Talk:HOWTOs

In 2009/3/19, we decided to translate BioPerl's HOWTOs into BioRuby. Below are discussion notes in 2009/3/19.

HOWTOs are narrative-based descriptions of BioPerl modules focusing more on a concept or a task than one specific module. BioPerl HOWTOs


 * Beginners HOWTO <- use bioruby tutorial (ask Pjotr to maybe add ideas from the bioperl one)
 * An introduction to BioPerl, including reading and writing sequence files, running and parsing BLAST, retrieving from databases, and more.


 * SeqIO HOWTO <- do, but with low priority
 * Sequence file I/O, with many script examples.


 * SearchIO HOWTO <- not now, but after NCBI-remote BLAST is completed
 * Parsing reports from sequence comparison programs like BLAST and writing custom reports.


 * Feature-Annotation HOWTO <- long; not highest priority; can maybe be shortened
 * Reading and writing detailed data associated with sequences.


 * SimpleWebAnalysis HOWTO <- high priority, but more work because from scratch; this is where bioruby can be very strong
 * Submitting sequence data to Web forms and retrieving results.


 * Flat Databases HOWTO <- lowest priority
 * Indexing local sequence files for fast retrieval.


 * PAML HOWTO <- skip
 * Using the PAML package using BioPerl.


 * OBDA Access HOWTO <- lowest priority, but should write bioSQL version
 * Using OBDA, a universal and customizable sequence retrieval system.


 * Trees HOWTO <- yep
 * Using BioPerl to manipulate phylogenetic trees.


 * PopGen/Perlymorphism HOWTO <- write wrapper for rsruby, and _then_ write the howto
 * Population genetics, molecular evolution, and BioPerl.


 * Graphics HOWTO <- first write Bio_Visualization
 * Creating beautiful graphics for sequence display and annotation.


 * Custom Glyphs HOWTO <- idem
 * Extend Bio::Graphics using custom glyphs (advanced).


 * Submit Patch HOWTO <- highest priority (refer to Jan's blog post)
 * The steps needed to get your modification to BioPerl into the code base.


 * Build Pipelines for Phylogenetic analyses HOWTO <- would be nice, but have to start from scratch
 * A framework for phylogenetic analyses from gene set to gene family to alignment to phylogenetic inference.


 * Writing tests for BioPerl modules HOWTO <- important, but have to start from scratch
 * A general guide on how to write BioPerl tests using Test::More.


 * Using EUtilities HOWTO <- nothing there, but we might write something on webservices
 * A guide on how to use Bio::DB::EUtilities for retrieving complex data and building customized data pipelines.


 * EUtilities Cookbook <- yes
 * Simple script examples using Bio::DB::EUtilities.


 * Getting Genomic Sequences HOWTO <- yes
 * Some examples of how to retrieve genomic sequences using Bioperl.

Candidate HOWTOs

 * BioSQL
 * manifest files (from next-gen sequencers) &lt;- write code first
 * combining lists? (extension to Set for biological uses)
 * using webservices (as a client)
 * storing data in database
 * how to manipulate structural information?

How is it possible to identified secondary structure/backbone with distance of 3 A around a ligand in 1E8W.pdb?