Article on Java modularity

Java 7 is out. Here's a good article explains some of the nice features.

InfoQ:Modular Java:What is it?

Data Analyst Job

Description
Description:

The bioinformatics department seeks an exceptionally talented and
motivated individual to assist with gene information curation and
database development, and provide data analysis supports for research
departments.

Responsibilities:

The successful candidate will perform regular data curation of the
in-house gene information databases. You will work with other
Bioinformatics scientists and programmers to identify needs and
opportunities in gene information integration and provide solutions.
The successful candidate will also work closely with lab scientists in
analyzing protein sequences, genomic structure and microarray data.
You will be encouraged to help design software for DNA and protein
sequence analysis and to pursue creative solutions to other tasks
commensurate with your experience and ability.

Requirements:

Applicants should possess a M.S. degree in bioinformatics, computer
science, or have equivalent experience. The successful candidate must
have strong programming experience in Java, Perl and database design.
Knowledge of R, and web application technologies is highly desirable.
You should have outstanding communication skills and the ability to
work independently and succeed in a complex, dynamic, team-oriented,
multi-disciplinary environment. You should be resourceful and pay
attention to details. Previous experience with biological databases
and sequence analysis are required.


DIVISION: Research
REQUISITION NUMBER: 08-1000025151 PROG ANALYST

R library som

Self-organizing maps for clustering, need large number of iterations.
A filtering function in the package,

filtering()

is very helpful to floor, ceil the input data table.

Corr

mantel.rtest {ade4},

This provides a comparison of two distance matrices.
Still looking for a good way of translating correlation to distance.

mahalanobis {stats}

Calculate the mahalanobis distance.

To calculate the mahalanobis distance require Cov estimate, and this can be done with either classic cov or robust cov estimate.

Procrustes Analysis

Procrustes analysis: procrustes() in vegan provides procrustes analysis, this package also provides functions for ordination and further information on that area is given in the Environmetrics task view. Generalised procrustes analysis via GPA() is available from FactoMineR.

clues package for clustering evaluation

clues contain the calculation of five different indexes when comparing two cluster/classifications.

adjustedRand(cl1, cl2, randMethod = c("Rand", "HA", "MA", "FM", "Jaccard"))

While the adjustedRandIndex from mclust can only compute for one.

ggplot2: Great plot libs

Just put up a post first. More details coming up soon.