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Archive of entries posted on November 2011

New: The “Talk” in “GeneTalk”

Last week, I worked on the “Talk” aspect of “GeneTalk”. Now, you can send private messages to other GeneTalk users. You’ll find your messages with the ‘envelope’ in the upper right corner or in the “My Profile” menu. No, we do not want to replace Googlemail , the main purpose for messages is for sharing [...]

New GeneTalk features

This week, there are basically two big improvements to GeneTalk. First, we got a server upgrade that makes the overall performance a little bit faster (and our provider complains about the large database… however). Also, there is a speedup in the gene set filtering that improves the performance even more. Second, the most important new [...]

Expensive function calls

I know, function calls are not ‘for free’ concerning runtime. This week I discovered that they can be quite expensive. I started with something like the following: Model “BigCollection” implements something like def test_something   big_collection.each do |small_collection|     small_collection.test_something Model “SmallCollection” implements something like def test_something   small_collection.each do |item|     item.test_something And the controller did inputfile.each do [...]

New features

Apart from a dozen minor bug fixes (including the ‘no valid email’ message when you try to log in with your user name(*) ) and layout improvements, I have completely redesigned the “gene sets”. Now, you can simply choose genes/chromosomal regions by gene name, entrez id or ccds id. Still you can use a set of [...]

how to edit gene sets

A customized gene set can be used to filter your VCF file for instance for variants that lie in the coding regions of genes that are of special interest to you. If there is consensus about the coding regions of a gene by the community (for us this means a CCDS ID exists), than it [...]

Features so far

The first features of GeneTalk are implemented. So far, you can Upload your variant sequence data as VCF file. Edit your linkage intervals and gene set filters. A linkage interval filter is simply a chromosomal region defined by its chromosome, start and end position. A gene set filter restricts your analysis to the exons of [...]

GeneTalk Blog Launched

Welcome to the GeneTalk blog. Here you will find everything concerning GeneTalk: Information about new releases, new features, tutorials… Have fun!