Author Archives: Mary

support_MODs

Video Tip of the Week: FlyBase TV, and a letter of support for model organism communities

This week’s video tip was prompted by a couple of things. First, it was a tweet from FlyBase, about their video channel. It’s been a while since we’d done a FlyBase Tip of the Week, so that was enough of a reason.

But it also came just after I was thinking about the importance of the model organisms, based on the campaign by the model organism databases to save their funding. Here’s a tweet from the yeast genome database (SGD) with a plea:

But this letter cites yeast, flies, WormBase, ZFIN, MGI, RGD and Gene Ontology as well.

mergeI have a soft spot for model organisms, not only because of the tremendous amount of great biology they’ve provided. I was a postdoc at The Jackson Lab, and I am acutely aware of how crucial it is to have the depth of the species specialists involved in creating and maintaining the resources that are appropriate for their organism. But it’s more than just institutional knowledge and data, of course. It’s also the importance of the community of researchers working on that organism, supporting them and having their needs met in many ways with species-specific resources.

So this week’s tip highlights some features of the FlyBase tools, as a way to remind folks of the great work that’s going on at model organism databases (MODs).

Now, if you haven’t already done so, please consider signing on to the letter of support for these databases. You can read more about the issue over at the site, but briefly:

NHGRI/NIH has recently advanced a plan in which the MODs will be integrated into a single combined database, along with a 30% reduction in funding for each MOD (see also these Nature and Science news stories). While increased integration will present many advantages, the plan will result in a loss of critical organism-specific datasets. The funding cut will also cripple core functions such as high quality literature curation and genome annotation, degrading the utility of the MODs. Given the large number of scientists that this policy change would affect and the importance of their work, this is a matter of extreme concern.

I have always shouted about the importance of high-quality curation. It’s so undervalued, but it’s only more and more crucial now that we are getting so much sequence data and we need the best existing knowledge to help guide us through it. Now is not the time to cut back on curation.

So if you have valued MOD data and community sites, please consider signing on to the letter of support.

Quick links:

FlyBase:  http://flybase.org/

Support Model Organism Databases letter: http://www.genetics-gsa.org/MODSupport/

References:

Hayden, Erica Check. “Funding for model-organism databases in trouble.” Nature News. () DOI: 10.1038/nature.2016.20134

Kaiser, Jocelyn. “Funding for key data resources in jeopardy.” Science 351.6268 (2016): 14-14. DOI: 10.1126/science.351.6268.14

Attrill, Helen, et al. “FlyBase: establishing a Gene Group resource for Drosophila melanogaster.” Nucleic acids research (2015): gkv1046. DOI: 10.1093/nar/gkv1046

SNPpets_2

Friday SNPpets

This week’s SNPpets have lentils. I love lentils. But also zombies. And a baronet established by DNA sequencing. A need for some CRISPR edting. And the sudden retirement of HapMap. There’s also an attempt to save the model organisms from retirement or zombie-ness. Wormbase/Flybase/ZFIN et al need your signature. I wish signaures could save science from the Brexit as well. But I suspect that’s unlikely.


SNPpets_2Welcome 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…


 

genonets_quickstart

Video Tip of the Week: Genonets, exploring genotype-phenotype relationships

Lately I’ve been keeping an eye on a lot of the tools that link individuals with sequence data, their phenotypes, and researchers/physicians who may either study or treat the associated medical issues (see MyGene2 most recently) . But there’s a lot of room upstream of these kinds of patient outcomes to explore genotypes and phenotypes. This week’s Video Tip of the Week is for Genonets, offering “Analysis and Visualization of Genotype Networks”, a tool that can help to explore these relationships for pre-clinical/research scenarios as well.

A recent paper explains the goals behind their tools, and they also have a series of videos on their web site to help you get going with Genonets. I’ll put the intro video here, but be sure to click over to their “Learn Genonets” page for a lot more. There’s also a text-based tutorial you can work through which is helpful.

You can also kick the tires a bit with a sample file that’s available from their search page. Just click the checkbox to load it up and try it out. And then be sure to explore those “deep dives” videos to go further.

