Go Back   SEQanswers > Site News > Wiki Discussion

Similar Threads
Thread Thread Starter Forum Replies Last Post
FastQC,kmer content, per base sequence content: is this good enough mgg Bioinformatics 10 11-06-2013 11:45 PM
Obtaining unique sequence tag file from fastQ format ramadatta.88 Introductions 0 09-26-2011 02:25 AM
how do I output the CS tag for BWA align of SOLID reads? KevinLam Bioinformatics 16 07-23-2011 11:06 PM
Bowtie MD tag format reference mendl7 Bioinformatics 2 02-23-2011 02:47 PM
SAM format NH tag question blu78 Bioinformatics 0 05-12-2010 06:07 AM

Thread Tools
Old 04-28-2010, 02:07 PM   #1
Location: Columbus, OH

Join Date: Feb 2009
Posts: 11
Default output format content & tag mayhem

(Eric already got this question and wanted me to post it here as well)

1. Currently, when people click on a output format, they see an empty page (at least the ones i checked). I think it will be nice to create a form for output format and allow people to paste 5-10 lines of sample and then explain each column in format.

2. Tagging of operating system, programming language, method and domain is great but I think it needs standardization (check out MacOSX variants).
I was trying to clean it up by updating each entry one by one. it's very slow, if there's an alternative interface (commandline, perl,..) to do this faster, I can do the cleanup..
alperyilmaz is offline   Reply With Quote
Old 05-02-2010, 03:31 PM   #2
wiki wiki
Location: Cambridge, England

Join Date: Jul 2008
Posts: 266

Yup, it helps to get wiki questions in one place here, if only to start getting a community together :-)

To answer point 1)

I set it up so that output and input format *should* take you to a form to describe the format (for example, try looking at the sam or fasta formats, where the form was used to create the page). I'm not sure why you are being taken to an empty page, so I'll have a look. I think it's a great idea to have forms to describe formats. If we get the ball rolling on this, SEQwiki could quickly be the biggest file format resource for bioinformatics on the web!

To answer point 2)

About cleaning up the tags... I know what you mean! My long term plan is to integrate the wiki with the EMBRACE software ontology (or similar), to provide a strict, community developed controlled vocabulary for describing bioinformatics software. I've been talking with Jon Ison and some people from 'BioCatalogue' about that. Unfortunately I haven't got round to that yet :-/

The next best thing is to decide how the tags should be used, and document that better on the form.

I noticed the 'MacOSX' heterogeneity too... wherever you think it appropriate, we can make the free text entries into drop down boxes (based on existing values) to provide a much stricter entry system (users would have to go through several steps to add a new value to the set of existing values). I've shied away from enforcing values on the user, but in some cases its probably appropriate.

Finally, yup, there is a Perl interface via the MW API!


This is the one I've been using (not a particular vote of confidence, but I'm familiar enough with it / have example scripts written using it):


I'll post some examples of bots I've written using this framework on the wiki itself. If you write a bot, don't forget to set the bot bit on your edits! It hides them from the default 'recent changes' lists.

All the best,
Homepage: Dan Bolser
MetaBase the database of biological databases.
dan is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:48 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO