jeffb's blog

COGs program is no longer supported

Please note that the COGs program is no longer supported.
All that we have for COG is here: http://www.ncbi.nlm.nih.gov/COG/ & ftp://ftp.ncbi.nih.gov/pub/COG/ . 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. http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters & ftp://ftp.ncbi.nih.gov/genomes/CLUSTERS/

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

Predictive Modeling of Metagenomes

Dan Knights
University of Colorado Boulder
Department of Computer Science

Tuesday, February 28, 2012
4:00pm
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 - http://bodegaphylo.wikispot.org/ 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.

doodle: http://www.doodle.com/m36gmg8e3me55xy9
mailing list: http://tinyurl.com/sourceform
-Michael Rosario
http://tinyurl.com/oebsource

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. https://bcrc.bio.umass.edu/courses/spring2012/micbio/micbio660/sites/def...

Bruno Strasser also gave an interesting historical talk for the 25th anniversary of GenBank - http://eutils.ncbi.nih.gov/About/genbank25/data/day1/strasser/

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 (https://depace.med.harvard.edu/), 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.

Advanced Systems Ecology, ECO 777

This course covers various methods in modeling in general. It will focus on using R to help parameterize a models. We can embed a model in a log-likelihood function and use R routines (such as optim) to find the most likely parameters given the data! There will be a meeting on Tuesday at 3PM in Room 312B Holdsworth to pick a time and place to meet. - Instructor Jack Finn

Top-down genomics: generating testable mechanistic hypotheses from genome-wide studies

A research seminar entitled: “Top-down genomics: generating testable mechanistic hypotheses from genome-wide studies.” will be presented by Dr. Aaron J. Mackey, Assistant Professor of Public Health Science and Biochemistry & Molecular Genetics, University of Virginia
Wed Feb 1 - Integrated Science Building Room 221 - 4-5pm

Welcome

Welcome to Bioinformatics and Genomics!

We will first meet on Tuesday Jan. 24 at 8am in Skinner 201.