Galaxy Exercises


I was wondering which files I should upload for the Galaxy Exercises...the ".bam" files are too fat.
Anyone knows?

COGs program is no longer supported

Please note that the COGs program is no longer supported.
All that we have for COG is here: & . Please note that neither the COGs website/ftp site, nor the data files have been updated in many, many years and will not be. We can’t supply any additional files or updates.

We strongly recommend that you take a look at the Protein Clusters database which is a newer and supported version of bacterial function domain annotations. &

However, this seems to be the same clusters that come with the CDD download.


To fix problem with R:

Open C: drive
Open Program Files
Find the R file
Right click on it and select properties
Once in the R properties click on the security tab
To change permission click on the edit button
Select the first listed user and check the box for full control
Do this for each user listed
Click apply

No class Tuesday 2/28/12

Just a reminder that class tomorrow is cancelled. (If I have the wrong week, hopefully someone will let me know!)

Predictive Modeling of Metagenomes

Dan Knights
University of Colorado Boulder
Department of Computer Science

Tuesday, February 28, 2012
Computer Science Building, Room 150 and 151
Faculty Host: Andrew McCallum

"Predictive Modeling of Metagenomes"

Human-associated microbial communities have been implicated in a variety of chronic diseases, including inflammatory bowel diseases, obesity, and autoimmune disorders like diabetes. Environmental communities are also important for bioconversion of waste products in biofuel production. However, microbiomes are highly complex systems involving mutualism and competition between many constituent organisms, and a variety of fundamental and interesting computational challenges remain in the modeling of pathogenicity and community-wide response to perturbations. In this talk I will discuss several computational and statistical approaches to predictive modeling of microbiome behavior using high-throughput metagenomic and transcriptomic sequencing data, including models that leverage biological structures such as phylogenies and gene ontologies to extract features and constrain model complexity.

Reception in atrium at 3:40pm

2012 Bodega Applied Phylogenetics Workshop

Applications are being accepted for the 2012 Bodega Applied Phylogenetics Workshop - Workshops and courses like this are great for professional development. They often target advanced graduate students, postdocs and faculty.

OEB's R group (SOURCE)

OEB's R group (SOURCE) is ready to kick off a new semester of R programming and learning! We welcome all levels of R users who want to learn more about implementing R in research. This semester, we invite our SOURCE members to bring in their own programming problems to the meetings. So if you've ever wanted to do basics statistics, write your own random walk function, model and simulate a game of table tennis using R, or would like FREE programming help on your project please consider joining us this semester! Our first few sessions will involve a review of last semester's material by deconstructing R scripts as a group, so please try to make the first few sessions if you would like a refresher in R coding.

mailing list:
-Michael Rosario

Next week's reading on Margaret Dayhoff - "Father and Mother of Bioinformatics"

Reading for next Tuesday: Collecting, comparing, and computing sequences: the making of Margaret O. Dayhoff's Atlas of Protein Sequence and Structure, 1954-1965. Strasser BJ. J Hist Biol. 2010 Winter;43(4):623-60.

Bruno Strasser also gave an interesting historical talk for the 25th anniversary of GenBank -

Visualizing large transcriptional networks

Angela DePace is an Asst. Prof in the Systems Bio Dept at Harvard Med and is coming to give the MCB seminar on Feb 7th at 4pm in ISB 221. Her work principally concerns how transcriptional networks are regulated on a global scale in Drosophila (, but is also generally interested in how to visualize large sets of scientific data in a constructive fashion (she's actually co-authored a book on this with Felice Frankel (MIT)).

Applications of Genomics

Li-Jun Ma is offering a course on Applications of Genomics that meets MF 2:30-3:20 in the CNS Greenhouse classroom, rm 103. The course will focus on the analysis of next generation sequencing data. There is some overlap with our course, but in a healthy way that is nonredundant. It is fine if you are taking both courses and to design a project that works for both course (if it is also ok with Li-Jun). Li-Jun will be giving a research seminar for our course and I will be giving for their course.