biocatalogue, filequirks, myexperiment
Post on 02-Jul-2015
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Summary from my fellowship in Manchester
e-Science in Manchester
Jerzy OrłowskiJerzy Orłowski
What will I talk About
Part one: Biocatalogue SearchByData
Searching for services that will analyze or process your data file
Other ideas, born meanwhile
Part two: Other things I've done meanwhile
Part three: How do they do it in MyGrid
New methodology that we could adopt
How can I help you, how you can help me
Part one:Biocatalogue SearchByData
Biocatalogue
The BioCatalogue is a catalogue of Life Science Web Services
A web service is a network application with programmatic interface
BioCatalogue relies on community annotation
Service providers
Users
Curator
Technology: Ruby on Rails
Browsing services
My contribution
Search ByData
Ability to find services not on tags, providers etc. but on exemple input files
Algorithm based on FileQuirks based in GeneSilico
User provides an real input file, which is matched with example inputs of all the services using regular expressions
Services most likely to analyze / process user file are returned
Other ideas – getting example input files
The main limitation of Search By Data is lack of example inputs for services
for 1169 services, more than 3000 operations there are no more than 500 example inputs
Most of inputs are numbers or ids
Idea – get more inputs:
From people executing the servicesTaverna Provenance
Soap Servlet
By executing services by bots with some data
Soap Servlet
Automatic generation of web interface for web services:
For users: allows to quickly test or execute a service
For us: allows to get example inputs for services
Currently – alpha version
Soap Servlet interface for Afold
Soap Servlet interface for Afold
Part 2:Other projects I've done meanwhile
GeneSilico web services
Turning some of our programs into SOAP services
ProteinSilico
ModeRNA
Parts of MetaServer
Parts of MetaRNA
See: https://wiki.genesilico.pl/GenesilicoSOAPServices
Good documentation on BioCatalogue, used to test Search By Data
FileQuirks
FileQuirks – web server for recognition of biological data types
New user interface
More data types
Help pages
Summary sent to NAR (waiting for decision)
http://filequirks.genesilico.pl
FileQuirks Help Pages
I decided to use Joomla CMS
Help pages have standard format
Joomla make them easy to write and update
GeneSilico home page is written in Joomla so it would be easy to migrate/merge and graphic template already exists
It easy to add help pages of other services
Software and server list on http://www.genesilico.pl/index.php/servers.html is outdated
Genesilico web services
Web service is a network tool with programatic API “program as a service”
Pros
Compatibility between languages (XML is the protocol)
Code reusage – no need to install programs
Easy linking with other tools
Automatic user interface generation
Cons:
You have to maintain the server
Harder to make it private
Example 1
MetaMQAP
Kudlaty Chimera MetaMQAP plugin uses MetaMQAP (wrote his own interface)
Toolkit uses MetaMQAP
I have also written scripts for using MetaMQAP
Conclusions:MetaMQAP needs to be installed and maintained on many
different systems by different people
Making a SOAP server will save people time
Example 2
Methods for RNA secondary structure prediction
They are used by RNA MetaServer
Tomek Puton uses them for CompaRNA
They were used by me for testing Search By Data
Conclusions:SOAP interface for fast methods exists
It just need updating and incorporating in other tools
GeneSilico web services
Instructions on:
https://wiki.genesilico.pl/GenesilicoSOAPServices
How do they do it in MyGrid?
Some methodology we might adopt or just be aware of
Working system
They do dot make science itself – they make tools for scientists
And science about how new technologies are adopted in science
Every project is collaboration with other groups
There is always more than one people working on a project
more than 25% of time spent on meetings
Code developers are not scientists, but employees
Working system2 “uncommon” positions
Project managerNot a scientist
Not a developer
Responsible for: keeping up with release schedule
grant schedule
cooperation between projects
Service curatorNot a developer
Responsible for keeping in touch with user community
Organizing meetings with focus group, jamborees etc.
Working system
No seminars
Instead weekly meeting with advances on all projects
A lot of project dedicated meetings and teleconferences
Sharing policy
Code and ideas are even from the beginning of the project
Scientific finding can be published only once but tools can be better and better
Selling your ideas enables cooperations and making tools compatible – better grants
Publishing your code (git, svn) get you more users – nice for publications and grants
Development
Languages: Java and Ruby on Rails
Every code is under version control
Massive branching and merging
Dependency management systems (maven)
All services are hosted
Collaborations (EMBL-EBI)
Corporate hosting
Clouds (Amazon EC2)
Making user community
Summary – what we could discuss
Programatic interfaces (Middleware)I can make SOAP interfaces for you,
deploy and publish them
I would require you to use such interfaces in your future code
What else I can give:CMS for public help pages for programs
and web servers
What I'd like to ask
Acknowledgments
MyGrid
Carole Goble
Charlotte Hooson-Sykes
Jithen Bhagat, Franck Tanoh, Soahib Sufi, Peter Li and others
University of Southampton
David da Roure
GeneSilico
Janusz Bujnicki
Iga Korneta
Piotr Iwaniuk, Jakub Jopek, Bartosz Bedyński, Artur
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