news and software updates at NIAID and NIH
RT @MICROUVic: There is a new, FREE journal that is devoted to publishing genomic sequencing data. Cancel all of your social plans! http://t.co/aOjI65QO
RT @John_Idol: Never been more proud of any other project in my life, new @openworm website is live – http://t.co/LmnNiydf
RT @DNAday: Join us 2/14 for Bob Waterston/Sir John Sulston talk on public access to genomic data. #HGP10 http://t.co/heieGnRO [Note--I asked if this would be streamed, here's the reply: This won't be streamed live but will be available ASAP on @genome_gov's you tube channel http://t.co/cu3jTV9i]
Zoiks: RT @neilfws: Ensembl Genomes release 17: http://t.co/2Mnhl4s1. “Due to this sheer number of new genomes…BioMart access is no longer possible” [But my favorite sentence this week was, actually: "A missing chromosome in beetle (Tribolium castaneum) was also reinstated, and its gene models updated"]
BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community 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 items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.
This week’s highlighted item is something that I’d love to try. Plant tissue-specific promoter design. I can really see the advantage of tools for this.
Design a synthetic plant promoter to control gene expression to specific plant tissues or times of day. RIKEN will synthesize the DNA, transform it into a plant, and measure the gene expression level using Firefly Luciferase to create glowing plants.
I wish I had time for this. Or that I had heard about it sooner. It ends on Friday. Hawaii time…but still…can’t get there this year. Maybe I’ll watch for it next year though! Will give me time to check out their software in more detail anyway.
When we do workshops, I sing the praises of the ENCODE data that’s genome-wide, and how it is offering amazing new opportunities to explore and discover new features of you genomic regions of interest. But I know that’s all I can do to introduce folks to the data in a short session–and they need to take it to the next level themselves. In the future I’ll be pointing them to MotifLab as a way they might want to proceed after their UCSC and ENCODE training.
MotifLab is a software tool that lets you take segments of interest and process them with a number of other useful data types and tools, integrated into one place. You can then apply various motif finding and analysis tools to assess the region. And you can layer on other data types to help you to further understand what’s going on in that spot.
In the past I might have taken regions of interest from the UCSC Genome Browser and gone to other sites to accomplish many of the things that are integrated into MotifLab. And some of those tools–while nice–don’t offer me the visual track-based additional data I want to consider once I’ve analyzed my stuff. I’d end up taking it back to UCSC as a custom track, uploading that, and then exploring some more. But over many regions, that can be hard to visualize simultaneously.
In fact, it reminds me of a question that a lot of trainees ask in our UCSC Genome Browser workshops: can I have several regions open at the same time? And I think that MotifLab will essentially let you do that, in one place.
They have a series of tutorials to work through to help you to understand what they offer and how to accomplish it. I will point you there, because I haven’t had the time to fully examine all the details myself. But I have plans to take some data I’m interested in, and run it through the paces there. It might not be the right tool for everyone, but it’s got the right combination of tools and graphics to work the way I like to think about the data.
The tutorials they have aren’t embeddable, so I link you to them with the screenshot above. Or you can go directly to the list. They take a while to load, and there’s no audio–you will click through the segments. But they give a good grasp of the kinds of things you can do.
Klepper, K., & Drabløs, F. (2013). MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis BMC Bioinformatics, 14 (1) DOI: 10.1186/1471-2105-14-9
Hey folks–as a public service announcement I’m posting this email from the Genetic Alliance folks. They’ve assembled a terrific webinar series that cover hot topics in genomics research and privacy issues. I’m posting part of the email, but then will direct you to their page for the full list of upcoming webinars.
I’ve read the report1 and I thought it was really well done. But I’ve seen little chatter about it since among the genoscenti. I’m eager to hear more discussion about it. And it heated up in the public sphere recently with the publication of that paper that identified donors to the 1000 genomes project2. One of the webinars is specifically targeted to ancestry information and WGS (the December 10th one).
++++++++
What about Privacy and Progress
in Whole Genome Sequencing?
The Presidential Commission for the Study of Bioethical Issues recently released a report entitled Privacy and Progress in Whole Genome Sequencing. In short, it concludes that “to realize the enormous promise that whole genome sequencing holds for advancing clinical care and the greater public good, individual interests in privacy must be respected and secured”. In their words: “As the scientific community works to bring the cost of whole genome sequencing down from millions per test to less than the cost of many standard diagnostic tests today, the Commission recognizes that whole genome sequencing and its increased use in research and the clinic could yield major advances in health care. However it could also raise ethical dilemmas. The Commission offers a dozen timely proactive recommendations that will help craft policies that are flexible enough to ensure progress and responsive enough to protect privacy.”
Many people contributed to this report over a year. The committee worked hard to distill a great deal of information into a cohesive set of recommendations. It is important that this information be disseminated, discussed and built upon. This year-long series will use the report structure as the basis for discussion. We’ll explore each recommendation, look for practical applications, and consider what else might be needed to realize the fruit of whole genome sequencing and respect privacy.
Genetic Alliance offers this series of monthly webinars, on the second Tuesday of each month at noon, beginning in February 2013 and ending in December. All webinars are free of charge and are also archived for later viewing. In general, the webinars will last one hour and leave ample time for questions and answers.
2Gymrek, M., McGuire, A., Golan, D., Halperin, E., & Erlich, Y. (2013). Identifying Personal Genomes by Surname Inference Science, 339 (6117), 321-324 DOI: 10.1126/science.1229566
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 @kbradnam: New blog post: Some brief thoughts on developing and supporting command-line bioinformatics tools http://t.co/TEKuhPxn
RT @bffo: MT @genetics_blog: Video introduction to #RNASeq by @rafalab https://t.co/lU1j8ACJ #bioinformatics #Rstats
RT @GenomeBrowser: White Rhinoceros (Ceratotherium simum) charging in with a new browser! http://t.co/dG125Jyr Sequenced/assembled by the @broadinstitute
RT @EncodeDCC: Uniformly processed ENCODE DNaseI hypersensitivity data available to view & download from @GenomeBrowser http://t.co/BzhxFryJ cc @ENCODE_NIH
RT @ProfLHunter: Bioinformatics at #davos #wef presented by Ewan Birney. Not sure if that means we’ve arrived or if we e now over the hill RT @ewanbirney
RT @DoubleXSci: Free Kits Help 10-Year-Olds See Their DNA | Budding Scientist, Scientific American Blog Network http://t.co/FEntnhjT via ...Friday, 02.15.13 21:50
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…
http://t.co/gZTgpJqr
Recent Comments