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Here’s another course for the summer aimed at PhD students and early career molecular biologists on mastering the use of pre-existing bioinformatics tools. The venue sounds amazing and it looks like the perfect place to learn or hone your existing bioinformatics skills. Francis Martin will be giving the keynote lecture so there is more incentive to attend! The summer is a great time to learn some new skills and really hone data analysis techniques. I think it’s best to learn some topics — bioinformatic tools and data analysis scripting in particular — as intense multi-day workshops or a week- or two-week long short courses. Here’s a few courses that are being held this summer that may be of interest to you. I’ll be sure to post more as I hear about them. Programming for Evolutionary Biology, Leipzig, Germany, April 3rd to April 19th, 2013
Informatics for RNA-sequence Analysis, Toronto, Canada, June 3rd to June 4th, 2013
Pathway & Network Analysis of -Omics Data, Toronto, Canada, June 10th to June 12th, 2013
Again, I’ve been in the midst of writing manuscripts and doing data analysis and haven’t been able to put as much time into this blog as I usually like. I’m also having some trouble with my server, so you’ll have to excuse the slow load times from my service provider. As well as having lots of papers in the pipeline, I am finishing up a few draft posts for the blog, so stay tuned as there is more on the way. Speaking of paper writing, the following video has made the rounds on the internet – and with the theme of this post – I’m reproducing it here. Computer Science graduate student Timothy Weninger recently submitted a paper to a conference and created a video of his writing process. The following short documentary film (world cat link) was produced by Pennsylvania’s Wild Resource Conservation Program and Commonwealth Media Services to highlight the role and social impacts that forest fungi have in the state of Pennsylvania. Since I’m located here and have some friends in the video, I thought I make it available to you for your viewing pleasure. Sorry for the lack of posts as of late, I’ve been a little swamped lately with writing and researching; unfortunately this blog has to suffer sometimes. I don’t have time to write a complete post right now – maybe soon in the future – but I’ve been closely following the cases of fungal meningitis derived from contaminated injections of the steroid methylprednisolone acetate. Looks like the main culprit is Exserohilum rostratum, although one person has been infected with a species of Aspergillus. Both of these fungi are extremely common in soils and are plant pathogens. Here’s some links from the CDC on the current infections: As of today, October 12th, the number of infections have been reported from numerous states:
Here’s a quick informational video on fungal meningitis: Here are some links to news articles published over the few weeks:
The video below is a little on the cheesy side, but it’s an interesting take on the making of a baseball bat from White Ash trees. I thought I would post it to you in honor of the professional baseball postseason in the United States right now. Ash trees across the Eastern United States, and particularly in Pennsylvania, are quickly being destroyed by the Emerald Ash Borer, an invasive beetle which spreads fungal infections from tree to tree, so many baseball bat manufacturers are moving to using Sugar Maple. There is a difference between the wood structure (i.e. cell wall morphology) between Ash and Maple and these slight differences in the wood grain effect how the ball is hit and how far it goes or how much control a batter has over where a ball is hit; at least some players tend to prefer one type of wood over another. I returned more than a week ago from Titus Brown’s two-week “Next Generation Sequence Data Analysis Workshop” at Michigan State University’s Kellogg Biological Station on Gull Lake in Hickory Corners. There’s really so much to say about this course and I can’t quite possibly cover it all here. I’m also still processing it all in my head and will probably be doing this for quite some time.
The course was a rigorous two-week workshop on current “next-generation” sequencing technologies and methods for data analysis. You could describe it as an advanced bioinformatics boot camp – exercises focused on text manipulation and data processing at the command line, Python scripting, and statistical analysis using the R language. You can find more information about the course, including all the tutorials, at Titus’s ANGUS website.
Titus, Ian Dworkin, and Istvan Albert instructed this intensive workshop – which sometimes consisted of ten hours of lectures and exercises a day. Guest speakers/lecturers included Corbin Jones (Sequencing technologies and data analysis), Erich Schwarz (Genome Assembly and WormBase), and Julian Catchen (RAD sequencing and the Stacks program for population genetics from next-generation sequencing data). We implemented Amazon Web Services (AWS) to create virtual UNIX machines. This standardized our exercises and also conveniently made the course equal opportunity for users of all operating systems. Course participants could use the virtual machines for the workshop tutorials or to begin analysis of their own data – the only requirement was to bring a laptop to access the internet. Amazon provided a learning grant to the instructors for all the course participants to use their Elastic Cloud Computing (EC2) service for tutorials and data analysis. I can see lots of benefits to both teaching and conducting research using disk images housed in the cloud. One such benefit is that all the students in the course – as well as anyone, for example, who might want to replicate your publication data analyses – can use an identical disk image you provide. This eliminates any issues a user may experience from differences in operating systems, program dependencies, and processing capabilities.
