Friday SNPpets

24 May, 2013 (08:06) | SNPpets | By: Mary

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…

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What’s The Answer? (genome data viewers)

23 May, 2013 (07:30) | What's the Answer? | By: Mary

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 question is one that comes up from time to time, but it’s probably worth re-examining for new choices or new features as technology changes. And I learned about a viewer that was new to me–Chipster. I’ll be checking out that one in the future.

Question: Other genomic viewer like IGV

Are there other genomic viewer like IGV ?

–marcodpc

You can get a sense of what tools people are actively using, and features that they like, from the answers. Go check ‘em out, and if you have other ideas bring them over.

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Video Tip of the Week: Canary Database for sentinels of human health

22 May, 2013 (08:32) | Tip of the Week | By: Mary

Recently we attended the Medical Library Association conference (#MLAnet13). Librarians are working so hard to wrangle information into usable forms, and to generate new connections among data types to reveal new information and leads for further studies. I ♥ librarians. In one of the sessions I attended on Medical Informatics, I heard several great talks. One speaker talked about a resource that connected types of information that hasn’t been well connected before: animal health + human health.

Sure–you think–we have information on cancer in mice. Rats. Disease models, etc. But this was different. Peter Rabinowitz was talking about connecting a different kind of animal information–data about non-model organism species that are part of the environment that we share. He and his team have been organizing that data into the Canary Database.

You might be aware of this already in some ways. Deer ticks and lyme disease. Horses and eastern equine encephalitis. Birds in China and #H7N9 flu. Agricultural animal transmission of antibiotic-resistant bacteria. But there are numerous other types of possible animal health consequences that could provide awareness and actionable information for environmental or human health interventions that would provide real benefits, or at least offer new leads to investigate.

Here you can watch a quick overview of the Canary Database:

This database has been around for some time, collecting this type of information. They have scoured numerous sources, including Medline/PubMed, CAB Abstracts, and Agricola. They curate this, and organize it in various ways to make it searchable and accessible. But it’s not easy to find the right papers, as we found out during the session at MLA.

In his talk Peter provided stories of the challenges of this work. There is no MeSH term for sentinel species types of data. So they had to text mine to find appropriate papers, and then filter through large amounts of work that wasn’t their target. For example–they were interested in companion animals that might have asthma symptoms. Cats in a home suffering from asthma might offer clues to interventions that could help humans who are affected. But a search for cats + asthma will provide lots of papers where the cats are possibly causing the breathing problems–and not the kind of work they wanted to feature for their database.

One way genomics folks could help them out would be to flag literature on this issue for them. Species research communities read a lot of papers, and if they find good examples of sentinel species it would help the Canary Database team out. Commenters at the talk also suggested contact with the MeSH folks to ask for a new category.

I can see the idea of this type of connection being really interesting and useful, though. And as we sequence more species, we could look for similar responses in a whole new range of organisms–and maybe identify new models of human illness that we hadn’t realized before. Or we can learn from the related genes and pathways. So in addition to the warnings of environmental hazards, we can study responses and interventions that would be helpful too.

So check out Canary Database, and learn about animals as sentinels for potential environmental and health warnings.

Quick links:

CanaryDB: http://canarydatabase.org/

References:

Rabinowitz, P., Scotch, M., & Conti, L. (2010). Animals as Sentinels: Using Comparative Medicine To Move Beyond the Laboratory ILAR Journal, 51 (3), 262-267 DOI: 10.1093/ilar.51.3.262

Rabinowitz, P., Gordon, Z., Holmes, R., Taylor, B., Wilcox, M., Chudnov, D., Nadkarni, P., & Dein, F. (2005). Animals as Sentinels of Human Environmental Health Hazards: An Evidence-Based Analysis EcoHealth, 2 (1), 26-37 DOI: 10.1007/s10393-004-0151-1

Rabinowitz, P., Cullen, M., & Lake, H. (1999). Wildlife as sentinels for human health hazards: a review of study designs Journal of Environmental Medicine, 1 (4), 217-223 DOI: 10.1002/jem.33

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Who’s your daddy?

21 May, 2013 (11:43) | General Science, Genomics Research | By: Mary

A new article in Slate describes a case of non-paternity unearthed as a result of a 23andme scan.

Who’s Your Daddy?

The perils of personal genomics.

By

I expect a bit of chatter from the genoscenti. I’ll collect responses below if I see them. I agree that the actual studies of non-paternity show values that are all over the map. But I suspect that there are going to be a lot of people affected by this who didn’t see it coming. And many of those stories will be quiet and private, and won’t be widely known. Some will turn into Jerry Springer, perhaps.

But I know of cases where this has already had serious impact, like the woman who was thrown out of her tribe as a result of her DNA test. This is a very heated topic in some circles: Tribal Enrollment and Genetic Testing Resources.

Interesting times.

All I could think of was this:

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Friday SNPpets

17 May, 2013 (07:41) | SNPpets | By: Mary

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…

 

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What’s the Answer? (unglamorous tasks)

16 May, 2013 (08:02) | What's the Answer? | By: Mary

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.

