Comments for Biorelated

Comment on A ruby class for screen-scraping plasmodb database by George

George — Sat, 28 Apr 2012 00:12:27 +0000

Though they are not intuitive to use. Would be cool to have a Ruby, Perl and Python wrapper to retrieve data easily. Why not have REST interfaces and data retrieval via json. That would be cool as well. Maybe I need to go through the available services again and see what can be automated. :)

Comment on A ruby class for screen-scraping plasmodb database by Omar Harb

Omar Harb — Fri, 27 Apr 2012 03:20:05 +0000

PlasmoDB has Web services (although they weren’t available in 2009 when you wrote this post :)). You can access them here:
http://plasmodb.org/plasmo/serviceList.jsp

Comment on Converting sequence data from csv to fasta format by rzenka

rzenka — Sat, 25 Feb 2012 22:43:47 +0000

I wrote a little Excel plugin that loads .fasta into Excel and can save as well. It is designed for relatively short protein sequences (splits them into two fields if too long, like in the case of titin). My colleagues love it. I will try to make it more generic and release it publicly.

Comment on My first Bioruby plugin calculates the isoelectric point of a protein by George

George — Sat, 28 Jan 2012 06:27:28 +0000

Thanks for pointing it out! I edited the post to reflect the changes! :)

Comment on My first Bioruby plugin calculates the isoelectric point of a protein by Ben Woodcroft

Ben Woodcroft — Fri, 27 Jan 2012 22:17:02 +0000

Sure – just wanted to lessen confusion. But you did change it anyway, didn’t you!

Comment on My first Bioruby plugin calculates the isoelectric point of a protein by George

George — Fri, 27 Jan 2012 18:01:30 +0000

The code in this blog post was posted a year ago and I had not updated the post. for more accurate update please follow the github repo README.

Comment on My first Bioruby plugin calculates the isoelectric point of a protein by Ben Woodcroft

Ben Woodcroft — Fri, 27 Jan 2012 00:40:26 +0000

Cool, good luck with that. I noticed just then that the code you have above Bio::Sequence::AA#calculate_iep should be Bio::Sequence::AA#isoelectric_point by the way.

Comment on My first Bioruby plugin calculates the isoelectric point of a protein by George

George — Thu, 26 Jan 2012 05:13:50 +0000

Thanks Ben! and am glad that the plugin is useful. There is no formal publication for the plugin yet, though am planning to prepare one. The only reference so far is the github repository URL(https://github.com/georgeG/bioruby-isoelectric_point)

Comment on My first Bioruby plugin calculates the isoelectric point of a protein by Ben Woodcroft

Ben Woodcroft — Thu, 26 Jan 2012 04:21:00 +0000

Good stuff. I’m likely to use this in a publication – is there a recommended reference?

Comment on Converting sequence data from csv to fasta format by biorelated

biorelated — Thu, 01 Sep 2011 05:53:31 +0000

You would run the script all at once. you would change the name of the file, i.e the path to the csv file and the name of the new fasta file. seq_name_col is the column number with the names of the sequences and the seq_data_col is the column number for the sequences.