The UNIX–based workshop participants (who were using Mac OS, Fedora, and Ubuntu) were able to ssh using their terminals while the DOS users used PUTTY to login into AWS. The command line was the focus of the course – obviously this is the way that programmers and bioinformaticians do things and this workshop was a confidence building crash course at the command prompt. Also relying on just the command line helped reduce band-width as we had close to 30 laptops using the wireless connection in the room. The Python workshop exercises were implemented using the newest version of iPython notebook, a platform for utilizing the iPython toolkit as a browser-based notebook remotely from our EC2 instances. While there were minor hic-cups from the iPython Notebook platform (see Titus’s blog post), I was extremely impressed with the power of programming in python from this interface, so much that I immediately tried installing iPython notebook on my computer (and when I had some issues with matplotlib dependencies in my native installation, I then opted for the educational Enthought version). Especially for my level of proficiency with programming in Python, this platform is fantastic for the interactive in-line visualization, the handiness and speed of de-bugging line-by-line, and the overall ease of use – it just makes me want to be programming in python. I’ve already spent more time programming in Python in the short time I’ve returned from the course than I have prior to the course.
The workshop also focused on the statistical programming language R to analyze and plot RNA-Seq based data from Illumina sequencing. We focused on using R at the command line, but I personally have used R in the RStudio platform for a few months now and would recommend this interface. In addition to Python, the R language and all the great add-on packages are amazing for graphical representation of data. We spent a couple of afternoons working on raw text manipulation using awk (see bioawk!), sed, and other UNIX commands. One of my favorite nights was when the instructors went to the computer to use tools they had never used before, with scripting and command line help from the other instructors.
Probably the best aspect of the course was the intimacy and interactions of all the students, instructors, and teaching assistants. We basically were together as a group everyday – daily from breakfast at 7 am to midnight talks by the campfire – for two solid weeks. All the participants in the course came from such different biological backgrounds, but we all had a desire to use sequencing data to address our research questions. We thought and laughed and debated and problem solved and bonded with each other and played lots of volleyball. It, with all seriousness, was two of the best weeks of my life. UPDATE: Check out fellow workshop participant Wayne Decatur‘s daily blog (and see also Proteopedia) on the workshop for more info!
I’ve already briefly mentioned initiatives in the past year to try to restrict access to tax-payed funded research. I’d like to bring to your attention a new bill, called the Federal Research Public Access Act, seeks to establish embargo limits and require that the proceedings from all tax-payer funded research is available to all people. The following statement comes from the blog Why Evolution Is True:
You can sign the Federal Research Public Access Act Petition Here. Many of you know that I am located in Pennsylvania, but you may not be aware that the state tree of Pennsylvania is the Eastern Hemlock (Tsuga canadensis). Hemlock is not high on the list of valuable trees – the wood is moderately important in the pulp/paper and woodworking industries and it was once highly valued for tannins optimal for leather treatment. As a symbol for the state of Pennsylvania and for its ecosystem services – which include being a carbon sink, habitat for wildlife, and foundation for ecosystem water retention and purification – the tree is extremely important.
When I was on the West Coast of the US working with the Forest Service, we frequently came across a native Woolly Adelgid, which occupies the Pacific rim. Adelgids were only first identified on Eastern Hemlocks in 1951 near Richmond, Virginia, probably introduced from nursery stock –like many other invasive species. Using phylogenetic techniques researchers have identified that the Hemlock Woolly Adelgid populations introduced in the Eastern US trace to those from Southern Japan, not from the Pacific Northwest of the US.
