Naohisa Goto edited this page Jun 14, 2016 · 1 revision

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) <- 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?

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