Hat tip: 

Quick link:

Genonets: http://ieu-genonets.uzh.ch

Reference:

Khalid, F., Aguilar-Rodríguez, J., Wagner, A., & Payne, J. (2016). Genonets server—a web server for the construction, analysis and visualization of genotype networks Nucleic Acids Research DOI: 10.1093/nar/gkw313

SNPpets_2

Friday SNPpets

This week’s SNPpets have a pretty typical list of both new and updated sites and tools. The wheat genome (not gluten-free). A couple of key bits for folks who are scripting calls to NCBI (need to use https soon), or for folks in Asia who could use a UCSC Genome Browser mirror site closer to their location: http://genome-asia.ucsc.edu/. But my favorite thing this week was the best postdoc ad on twitter evah–see the snake one.


SNPpets_2Welcome 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…


https://twitter.com/Sara_and_Snakes/status/742891484064546816

UCSC Genome Bioinformatics

Video Tip of the Week: UCSC Genome Browser Exon-only Mode

The team at UCSC Genome Browser continues to update their resources and offer new ways to find and visualize features of interest to researchers. One of the newer features is the “multi-region” option.  When it was first launched, I did a tip on how to use that, with some of the things that I noticed while I was testing it pre-launch. But now the folks at UCSC have their own video on the exon-only display that you might also find useful.

One of the things that is illustrated here is how the exon-only mode is handy to enhance your exploration of RNA-Seq data. It also uses a great ENCODE data set as an example, and if you haven’t been using that collection it’s a good reminder of the kinds of things you can find in that resource still. And this extensive data set shows how much easier it is to look at different isoforms in the data in this new exon-only mode.

So have a look at this display option if you haven’t before, especially how it can help you to see transcript differences. If you aren’t familiar with the ENCODE data that’s being used, you can also see our training on that which will help you to understand how to use that data and the filtering features that are also used in this video.

Special note: I have updated the UCSC Intro slides to include the new Gateway strategies as well. So download those slides for the latest look. 

+++++++++++++

Disclosure: UCSC Genome Browser tutorials are freely available because UCSC sponsors us to do training and outreach on the UCSC Genome Browser.

Quick links:

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

UCSC Genome Browser training materials: http://openhelix.com/ucsc

ENCODE: http://www.openhelix.com/ENCODE2

References:

Speir, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., Hinrichs, A., Heitner, S., Harte, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Barber, G., Haussler, D., Kuhn, R., & Kent, W. (2016). The UCSC Genome Browser database: 2016 update Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1275

The ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome Nature, 489 (7414), 57-74 DOI: 10.1038/nature11247

SNPpets_2

Friday SNPpets

This week’s SNPpets offer a rather eclectic collection. Visualization with PanViz, LepBase for lepidopterans, a simulated data generator, and a new collection of community-curated phylogenetic estimates. But the big noise was the cancer “moonshot” data commons and the clinical trial for NCI-MATCH and precision medicine. Also newborn genome sequencing. Funniest thing: passive-aggresive bioinformatics. Coolest thing: Paul Simon and CRISPR (scroll to the bottom of the list).


SNPpets_2Welcome 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…


Mygene2_vid

Video Tip of the Week: MyGene2, connecting families with rare conditions with each other

Last week’s tip encouraged people to think about how their DNA may be used by various stakeholders. This could be researchers, physicians, pharmaceutical companies, and so on. But one thing it didn’t really cover–now that I think of it–was connecting with other families who may share variations that impact the health of someone in their household. If there isn’t research, or treatment, this connection alone might be worth it for some families.

So when NPR recently had a story on a database for families with rare genetic conditions, I went to have a look: Families Isolated By Rare Genetic Conditions Find New Ways To Reach Out.

The site is MyGene2, and it can help unrelated folks who have the same genome challenges connect with each other. It also can connect folks to researchers interested in the topic. But it does seem to be aimed more specifically at families seeking each other. It was recently awarded  a chance to compete for the final prize in the Open Science Prize effort, and they got a funding boost to keep going.

There is a “welcome” video that they’ve made, but it’s light on the software details. Still, though, I wanted to share the information so families may find it, and researchers may want to know about this resources as well. The video isn’t embeddable, though, so you’ll have to click to view it:

Mygene2_vid

You can learn more about the resources from their FAQ collection. I’ve found a couple of references (below) that provide some further information about the project [Note: the Genetics in Medicine one goes to a paywalled, piece–but you can access the pre-print version PDF at bioRxiv]. As more and more families who are seeking answers will have sequencing information available, they’ll need a place to go with that. I hope they find each other, and find answers.

