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
Two upcoming meetings in the state of Massachusetts may be of interest to you, one of which I have already told you about.
The Plant Biology Graduate Program at the University of Massachusetts Amherst will be holding their 10th Annual Symposium in Plant Biology on Saturday October 6th, 2012. This year’s focus is pertinent to readers of Cyme & Cystidium — it’s titled “War or Peace? Interactions Between Plants and Microbes“. The symposium is free but you have to register to attend.
Those that know me know that I’ve got a thing for orchids. From my point of view, what’s not to like: they have exceptionally diverse morphology, have complicated natural histories, have equally diverse interactions with pollinating insects, and – most important for me – are obligate mycorrhizal formers with a wide array of fungal symbionts. I’m quite surprised we don’t have more scientists studying them.
The journal New Phytologist has already sponsored 30 symposia on plant biology – the 31st symposium has been announced and will be focused on orchids and their interactions with mycorrhizal fungi and insects. The goal of this meeting will be to bring together scientists studying orchids and advance the study of orchids and their symbiotic fungi and co-evolved insects. As someone who has attended in the past, I cannot place enough emphasis on how rewarding these New Phytologist symposia have been to me. There is plenty of time to register and apply for a travel grant.
This particular symposium will be held in conjunction with the 5th International Orchid Workshop this upcoming spring. Both meetings will be held back to back at very close locales in Italy.
I enjoy going to academic meetings and very frequently post information about upcoming meetings and symposia. Some people have recently asked me why I put so much emphasis on meeting information on the blog and others have asked how I decide which meetings to attend, including this recent comment. I go to meetings for many reasons – some of which I will cover here – but, specifically for me, the main reason I go to meetings is to interact with other scientists in my discipline.
I believe going to scientific meetings is a vital part of mastering how to communicate your research. The types of communication you have the opportunity to master can range from giving an oral presentation to hundreds (or perhaps thousands!) of other scientists to speaking with someone for 30 seconds in an elevator. Academic meetings give you an opportunity to master your communication skills.
Meetings are also great places to learn about the cutting edge of your research area. Often scientists will present their most recent findings prior to publication. You might be able to learn about new technologies or novel ways to analyze data before you read about them in publications. Often during the question and answer portion of talks, theories and controversial topics are discussed, with a debate in real time. I tend to return from meetings mentally energized with lots of new ideas to investigate and think about.
Meetings are great places to network and meet people in your research area. It’s easier to strike up a conversation or collaboration via email if you’ve met someone in person at a meeting. Also, if you are in academia, the people you speak with at meetings will likely be the ones who are reading your grant proposals and reviewing your manuscripts. Future job contacts and impromptu pre-interviews happen at meetings. Most importantly, there’s the added bonus of developing friendships with your fellow scientists.
Lastly, I enjoy traveling, so going to academic meetings is a way for me to mix business with pleasure, so to speak. I’ve gotten to see some truly beautiful places under the auspices of attending scientific meetings.
If you are a student or a post-doc – or have been asked to present a talk – there may often be registration discounts for meetings and symposia. You may be able to get a discount if you volunteer to help out at the registration desk or other planned events. You might also be asked to provide financial need. You should check with the meeting organizers as soon after the meeting is announced for these types of discounts.
When it comes to choosing a meeting to attend, I prefer smaller more intimate meetings, with a range of participants in the hundreds, and not thousands like you have a tendency to find at large meetings. Large meetings can be valuable, but I personally find that it’s more difficult to see attend all the talks you want to and to locate the people you want to speak with. I will often speak to people who have attended specific meetings in the past and ask them about their experiences.
Before going to a conference, I usually get an idea of which talks I would like to see and who I would like to speak with at the meeting. This can happen before I leave for a meeting if the conference booklet is posted online, but it typically happens right after I arrive at the registration desk. Some people prepare by bringing business cards, and although I haven’t used business cards, this could help people remember you after the meeting. You also want to prepare your “talk” – whether it’s for a speaking presentation, a poster presentation, or just speaking in the hallways or at a dinner of the meeting – you should be able to communicate your research clearly in many different formats.
During the meeting, I have different strategies depending on the meeting size and the types of talks. I try to pick the talks that are most relevant to my interests, but sometimes this leaves me running between sessions. This can be a great time to “bump” into someone you want to speak with, but you may also miss important talks this way too. Sometimes, particularly at the end of meetings when my mind is overwhelmed, I sit through entire sessions just to see if there is something interesting in a disparate research area that can be applied to my research. I’ve gotten some great ideas listening to talks I thought would not be pertinent to my research. I take notes and make sure to write down literature to look up and read when I get home from the meeting.
