My MacBook Pro hardware configuration

If you run TopHat (rna-seq aligner) or any other program that can run on a multi-core system, it is useful to know the number of cores in the system. My MacBook pro revealed to me that it is a single processor but 2 core, which can be specified on the TopHat command line: 

Model Name:    MacBook Pro
  Model Identifier:    MacBookPro6,2
  Processor Name:    Intel Core i5
  Processor Speed:    2.4 GHz
  Number Of Processors:    1
  Total Number Of Cores:    2
  L2 Cache (per core):    256 KB
  L3 Cache:    3 MB
  Memory:    4 GB
  Processor Interconnect Speed:    4.8 GT/s
  Boot ROM Version:    MBP61.0057.B0C
  SMC Version (system):    1.58f16
  Serial Number (system):    ()
  Hardware UUID:    ()
  Sudden Motion Sensor:
  State:    Enabled

R for Mac OS X: new version on 3rd Oct

Universal R 2.13.2 released on 2011/10/03

This binary distribution of R and the GUI supports PowerPC (32-bit) and Intel (32-bit and 64-bit) based Macs on Mac OS X 10.5 (Leopard), 10.6 (Snow Leopard) and 10.7 (Lion). It is possibly the last distribution supporting Mac OS X 10.5 (Leopard) and PowerPC architecture. This update is highly recommended to R.app GUI users on Mac OS X 10.7 (Lion) since it works around several issues in Lion.
Read more at http://cran.r-project.org/bin/macosx/

scp vs sftp

On Unix hosts, we have an option of using sftp or scp for secure file transfers. Both encrypt the password as well as the files being transferred. However, I learnt that the difference between the two lies in SSH support.  sftp only works with servers running ssh version 2, while scp will work with both ssh version 1 and ssh version 2.

seqMINER: good tool for ChIP-seq data visualization

A java tool that runs in Win/Linux/MacOSX that lets you upload alignments from chIP-seq datasets to view profiles around TSS or chosen genome co-ordinates:

Paper: http://www.ncbi.nlm.nih.gov/pubmed/21177645?dopt=Abstract

Software: http://bips.u-strasbg.fr/seqminer/tiki-index.php

Beyond the Genome 2011: Day 3: Microbiome sequencing

The focus was on large scale microbial sequencing efforts under the NIH microbiome grant. Presentations by JCVI, NIAID, Scripps.

Beyond the Genome 2011: Day 2: Exome sequencing

A complete overview of all challenges, achievements, case studies and future plans on using exome sequencing.

Beyond the Genome 2011: Day 1: Cancer Genomics

Today's presentations highlighted how challenging it is to study the cancer genome. Also highlighted the need for bioinformaticians to get a grip on human genetics in order to correctly interpret genomic datasets, specially sequencing results.

2011 NAR Database Summary Paper Category List

Nucleotide Sequence Databases

RNA sequence databases

Protein sequence databases

Structure Databases

Genomics Databases (non-vertebrate)

Metabolic and Signaling Pathways

Human and other Vertebrate Genomes

Human Genes and Diseases

Microarray Data and other Gene Expression Databases

Proteomics Resources

Other Molecular Biology Databases

Organelle databases

Plant databases

Immunological databases

Beyond the Genome 2011: Workshop

Informatics workshop:
Cutting edge presentations by Mike Schatz, Ben Langmead and James Taylor, highlighting implementations of reproducible bionformatics workflows on the Amazon EC2 cloud computing platform.