Quick links:

MyGene2: http://www.mygene2.org

Follow them on twitter: https://twitter.com/MyGene2

Find them on Facebook: https://www.facebook.com/MyGene2/

(The Genetics in Medicine piece also notes My46.org, “a web-based tool for managing return of genetic test results”.)

References:

Panko, B. (2016). Six finalists to compete for Open Science Prize Science DOI: 10.1126/science.aaf9980

Chong, J., Yu, J., Lorentzen, P., Park, K., Jamal, S., Tabor, H., Rauch, A., Saenz, M., Boltshauser, E., Patterson, K., Nickerson, D., & Bamshad, M. (2015). Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features Genetics in Medicine DOI: 10.1038/gim.2015.161

SNPpets_2

Friday SNPpets

This week’s SNPpets offer quite the range of stories and links. Genomics for nurses and rice breeders. CRISPR tricks. A database retirement (Epigenomics DB), and a new collection of miRNA tools among other new resources and data. There are multiple forays into visualization of data, and a visual search engine for scientific diagrams. There’s an important story about genetic drift in research model mice. And a distressing story about how even a highly informed patient/family has difficultly getting tumor genomics investigations accomplished.


SNPpets_2Welcome 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…


https://twitter.com/BioMickWatson/status/736206222144221184

ga4gh_vid

Video Tip of the Week: Your DNA, Your Say. GA4GH wants to hear from you. And you.

The Global Alliance for Genomics and Health (GA4GH) has come up a few times on our blog. The last time we highlighted them for a tip, it was about their Beacon tool. The idea of the Beacon is that it could interrogate a database but in a very subtle way, without needing access to the entire sequence information of a patient. It would ask a simple yes/no question about a given sequence variant–and if a “yes” came back, then a researcher could go through the process of getting proper access to protected patient data.

So it was a way to keep people from pawing through data that they don’t need. And yet it could still connect people who might benefit from research, with researchers who need information.

But certainly issues of patient or donor privacy are hot topics. More and more data will come in from large projects, or from diagnostic samples, and cancer vs normal tissue comparisons, and we are going to struggle with the access vs. privacy matters for a while. The general public is only now becoming aware of the impacts. But we certainly need people to understand and we’ll want them to contribute to expanding our knowledge about health and disease.

That’s why the folks associated with GA4GH, the Wellcome Trust, and the Wellcome Genome Campus are eager to engage the public on their feelings on use of genomic sequence data. They have launched a project called “Your DNA Your Say”[PDF], in the form of a survey with videos to help understand where people are on this issue. Here’s the intro video to entice you to answer the survey:

I answered the survey because I do have concerns about access to information that will help us drive the science forward, as well as about the potential for misuse of the information. But I would like them to hear from as many people as possible, so that we can understand the barriers to research and donation that are looming. Have your say. And spread the word.

You can learn more about their ideas in a variety of publications–I’ll link to one below, but there are other publications and more details about the overall projects and individual tools at the GA4GH web site.

Quick links:

Survey site: YourDNAYourSay.org

GA4GH: http://genomicsandhealth.org/

References:

Lawler, M., Siu, L., Rehm, H., Chanock, S., Alterovitz, G., Burn, J., Calvo, F., Lacombe, D., Teh, B., North, K., Sawyers, C., & , . (2015). All the World’s a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health Cancer Discovery, 5 (11), 1133-1136 DOI: 10.1158/2159-8290.CD-15-0821

SNPpets_2

Friday SNPpets

This week’s SNPpets consist of the usual stuff–new data, new databases, old problems. For the US holiday weekend we’ll also include a styrofoam cooler guide. Ok, it’s for lab stuff, and you want to avoid pathogens. But still, useful. And during your picnic, think about what your Dog DNA is trying to tell you. Try to keep ants away from your picnic, unlike the one in the robot shown here. Probably the biggest surprise this week: DAVID has finally been updated.


SNPpets_2Welcome 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…