Video Tip of the Week: GOLD, Genomes OnLine Database

Yes, I know some people suffer from YAGS-malaise (Yet Another Genome Syndrome), but I don’t. I continue to be psyched for every genome I hear about. I even liked the salmon lice one. And Yaks. The crowd-funded Puerto Rican parrot project was so very neat. These genomes may not matter much for your everyday life, and may not exactly be celebrities among species. But we’ll learn something new and interesting from every one of them. It’s also very cool that it’s bringing new researchers, trainees, and citizens into the field.

The good news is there is opportunity still for many, many more species. And decreasing costs will make it possible for more research teams to do locally-important species. But–it would be a shame if we wasted resources by doing 30 versions of something cute, rather than tackling new problems. A central registry for sequencing projects may help to manage this. Genomes OnLine Database has been cataloging projects for years, and it would be great if folks would register their research there.

I was reminded of this by a tweet I saw come through my #bioinformatics column. This is what I saw flying by:

As much as I enjoy Twitter and think that science nerds are pretty good at it, it’s hard to know if the right people will see a tweet. Anyway, I suggested that this researcher check out GOLD and BioProject to see if anyone had registered anything.

I realized that although we have talked about GOLD in the past, it hadn’t been highlighted in our Tips of the Week before. So here I will include a video from a talk about GOLD. Ioanna Pagani gives an overview of GOLD, the foundations and the purpose. And then she goes on to demonstrate how to enter project metadata into their registry (~12min). Watching this will help you to understand the usefulness of GOLD, and what you can expect to find there. She describes both single-species project entry, and another option for entering metagenome data projects (~25min).

In the News at GOLD, they mention that their update this summer resulted in some changes to the interface–so the specifics might be a bit different from the video. But the basic structural features are still going to be useful to understand the goals and strategies. It may also help to convey the importance of appropriate metadata for genome projects. If you are involved with these projects, checking out the team’s paper on the structure and use of metadata is certainly worthwhile.

In times of all this sequencing capacity, people are going to start looking for new organisms to cover. Of course, some people will want to look at another strain, isolate, geographical sample for good reasons–but keeping a lot of unnecessary duplication from happening would be nice too. And it would be great if submitters also conformed to the standards for genome metadata–the ‘Minimum Information about a Genome Sequence’ (MIGS, now in the broader collection of standard checklists in the MIxS project) standards being developed by the Genomic Standards Consortium. (You can see how GOLD conformed to this in their other paper below.) Let’s spread the resources around to get new knowledge when we can. I would like to see a more formal mechanism that connects people who have some genome of interest with researchers who might have the bandwidth to do it, as well. Social sequencing?

Quick links:

GOLD: http://www.genomesonline.org

Genomics Standards Consortium: http://gensc.org/

References:
Pagani I., J. Jansson, I.-M. A. Chen, T. Smirnova, B. Nosrat, V. M. Markowitz & N. C. Kyrpides (2011). The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata, Nucleic Acids Research, 40 (D1) D571-D579. DOI: http://dx.doi.org/10.1093/nar/gkr1100

Liolios K., Lynette Hirschman, Ioanna Pagani, Bahador Nosrat, Peter Sterk, Owen White, Philippe Rocca-Serra, Susanna-Assunta Sansone, Chris Taylor & Nikos C. Kyrpides & (2012). The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness, Standards in Genomic Sciences, 6 (3) 444-453. DOI: http://dx.doi.org/10.4056/sigs.2675953

Field D., Tanya Gray, Norman Morrison, Jeremy Selengut, Peter Sterk, Tatiana Tatusova, Nicholas Thomson, Michael J Allen, Samuel V Angiuoli & Michael Ashburner & (2008). The minimum information about a genome sequence (MIGS) specification, Nature Biotechnology, 26 (5) 541-547. DOI: http://dx.doi.org/10.1038/nbt1360

Friday SNPpets

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…

What’s The Answer? (gene essentiality)

Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars 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 Biostars.

This was a new and interesting question, one I haven’t seen before. Are there resources specifically highlighting essential genes in fly? I can see how a dedicated set of these would be useful, and how it could be challenging to extract that from other, more broad, tools and collections.

Question: database of gene essentiality in Drosophila?

I am looking for annotation of gene essentiality in Drosophila. The ideal resource would be a knockout or a RNAi screening which would tell me, for every gene, whether its deletion or silencing is lethal or not.

