Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits. Why not let us know how they compare to the tools that you use in the comment threads?
Mary Mangan has been fascinated with biology since spending summers at the beach engrossed by the tide pools. This led to degrees in Microbiology, Plant Cell Biology, and eventually a PhD in Cell, Molecular, and Developmental Biology. Moving to computational biology, bioinformatics and genomics as those fields emerged, Mary finds databases are the new tide pools for her. And new waves keep washing interesting things in! Mary is currently the President of OpenHelix since its founding in 2003. OpenHelix provides online and onsite training on bioinformatics and genomics resources. Previously, she successfully founded and operated Biological Software Testing Services, Inc. This company provided software testing from a biological scientist’s perspective for the bioinformatics industry. For some publications, you can see her Google Scholar profile.
Do you RTFM? C’mon—tell the truth. When you approach some new software, do you read the freakin’ manual first? Yeah. Thought so. Not to worry, it’s a common phenotype. In fact, we’re pretty sure that the scientists at OpenHelix are among a tiny fraction of people with a rare allele for software manual reading. But the good news is we’ve found a way to help non-rare allele people. We make short videos on biomedical research software tools, hosted at SciVee, where the goal is “making science visible”. (http://www.scivee.tv/ )
Isn’t that a better way to dive in to new software? Yeah, we think so too.
The Human Genome Project (HGP; http://www.genome.gov/10001772 ) changed nearly everything in biomedical research. The delivery of the human sequence data was certainly key—but there are other aspects of how that effort changed the ways biomedical science researchers work that people may not realize. There were databases and software tools for biologists before the HGP. But the explosion of data, and the concurrent development of new sequencing technologies, has provided a bonanza of data bits. The need for more sophisticated analysis tools, combined with a thriving open source software community, has changed the research culture as a result.
A huge array of databases and tools that support genome research are now available to everyone with an internet connection (nice collections include OBRC from University of Pittsburgh http://www.hsls.pitt.edu/obrc/ and the bioinformatics.ca directory http://bioinformatics.ca/links_directory/index.php). Researchers around the world provide and use the tools. However, the outreach, support, and training on these terrific resources varies a bit. The traditional means of getting the word out in science—the scientific paper, conferences, seminars—continues to provide means of learning about these tools. But the static nature of papers and posters can’t convey some of the best features of using this software. And if you weren’t at that conference or seminar, you simply might not know about a tool. Further, for many of the “big data” projects running now—access to the data is offered long before publication: you have to know how to use the databases to mine that information effectively. Even after publication, sometimes the bulk of the data isn’t provided in the literature itself, but in a companion database (http://blog.openhelix.com/?p=11705 ). And we all know: nobody reads the documentation. And before you even decide if reading the documentation is worth your time, a gentle intro to the basic functions might be really helpful.
So here at OpenHelix we’ve made it our mission to provide outreach and training for these data and tools. Primarily we aim to reach active scientists and young scholars. But increasingly the biohacking public will want and need to know more about them too. For some tools we have seminar-length training available (such as the materials sponsored by the UCSC Genome Browser; http://openhelix.com/ucsc ). For other tools, though, we provide appetizers of awareness with a weekly “Video Tip of the Week” (http://blog.openhelix.eu/?cat=10 ). For years now every week we offer a short movie on some tool, or tool feature, that we think is useful to the community; generally, they are no more than 5 minutes long. We record a live-action interaction with the software, and in the audio describe the features we want to highlight. Then we make these available to anyone using SciVee.
SciVee is a robust hosting platform for “making science visible”. We like the emphasis they place on science—it’s not just full of pet and celebrity videos (which are also fun, but not exactly what students and researchers need…). Anyone can take the embed code for the videos and use them elsewhere. SciVee has been a great place for us to organize and host our videos. Posting our videos is free, the SciVee team knows the arena – it was originally developed by Phil Bourne’s lab to meet this growing need for new outreach strategies – and it’s a service that has been available for as long as we’ve been doing our tips (since 2007), which isn’t true of some other video hosting options available now.
The Cannabis genome project is using a custom version of the UCSC Genome Browser, in this video you can see some of the data and how you can interact with it.
There are so many great open source software projects out there, for a huge range of research areas. Recently we featured a fun new browser tool that lets you interact with a 3D C. elegans worm (http://blog.openhelix.com/?p=11669). Previously we offered a peek at a new Cannabis genome browser—as a sort of gateway database to entice people to appreciate plant genomics! (http://blog.openhelix.com/?p=11320 ). Another popular tip was a look at how I use Twitter for bioinformatics (http://blog.openhelix.com/?p=6591 ). Even some of the most long-lasting databases sometimes need a fresh look, and recently we offered a tip on the new OMIM interface which has been really popular too. (http://blog.openhelix.com/?p=8539 )
The scope of freely available resources is just tremendous, and we aim to connect researchers to the right tools for their needs. We hope that these short introductions to great software help people to learn about the projects and the features available. The opportunity to generate and deliver science videos has been a valuable way to get the word out about excellent open source tools available to all.
van Bakel, H., Stout, J., Cote, A., Tallon, C., Sharpe, A., Hughes, T., & Page, J. (2011). The draft genome and transcriptome of Cannabis sativa Genome Biology, 12 (10) DOI: 10.1186/gb-2011-12-10-r102
You can follow the online conversation on Twitter with the #ToolTales hashtag and you can read Dr Peter Etchells’s Tool Tale here, Alan Cann’s here, Jerry Sheehan’s here, Boris Adryan’s here, Anthony Salvagno’s here, Daniel Burgarth and Matt Leifer’s here, Zen Faulkes’s here, Jenn Cable’s here , Mike Biocchi’s here, Susanna Speier’s here, Derek Hennen’s here, Musa Akbari’s here, Benedict Noel’s here, Chris Surridge’s here and Gerd Moe-Behrens’s here.