Heh. Ok, so it’s not all glamour–this discussion made me laugh. Posed in the forum:

Forum: What do you waste your time on

Like in everything else we do, the 80%-20% rule works great in bioinformatics. What is your 80% of the time wasted on? I can suggest: 1. converting accession numbers between databases 2. parsing output The bottom line of the post is how to avoid these time consuming tasks.

–Asaf

Converting accession numbers and file formats was pretty popular. But the pointing-to-documentation one made me chuckle too. Go see the full spectrum of bioinformatics glory duties.

 

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Video Tip of the Week: Influenza Research Database (IRD)

15 May, 2013 (08:33) | Tip of the Week | By: Mary

It may not be traditionally what you think of as flu season, but lately there’s been a great deal of talk about some viruses that are concerning public health officials and infectious disease specialists. You might have heard of the H7N9 situation in China, and the NCoV virus in France that made headlines.

But researchers are working all the time to understand, characterize, and evaluate viral sequences. They will access a number of different tools to do so. We talked last month about GISAID and EpiFlu as our Tip of the Week, and how the special access agreement they have developed has provided some otherwise reluctant governments to share the newest sequence data. So if you want the most current sequences–you would turn to EpiFlu.

There are other virus resources that you should investigate too. Another important site is the IRD, or Influenza Research Database. They have developed an extensive repository of many flu sequences, and have provided a wide range of tools to help researchers investigate and evaluate the data. In addition, they have incorporated some tools that provide novel analyses of the underlying data. This includes predictions of cytotoxic T-cell epitopes, and a sequence feature variant type analysis that they mention in their recent paper.

For this week’s video tip, I include their first of eight videos that will help you to understand their organization and tools. But be sure to keep going for the other 7 that they offer at their YouTube pages.

Be sure to also read the paper that they recently published–it has a nice overview of their tools, their strategies, and also provides a nice use case example of how to flow through a typical evaluation. And if you want other virus data besides flu check out the companion site Virus Pathogen Database and Analysis Resource. You’ll see a similar organization but with a wider range of sequences available. They have a separate thread of videos for the ViPR tools as well.

Quick links:

IRD, Influenza Research Database: http://www.fludb.org/

Other viruses not just flu are in the Virus Pathogen Resource (ViPR) that offers a similar structure and tools: http://viprbrc.org

References:
Squires, R., Noronha, J., Hunt, V., García-Sastre, A., Macken, C., Baumgarth, N., Suarez, D., Pickett, B., Zhang, Y., Larsen, C., Ramsey, A., Zhou, L., Zaremba, S., Kumar, S., Deitrich, J., Klem, E., & Scheuermann, R. (2012). Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance Influenza and Other Respiratory Viruses, 6 (6), 404-416 DOI: 10.1111/j.1750-2659.2011.00331.x

Pickett, B., Sadat, E., Zhang, Y., Noronha, J., Squires, R., Hunt, V., Liu, M., Kumar, S., Zaremba, S., Gu, Z., Zhou, L., Larson, C., Dietrich, J., Klem, E., & Scheuermann, R. (2011). ViPR: an open bioinformatics database and analysis resource for virology research Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr859

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Decoding Annie Parker: film about the BRCA hunt

10 May, 2013 (18:12) | Genomics Research | By: Mary

I didn’t know that this film was even in the works.

I know there’s controversy over the patents, but you have to acknowledge that the underlying science was really important. And I’m rather pleased to see a woman scientist in film. Looking forward to seeing it somewhere.

Here’s the film website: http://decodingannieparker.com/

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

Hat tip David Bachinsky via twitter:

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

EDIT: I just wanted to add some information that’s breaking now about Angelina Jolie’s recent announcement of her double mastectomy due to her BRCA1 testing. And here’s a good piece about some context for that: A Cautionary Perspective On Angelina Jolie’s Double Mastectomy

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Friday SNPpets

10 May, 2013 (07:44) | SNPpets | By: Mary

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…

 

 

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What’s the Answer? (data access #fail)

9 May, 2013 (07:55) | What's the Answer? | By: Mary

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 question got a lot of votes! Sadly, it’s far too common. And probably most people have run into this problem in bioinformatics and genomics at some point. Sometimes it’s data, sometimes it’s software.

Question: What if authors do not share their published data ?

Dear biostars,

I am wondering what do you do if any author do not share his/her published data with you ? Usually I send an email request after checking their supplemental and public database (ex: GEO) links or others in their paper carefully. Most of the time they do respond to my requests. However sometimes I never get any response from either first or corresponding author regrading sharing their data even after multiple requests. It is really frustrating as the guidelines of that journal (Cell, Nature) clearly state that the data should be public. Do you have any similar experience ? If you write any complaint to the editor, does it work ?

Thanx in advance
Sorry that it is not really a bioinformatics question

–repinementer

Zev Kronenberg gives an excellent stepwise answer. Be sure to look at step zero! But there are a couple of other items you can read through as well. Go have a look at the answers.

But there’s no excuse for this now. With FigShare, GitHub, and other existing options for various types of things that need to be made available, it needs to improve. Reviewers need to demand this, and editors have to insist on this. And those who don’t deliver will likely be subject to some public shaming–because that’s the last step when all else fails (see Zev’s step 7).

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