= Satellite meeting for Use-cases development and documentation =

== Topics ==

Several examples of the biological data are provided by users.
The service developers explained how to use their programs for the data.
Finally, users described the several potential work-flows for the computational part of their research.

== Participants ==

 * Toshiaki Katayama
 * Young Joo Kim
 * Keun-Joon Park
 * Yunsun Nam
 * Arek Kasprzyk 
 * Syed Haider
 * Shuichi Kawashima
 * Takeshi Kawashima
 * Raoul JP Bonnal
 * Tatsuya Nishizawa
 * Oswaldo Trelles 
 * José M. Fernández
 * Paul Gordon 
 * Vachiranee Limviphuvadh
 * Tobias Gattermayer
 * Riu Yamashita 
 * Fumikazu Konishi 
 * Takatomo Fujisawa

== Targets ==

 

== Date ==

 * 2009/3/19 15:00-18:00
 * anytime


== Room ==

 * 3F 

== Notes ==

'''Data for testing'''

1) SNPs data contain 262,338 SNPs (Stroke patient vs. normal) from Affymetrix GeneChip (provided by Prof.Kim)[[BR]]
2) Amino acid sequences of 53 genes (multifasta format) which are located at disease map locus of one form of epilepsy (provided by Vachiranee)[[BR]]
3) Nucleotide sequences (multifasta format) (provided by Riu)[[BR]]
4) Genome data (provided by Takeshi)[[BR]]


'''Softwares''' 

1) BioMart[[BR]]
2) Galaxy[[BR]]
3) jORCA[[BR]]
4) ANNOTATOR[[BR]]


== Results ==
  

Question
- Takeshi asked about how to annoate in-house data with comparing with public genome data using BioMart.
- For example, how to annotate Halocynthia roretzi or Molgula tectiformis ESTs comparing with Ciona intestinalis and Ciona savigni using BioMart.
Answer
- Convert Halocynthia data into BioMart format. Install BioMart server locally. Then merge public DB and local data together.
- BioMart format is simple.


Takeshi present an example
- minor animal (ex, H.roretzi, closest animal of Ciona)
- how can analyze Halocynthia roretzi and M.tectiformis which are rare annotation.
- type of data is ESTs, assembled EST cluster,,,etc,,
- potential flow: BioMart -> ANNOTATOR -> TogoDB

[[Image(bh2009-usecase_1.pdf)]]

'''*SNPs data'''[[BR]]

ANNOTATOR currently can not analyse SNPs data itself but can analyse genes data which contain SNPs of interested. [[BR]]
Galaxy (http://galaxyproject.org) and RGenetics (http://rgenetics.org/)
        quality control, ancestry, case-control analysis, tdt, oter statistical tests[[BR]]
-can link dbSNPs to Galaxy for further analysis

[[Image(bh2009-usecase_2.pdf)]]

'''*Multifasta format (amino acid sequences)'''[[BR]]

ANNOTATOR can upload multifasta format of amino acid sequences -> Prim-seq-an algorithm[[BR]] 
BioMart can upload GeneID but not the sequences to retrieve information associated to the GeneID[[BR]]
jORCA provide list of analysis which can do with FASTA format[[BR]]



'''*Multifasta format (nucleotide sequences)''' [[BR]]

ANNOTATOR can upload multifasta format of nucleotide sequences -> Prim-seq-an algorithm[[BR]]


'''*Genome data'''[[BR]]


DL ESTs of Halocynthia roretzi from NCBI/Taxonomy

TogoDB by Toshiaki
- upload table format  (table services for uploading data will be able to access using WS)

'''*Other comments from Developper side'''[[BR]]

jORCA by Oswaldo

-mapped WABI services
- jORCA: WABI WSDL application can run in local machine after installation
- jORCA can tell which kind of analysis can do with our multifasta format file or anykind of format. For example, using Magallanes: INB*,
if put "FASTA" in Find box, the result come up with 23 tools that can use for analysis. For analysis use myexperiment.org
*Magallanes: INB (Services discovering that discover what kind of analysis can provide for your data format)



== TODOs ==

1) How to combine the inhouse data into Public BioMart? => KAAS, blast2GO etc.[[BR]]
2) How easy to install the BioMart in local?[[BR]]
3) How modify the design of the interface of TogoDB?[[BR]]
4) User didn't have their own Data Repository site. (for TogoDB)[[BR]]

== Requests from use cases to developper ==

*(TO: [http://www.ebi.ac.uk/intact IntAct], Cytoscape) [[BR]]
It would be nice if user can retrive PPIs which are expressed in any tissues by using option function. (From: Vachiranee)[[BR]]

At this moment the only way that Bruno@!IntAct knows of doing this is to get the list of proteins from a specific tissue (using [http://www.ebi.ac.uk/pride PRIDE]) and then using the list of proteins accessions to find PPIs in the molecular interaction databases, such as [http://www.ebi.ac.uk/intact IntAct]. If there is interest, we (!IntAct) could find a way to include this option in a future release.

*(TO: ANNOTATOR)[[BR]] 
In the conversation with mostly biology-oriented participants of the Hackathon,[[BR]]
we found the following requests for ANNOTATOR to suit their needs:[[BR]]

- Ability to do batch jobs, i.e. large number of proteins annotated by our software (request came from many)[[BR]]
- ANNOTATOR should be downloadable and deployable somewhere local[[BR]]
- We were offered a potential collaboration in terms of using computing power of a Titec TSUBAME supercomputer. This means the ANNOTATOR's jobs need a mechanism to be submitted to an external site.[[BR]]
- For better results, consistency and the ability to replicate the annotator pipeline in a remote location, we need periodic and automatic updation of the underlying databases of the algorithms.[[BR]]
- How differences between ANNOTATOR and InterProscan[[BR]]
- Ability to save results of analysis as xml format for further analysis[[BR]]

*(TO: Galaxy)[[BR]]
- I'd like to input the list of ID on galaxy (such as Gene ID, IPR No.) to text form of biomart filter.