One report in a recent meeting proceedings described five genera, which included Lactarius (16 species), Amanita (13 species), Russula (six species), Tricholoma (four species), and Cortinarius (four species), that were all collected in large mono-dominant Eastern Hemlock forests. Whether or not these fungi are obligate symbionts of Eastern Hemlock have yet to be determined, but that list is a start, nonetheless. I have been collecting under Hemlock in one form or another for about 15 years –not a long period of time I admit – but I have been hard pressed to find some of these fungi in the same locations in recent years. These mushrooms seemed common in past years in some specific locations, but I haven’t collected Lactarius subpurpureus for many years now. I have observed Hemlock Woolly Adelgid in all of these locations. Trees that have insect infestations do not have extra photosynthate to provide to the fungal symbionts. A lack of carbon for the fungus should translate into a lack of, or at least lessened, reproductive fruiting. An opposing argument is that trees that are losing photosynthate are more reliant on symbionts for nutrient uptake to compensate for nutrient loss, so there would be a greater reliance on, and therefore more frequently observed, mycorrhizal roots.
This recent public interest in the demise of Eastern Hemlock has again kick-started my thinking about fungi associated obligately with Hemlock. Amateur mycological and botanical societies could play a huge role in documenting species presence at forays and weekend gathering, as well as playing a leading role in establishing multi-year surveys of hemlock fungal symbionts. Would anyone like to provide any input here? Are there resources that I am unaware of that are provided by amateur scientists? Would anyone like to start a citizen science brigade with me to survey in and around Eastern Hemlock for fungi (particularly Lactarius subpurpureus)?
UPDATE: I have received a few questions about the photos posted here. If you click on a photo, the link will take you to the source of the photo. The two photos of the Hemlock Wooly Adelgid infestations on Eastern Hemlock (the photo where I am showing you the underside of the hemlock branch and the photo just about this comment showing the top portion of the branch) were taken from a tree right outside my office on the campus of Penn State. Some of these trees have been sprayed with a pesticide (not sure which one) in previous years, but the Hemlock Woolly Adelgid infestations have continued. The future of these campus trees is uncertain. Check out the re-blog on the great site: The Hyphal Tip!
I really enjoyed this video assembled from time-lapse photography of plant growth and flower opening. Now would someone do one for fungi?
I’m sure you’re aware of the recently proposed (and three page!) Research Works Act (Bill H.R. 3699) that has been introduced in the House of Representatives here in the US? If not, then you should read the bill, and then most especially read: 1. An Op-Ed piece ’Research Bought, Then Paid For‘ in today’s New York Times from Michael Eisen. See also this post from Michael Eisen’s Blog. 2. A post in the Scientific American Blogs called ‘Scientists, Fight For Access!‘ written by Kevin Zelnio (Twitter & Blog). 3. A series of posts on the issue of public access to publicly funded research from Jonathan Eisen’s Blog, and see ‘Scientists Embrace Openness’ through the Journal Science.
In yesterday’s New York Times is a nice opinion piece from Ian Lipkin on real life and real life infectious outbreaks. You should read it. Here’s an interesting short film on the “viral” marketing of the movie Contagion. Obviously, it’s not viral, but bacterial and fungal marketing. I haven’t seen the movie, so I can’t endorse it one way or another, but I will say Steven Soderburgh has a pretty great track record when it comes to movies. The above video shows a fascinating way to advertise this movie to audiences (See Jonathan Eisen’s blog post on the subject here). The recently established website extention.org is a agricultural cooperative extention collective of 74 land grant universities which seeks to serve the public though education and service.
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I'm a biologist with broad interests, focused mainly on fungal and plant genomics and understanding how these two diverse groups of organisms interact with each other. I am mainly interested in the mycorrhizal fungal symbiosis, the meta-taxonomic and metagenomic assessment of plant-associated environments, and the dissection of interactions of fungus and plant: from cell-to-cell contact to the modification of gene expression resulting from these communications. I typically use laboratory techniques and field studies addressing more specific questions using controlled experiments. I have increasingly turned to bioinformatic techniques to handle the analysis of genomic data so I spend a lot of time in front of a computer.
You can read more about me and my interests at my website. Please get in touch with me by emailing me at josh...@gmail.com |
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One Hundred Important Questions Facing Plant Science Research
The October issue of the journal New Phytologist contains a commentary article by a group of plant scientists who conducted a survey to identify the 100 most pressing scientific questions facing plant biologists. The article “One Hundred Important Questions Facing Plant Science Research” is very thought provoking.
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