I saw that there are many resources online, from flybase to UCSC, but I could not find any annotation on gene essentiality there. There are also a lot of screenings published, but they all seem to be related to specific conditions (e.g. exposure to a DNA damaging factor, stress, etc..), but I could not find any screening in which no special conditions were applied. In general, I not familiar with Drosophila, and I am not sure what an expert in the field would use. Which resource do you recommend me?

–Giovanni M Dall’Olio

Giovanni found a couple of answers and brought them over, but if you know of any other useful collections it would be handy to have that information. I know there are various species knock-out projects, and likely more to come. But I was not familiar with the OGEE (Online GEne Essentiality Database) set. It’s not limited to flies, btw. And as I was reading up on OGEE, I saw a reference in PubMed to another essential gene database that was new to me: DEG, Database of Essential Genes. Reading up on that now too.

References:

Chen W.H., M. J. Lercher & P. Bork (2011). OGEE: an online gene essentiality database, Nucleic Acids Research, 40 (D1) D901-D906. DOI: http://dx.doi.org/10.1093/nar/gkr986

Luo H., Lin Y., Gao F., Zhang C.T. & Zhang R. (2013). DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements., Nucleic acids research, PMID: http://www.ncbi.nlm.nih.gov/pubmed/24243843

Video Tip of the Week: #Docker, shipping containers for software and data

Breaking into the zeitgeist recently, Docker popped into my sphere from several disparate sources. Seems to me that this is a potential problem-solver for some of the reproducibility and sharing dramas that we have been wrestling with in genomics. Sharing of data sets and versions of analysis software is being tackled in a number of ways. FigShare, Github, and some publishers have been making strides among the genoscenti. We’ve seen virtual machines offered as a way to get access to some data and tool collections*. But Docker offers a lighter-weight way to package and deliver these types of things in a quicker and straightforward manner.

One of the discussions I saw about Docker came from Melissa Gymrek, with this post about the potential to use it for managing these things: Using docker for reproducible computational publications. Other chatter led me to this piece as well: Continuous, reproducible genome assembler benchmarking. And at the same time as all this was bubbling up, a discussion on Reddit covered other details: Question: Does using docker hit performance?

Of course, balancing the hype and reality is important, and this discussion thrashed that about a bit (click the timestamp on the Nextflow tweet to see the chatter):

To get a better handle on the utility of Docker, I went looking for some videos, and these are now the video tip of the week. This is different from our usual topics, but because users might find themselves on the receiving end of these containers at some point, it seemed relevant for our readers.

The first one I’ll mention gave me a good overview of the concept. The CTO of Docker, Solomon Hykes, talks at Twitter University about the basis and benefits of their software (Introduction to Docker). He describes Docker of being like the innovation of shipping containers–which don’t really sound particularly remarkable to most of us, but in fact the case has been made that they changed the global economy completely. I read that book that Bill Gates recommended last year, The Box, and it was quite astonishing to see how metal boxes changed everything. This brought standardization and efficiencies that were previously unavailable. And those are two things we really need in genomics data and software.

Hykes explains that the problem of shipping stuff–coffee beans, or whatever, had to be solved, at each place the goods might end up. This is a good analogy–like explained in the shipping container book. How to handle an item, appropriate infrastructure, local expertise, etc, was a real barrier to sharing goods. And this happens with bioinformatics tools and data right now. But with containerization, everyone could agree on the size of the piece, the locks, the label position and contents, and everything standardized on that system. This brought efficiency, automation, and really changed the world economy. As Hykes concisely describes [~8min in]:

“So the goal really is to try and do the same thing for software, right? Because I think it’s embarrassing, personally, that on average, it’ll take more time and energy to get…a collection of software to move from one data center to the next, than it is to ship physical goods from one side of the planet to the other. I think we can do better than that….”

This high-level overview of the concept in less than 10min is really effective. He then takes a question about Docker vs a VM (virtual machine). I think this is the essential take-away: containerizing the necessary items  [~18min]:

“…Which means we can now define a new unit of software delivery, that’s more lightweight than a VM [virtual machine], but can ship more than just the application-specific piece…”

After this point there’s a live demo of Docker to cover some of the features. But if you really do want to get started with Docker, I’d recommend a second video from the Docker team. They have a Docker 101 explanation that covers things starting from installation, to poking around, destroying stuff in the container to show how that works, demoing some of the other nuts and bolts, and the ease of sharing a container.

