Hi! A few weeks ago I asked for teaching material for an introductory course in bioinformatics on evoldir. Please find the suggestions/answers below. If you want to use any of the suggested material/links, please give the original authors/sources credit and for some of the material you may need to contact them to clarify under which terms you are allowed to use the material. I have not included email addresses here to avoid that contributors receive a lot of spam. However, the affilations and the names are given so that it should be easy enough to find and contact people if needed. Thanks a lot to all of you who have responded to my inquiry. It is greatly appreciated! Cornelya Answers: 1. Ian Dworkin (Michigan State University) Cornelya, I saw your post of EvolDir. I have a couple of suggestions. My colleague Titus Brown and I have been teaching a short course (2 week workshop) on the analysis of next generation sequence data. We post all of the materials online for free, including tutorials and some lectures. http://ged.msu.edu/angus/tutorials-2011/ http://ged.msu.edu/angus/tutorials-2012/ We use the Amazon EC2 cloud computing system to run everything (so students do not need any special computer). While you normally have to pay, if you contact Amazon they usually provide 100$ educational credit for EC2 for each student. In 2010 & 2011 we primarily used unix shell scripting and python, while this past summer Titus integrated a fair bit of the ipython notebook framework (which I would not suggest unless you have some familiarity with it. It is great for teaching, but the teacher needs a fair bit of background). I also highly recommend teaching the tutorials within the context of very simple scripting/programming. This could all be unix shell scripting or in a language like python or R (or perl if that is what you know). The problem with galaxy and other systems is that the point and click model does not real provide any extra added value (like the basics of programming), and since the shelf life of such programs is not so long (3-4 years usually), what is learned can become obsolete quickly. I am not sure what background you have though, so it clearly depends on this. I am mostly involved with the more statistical side of bioinformatics for expression data and genome mapping, but I can also make some suggestions for materials if you like. btw.. I am a Trent alum, graduated in 1997. I worked really closely with Carolyn Kapron, Michael Berrill and Jim Sutcliffe. If you see any of them, say hi for me ( I saw them all 2 years ago at Michael's retirement party). Cheers Ian 2. Lourdes Pena-Castillo (Memorial University of New Foundland) Hi Cornelya, I am teaching an introductory course in bioinformatics this fall at Memorial University so I have some teaching material. I am attaching my slides and one lab for the first two topics in your list. For Galaxy I selected a couple of tutorials available on the web starting with Galaxy 101. In the slides I removed those figures which can't be distributed without violating copyright, but I left the references so you could get them if you wish to. In the slides U.B. refers to the textbook Understanding Bioinformatics published by Garland Science (which is the textbook I use). Figures without a reference are my own figures and you can use those and my slides under the CC BY-NC-SA 3.0 license (http://creativecommons.org/licenses/by-nc-sa/3.0/). Hope you find this material useful. All the best, Lourdes 3. Sarah Stockwell (Cornell University) Have you tried the ABLE labs? Looks like they have 17 bioinformatics labs in their archive: http://www.ableweb.org/volumes/archive.htm Cheers, --Sarah 4. José Lourenço (Oxford University) Dear Cornelya, I have just read a twit with your request for teaching material. Maybe you should check this page at the University of Oxford: http://www.stats.ox.ac.uk/research/genome/teaching5. Pedro Fernandes (Inst. Gulbenkian de Ciência, Oeiras, PT) Hi Cornelya There are various materials that you can freely download from the BTN website www.biotnet.org Please let me know if you have difficulties or need more. I have additional stuff, on those and other subjects, but the BTN ones have been checked and rated. Maybe better to start at BTN. My materials are often interdependent, therefore not readily usable as standalone courses. Cheers Pedro 6. Donald Forsdyke (Queen's University) These links may be of help: http://post.queensu.ca/~forsdyke/videolectures.htm http://post.queensu.ca/~forsdyke/book05.htm 7. Joseph Bielawski (Dalhousie University) Hi Cornelya, The workshop on molecular evolution at the MBL has many on-line activities. Some are easier than others to use outside of the workshop, but they are available to anyone. This workshop covers items 1-3 on your list below. Here is the main page: https://molevol.mbl.edu/wiki/index.php/Main_Page This is the schedule page: https://molevol.mbl.edu/wiki/index.php/Schedule Links on the schedule page should bring you to the pages that have tutorials etc. ALIGNMENT LAB: https://molevol.mbl.edu/wiki/index.php/MSA_lab FASTA/BLAST LAB: http://fasta.bioch.virginia.edu/mol_evol/ PAML LAB: http://myweb.dal.ca/js551958/PAML_lab/lab.html There are several phylogenetics labs but the vary in degree of accessibility and practicality. There is alos a European workshop with on-line resources: http://evomics.org/workshops/workshop-on-molecular-evolution/2013-evolution-cesky-krumlov/ Good luck, Joe 8. Brian Golding (McMaster University) my notes are available online at http://helix.mcmaster.ca/3S03.pdf. I also have slides but they are in LaTeX (Beamer) if you would like them. Brian 9. Mike Bunce (Murdoch University/Western Australia) Hi Cornelya, I would look seriously at the geneious program - I wrote some tutes for this (they are available on their website).... there is a free version and a paid version. The company is usually very good with teaching licences with regards to cost). http://www.geneious.com/web/geneious/tutorials good luck! cheers Mike 10. Steve M. Thompson (Florida State University) Cornelya - My stuff's becoming dated, but it's still all available, and you are welcome to use any of it as long as you give me credit. See my home page below and use the side index to go to "Steve's FSU Intro' to Bioinfo'": http://www.bio.fsu.edu/~stevet/IntroBioInfo/Lab.html And if you dig around on that site, you'll find several lectures as well. Good luck! Cheers - Steve Cornelya FC Kluetsch, Ph.D. Trent University Biology Department Peterborough, ON K9J7B8 Phone 705-748-1011 ext. 6334 Fax 705-748-1003 E-mail: cornelyaklutsch@trentu.ca Cornelya Klutsch