After the meeting is over it’s important to follow up with those you have started collaborations with and those whose research papers you want to read. If you’ve taken notes, review them and think about posting them to a public forum, like a blog, so that others can share in on your meeting experience.
Here’s three upcoming mycological meetings which may be of interest to you:
As part of the 10th European Conference on Nitrogen Fixation held in Munich a satellite meeting called the 1st Molecular Mycorrhiza Meeting will be held over two days: Thursday, September 6th to Friday, September 7th. The list of speakers is pretty amazing if (like me), mycorrhizae is your thing. See here for registration and see here for abstract submission.
The British Mycological Society will be having a meeting for Fungal Interactions on September 3rd to 6th, 2012, in Alicante, Spain. The sessions look to be diversely balanced and focused on fungal interactions with all types of organisms. See here for the preliminary meeting program and to register see here.
Finally, if you live in the New England area of North America (or don’t mind the travel) the first regional meeting of mycologists from the state of Massachusetts and the surround area will be held on October, 27th 2012. It will be aptly named MassMyco. The meeting will be held at Clark University and hosted by the Hibbett Lab. I love these small regional meetings, so perhaps I’ll try to make the trek for this one. Registration is not open yet, but check back soon.
Perhaps because I study mycorrhizae the ICOM meetings have a special place in my heart, so I’m excited to tell you that the next ICOM — the 7th International Conference on Mycorrhiza (ICOM7) — is open for registration. The meeting will be held in New Dehli in January of 2013. Here is the call for abstracts. Here’s some more information from the meeting website:
This meeting, “Aboveground-belowground interactions: technologies and new approaches” looks to be an interesting one. The meeting is co-sponsored by three British organizations — the British Ecological Society, the Biochemical Society, and the Society for Experimental biology — and will be held at Charles Darwin House, London, from October 8th to 10th, 2012.
Here’s more information from the meeting website:
The IUFRO (International Union of Forest Research Organizations) working group has organized the “Genetics of Fagaceae & Nothofagaceae” meeting to be held in Bordeaux, France from October 9th to 12th, 2012.
This meeting will build upon a successful “Genomics of Forest and Ecosystem Health in the Fagaceae (Beech Family)” meeting held in North Carolina Research Triangle Park in 2009.
The aim of this international conference is to present new scientific findings in the area of genetics and genomics of species within the Fagaceae and Nothofagaceae.
Registration is open.
I haven’t been sure what to make of the BGI/ICG series of meetings thus far (see here and here), but at least the first foray into the Americas – The First International Conference of Genomics in the Americas, to be held September 27th to 28th 2012 in Philadelphia – looks to be interesting. There is a good group of speakers lined up for this meeting, even though the BGI have rightfully taken some criticism for skewing the speaker list a little on the male-side of the genomics spectrum. Registration is open now.
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.
Last year I told you about two short courses for using Blast2Go for automated functional annotation. These courses will again be held this year. Here’s information about this year’s courses:
Galaxy is a free web-based platform for bioinformatics and data mining initiated by some of my colleagues at Penn State’s Center for Bioinformatics and Genomics. The are Galaxy platforms popping up all over the place: JGI, JCVI, and you can run it on your own desktop or computer cluster. In case you’d like to gain hands on experience using the platform or want to learn more about setting up your own Galaxy platform you can attend the 2012 Galaxy Workshop and Community Conference:
I’ve been having some issues with posts because my server was hacked into again. I don’t know what is so interesting to anyone trying to break in and leave malware. So, I apologize. I’m getting back into the swing of things and trying to fix some problems after a couple weeks of travel.
I recently returned from the 7th Annual DOE-Joint Genome Institute User Meeting on the Genomics of Energy and the Environment. The keynote address by Carl Zimmer has been posted online:
This EMBO Practical Course in Plant-Microbe Interactions looks like a great short course. The course takes place at the The Sainsbury Laboratory, Norwich Research Park, from the 18th until the 19th of June 2012. Registration is open.
If I was still an undergraduate student I would certainly like to take this course in genomics and computational biology at Oxford. Please pass this information on to a deserving applicant.
The 18th Congress of the International Society for Human and Animal Mycology (ISHAM 2012) will be held in Berlin, Germany, from June 11th to 15th, 2012.
Copyright © 2009-2013 Cyme & Cystidium - All Rights Reserved
Powered by WordPress & Atahualpa