So this is making waves among the genomics folks. This also drifted through my feed:

Check it out–there seem to be some really nice features of Docker that can impact this field. It doesn’t solve everything–and it shouldn’t be used as an escape mechanism to not put your data into standard formats. And Melissa addresses a number of unmet challenges too. But it does seem that it can be a contributor to reproducibility and access to data issues that are currently hurdles (or, plagues) in this field. Docker is also under active development and they appear to want to make it better. But sharing our stuff: it’s not trivial–there are real consequences to public health from inaccessible data and tools (1). But there are broader applications beyond bioinformatics, of course. And wide appeal and adoption seems to be a good thing for ongoing development and support. More chatter on the larger picture of Docker:

And this discussion was helpful: IDF 2014: Bare Metal, Docker Containers, and Virtualization.

And, er…

I laughed. And wrote this anyway.

Quick links:

Docker main site: http://www.docker.com/

Docker Github: http://github.com/docker/

Reference:
(1) Baggerly K. (2010). Disclose all data in publications, Nature, 467 (7314) 401-401. DOI: http://dx.doi.org/10.1038/467401b

*Ironically, this ENCODE VM is gone, illustrating the problem:

encodevm_gone

Friday SNPpets

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…

What’s The Answer? (elab notebook, open source)

Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars 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 Biostars.

Recently I was watching the genoscenti talk about electronic lab notebooks. I had used the chatter as a post to make a point about the value of the Biostar information on that topic. It seemed to be popular. Lo and behold–there’s a new post on Biostar on this topic. And some nice open-source lab notebook software.

Tool: Introducing eLabFTW : free open source electronic lab notebook

Hello everyone,

I work in Institut Curie, Paris, France, as an engineer in a research lab. I developed a php/mysql application to keep track of experiments (lab notebook). It’s free and open source and I believe this community could be interested in such a thing.

You can run it on a server, for a whole departement if you want, or just locally on your machine.

Please visit the website and try the demo : http://www.elabftw.net https://demo.elabftw.net

Any question, suggestion or remark you might have, I want to read it :) Your input help me makes a better software.

Thank you :D

Regards,

~Nico

elab

The post got a good upvote number, so others found it interesting too. I went to give the software a try, and I thought it was very handy. And Nico was very responsive to my thoughts and working through an idea that I had, as you can see in our exchange. Although I’m not in a wet lab at this point, I really have been musing on the best way to store my thought process and series of steps I’m taking to accomplish certain things I need to do–sometimes in data mining, sometimes in software testing, etc. A system like this could work for my purposes.

Anyway–check it out, eLabFTW. There’s a way to test on a web installation demo that Nico has set up, or you can pull it down locally and run it.

Video Tip of the Week: NIH 3D Print Exchange

The other day I was joking about how I was 3D-printing a baby sweater–the old way, with yarn and knitting needles. And I also mentioned that I assumed my niece-in-law was 3D-printing the baby separately. I’ve been musing (and reading) about 3D printing a lot lately–sometimes the plastic model part, sometimes the bioprinting of tissues part. So when I came across this new NIH 3D Print Exchange information, it seemed worthy of highlighting.

Although I haven’t had access to a 3D printer setup yet (although I’m planning to take a course soon at the local Artisan Asylum), I’ve been seeing quite a bit of chatter about it. Some folks are designing gel combs (rather than paying ridiculous catalog prices). Some folks print skulls and other bones. There is so much opportunity for a wide range of helpful scientific applications across many fields that it seems an introduction to this topic would be wise for a lot of folks.

So when someone pointed me to the 3D printing initiative at NIH, I was hooked. The public announcement and site launch was in mid-June, according to their blog and press release. I was catching up by reading other items on their site, including some press coverage that provides context for this and other government initiatives on 3D printing. Make Magazine’s piece “The Scramble To Build Thingiverse.gov is On!” notes that the Smithsonian and NASA also have projects underway. But for me, molecules in 3D are what I’m most interested in, so I’ll focus on this NIH version below.

An intro video provides an overview of the kinds of things that will be available on their site. But there’s also a YouTube channel with more.

At the site now you will find a number of ways to get started. At the “Share” navigation area you will find already there is a section for custom lab gear, anatomical stuff, and biological structures and even some organisms. So if you have models to share, you can load ‘em up. With the “Create” space you can quickly generate some items with a handy quick start feature. Because I’m fascinated with the beautiful structures of hemolysins (have you seen these things?) I picked one out, entered a PDB ID, and within a half hour I was notified that the printable model was available to me–and you can see it here. But you can build your own from scratch as well, of course. There are other tutorials that will help you get some foundations in place.

Hemolysin 3D printable modelOr you can look around–from the “Discover” page you can browse or search for examples of models people have done. At this time, there are 347 (including the one I just did yesterday). But there will be more. I want to get mine printed up, and then see some other proteins too.

Ok, so it’s not like I made a kidney or something (although we know that day is coming). Being able to think about the 3D printing process, file types, and various options are probably worth noodling on. Getting your feet wet with a little protein structure or organelle might be a good way to get started. Check it out, and start thinking in other dimensions.

Quick links:

NIH 3D Print Exchange: http://3dprint.nih.gov/

Hemolysin for image: http://www.pdb.org/pdb/explore/explore.do?structureId=3B07

Model Generated for hemolysin from PDB record: http://3dprint.nih.gov/discover/3dpx-000507

Reference:
Murphy S.V. (2014). 3D bioprinting of tissues and organs, Nature Biotechnology, 32 (8) 773-785. DOI: http://dx.doi.org/10.1038/nbt.2958

Friday SNPpets

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…

 

What’s the Answer? (resource gone missing)

Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars 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 Biostars.

So, once again a resource that was published became unavailable. And this had consequences for one researcher–a paper was dinged by reviewers because the resource couldn’t be checked.

Question: What happened with miRecords mirna database website ?

What happened with miRecords mirna database website ? The webpage is not available and I used it’s data as part of an analysis in my paper. Now the reviewer can’t see the page and asks for an explanation.

Edit:

Sorry, I forgot to post the link. The miRecords was suppose to be available at http://miRecords.umn.edu/miRecords.

makaonte

Well, at least the resource is now back up, according to the comments. It was definitely down when I had tried. Apparently writing to the folks on the paper hadn’t succeeded. But is that a win for social media? Or just a temporary appeasement until the next time someone can’t be bothered to restart the server?

Alas. We still need a better way to retire stuff for situations like this.

Video Tip of the Week: Phenoscape, captures phenotype data across taxa

Development of the skeleton is a good example of a process that is highly regulated, requires a lot of precision, is conserved and important relationships across species, and is fairly easy to detect when it’s gone awry. I mean–it’s hard to know at a glance if all the neurons in an organism got to the right place at the right time or if all the liver cells are in the right place still. But skeletal morphology–length, shape, location, abnormalities can be apparent and are amenable to straightforward observations and measurements. Some of these have been collected for decades by fish researchers. This makes them a good model for creating a searchable, stored, phenotype collection.

The team at Phenoscape is trying to wrangle this sort of phenotype information. I completely agree with this statement of the need:

Although the emphasis has been on genomic data (Pennisi, 2011), there is growing recognition that a corresponding sea of phenomic data must also be organized and made computable in relation to genomic data.

They have over half a million phenotype observations cataloged. These include observations in thousands of fish taxa. They created and used an annotation suite of tools called Phenex to facilitate this. They describe Phenex as:

Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

That’s great data to capture to provide important context for all the sequencing data we are now able to obtain. I think this is a nice example of combining important physical observations, mutant studies, and more, with genomics to begin to get at questions about evolutionary relationships among genes and regulatory regions that aren’t obvious only from the sequence data. You may not be personally interested in fish skeletons–but as an informative way to think about structuring these data types across species to make them useful for hypothesis generation–this is a useful example.

Here’s a intro video provided by the Phenoscape team that walks you through a search starting with a gene of interest, and taking you through the kinds of things you can find.

So have a look around Phenoscape to see a way to go from the physical observations of phenotype to gene details, or vice versa.

Quick links:

Phenoscape: http://phenoscape.org/

Phenex: http://phenoscape.org/wiki/Phenex

References:
Mabee B.P., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J. & Westerfield M. (2012). 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton., Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology, PMID: http://www.ncbi.nlm.nih.gov/pubmed/22736877

Balhoff J.P., Cartik R. Kothari, Hilmar Lapp, John G. Lundberg, Paula Mabee, Peter E. Midford, Monte Westerfield & Todd J. Vision (2010). Phenex: Ontological Annotation of Phenotypic Diversity, PLoS ONE, 5 (5) e10500. DOI: http://dx.doi.org/10.1371/journal.pone.0010500