NERC Environmental Bioinformatics Centre

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Oct 1, 2013 (3 years and 9 months ago)

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NEBC
Workshop

Tuesday 17 July

2007


Agenda


Venue:







-

EBI, Cambridge


Attendees:


Dawn Field



-

NEBC



Bela Tiwari



-

NEBC



Tim Booth



-

NEBC



Stewart Houten



-

NEBC

Ashley Morley



-

NEBC



Susanna
-
a
ssunta
Sansone

-

EBI
, Cambridge



Philipp
e Rocca
-
Serra


-

EBI
, Cambridge




Marco Brandizi



-


EBI, Cambridge



Nataliya Sklyar



-

EBI, Cambridge





Chris Taylor



-

NEBC

Norman Morrison


-

NEBC



Dave Hancock



-

NEBC



Jason Snape



-


Astrazeneca




10.00


10:15

Arrive
-


Book in at recept
io
n



10.15


10.30

Jason
-


Overview of Post
-
genomics and Proteomics Programme status.



10.30



12.00

NEBC

-



Update on NEBC core
support activities
:





Bio
-
Linux, including update on National Grid Service access (Stewart)





Update on Envbase status
(Ashley)





Review of contact with PGP researchers for design, analysis, etc. (Bela)





Course plans (Bela)





Barcoding and Genquery update (Tim)





MIBBI update (Chris)





Ontology and standards (Norman)



12.00


12.15

Bela
-



NEBC PGP September r
oadshow plans





NERC PGP Science meeting 24
-
25
th

S
e
pt
e
mber, Milton Keynes.


12.15


13.00

Lunch

-


Time may vary depending on above schedule



13.00


14.00

Susanna

-


BioMAP
-
TAB and the Bio
-
Investigation model (format as a common way to





s
ubmit

mul
ti
-
omics investigation to ArrayExpress, Pride, Meda
-
to
-
be)


14.00


14.30

Dave
-



Update on the O'Mixed project



14.30


15.00

Susanna
-


Bio
-
Investigation Index (using Investigation, Study, Assay)




15.00



16:00



General discussion on topics raised d
uring the day.




16.00


Close



Notes from NEBC
-
EBI workshop 19
-
20 Feb 2007.


Monday 19
th

Feb.


Dawn introduces workshop.


Round table introductions from all attendees.


Dawn briefly reviewed the minutes from the previous workshop. Slides still need to b
e supplied from those
that presented them at the Dec 06 meeting in Cambridge.


The agenda for this two day meeting was discussed and agreed as appropriate.


Logistics. Dawn stated that CEH had not yet arranged the transfer of money to the EBI for Chris Tay
lor’s
position as MIBBI programmer. Dawn is waiting for Will Thomas, NERC EG Science Programme
Administrator, to confirm the transfer.


Dawn and Bela gave a brief overview of the NERC Omic Data Strategy Meeting that took place on 2
nd

Feb at
the MRC, London
. The meeting attendees are forwarding a plan to NERC ISG that outlines what they
require.


Dawn mentioned that NEBC has a new website since July 2006 and has a Wiki that will be used to post the
minutes and presentations from this workshop.


Norman stated

that there is no change in the status of the MSI paper.


The OBI meeting in San Diego was then discussed. Many of the workshop attendees went to this OBI
meeting, and the talks revolved around the OBI milestones set in San Diego and that a Google calenda
r was
available that displayed the key dates.


Chris Taylor presented the MIBBI website and explained what MIBBI is. It has superseded the MICheck
name as that URL was already taken. It has several participant projects. It uses XML forms. Lots of MIAME
bas
ed projects.


Tim gave an update on MIBBI, MIGS and EnvBase websites using GCat. He reviewed the use of Orbeon (did
not like it as a programming tool). Action to check website for terms


Dawn search on google?


Tanya reviewed the GCat
-
GSC background and l
atest actions.


Dawn suggested a meeting between Tim, Chris, Tanya and Dawn to discuss GCat
-
GSC.


Lunch at 12.45




After lunch, David Shotton gave a brief talk on his project at the Zoology Department, Oxford University.
They are building a web
-
based imag
e database for biology. The plan is to have researchers enter their
metadata about images on a web based form as soon as the images are created, and to use this data and
database as part of any paper submission. This will hopefully make the database useful

to those inputting
the data as an aid to publishing papers, and to those requesting the data at a later date.

They will have RDF support.


Graham Klyne followed David’s talk with details about the methods they will use for the database and how it
will be
a distributed database accessible from the web. It will use public repositories and individual servers.
Mash
-
able sources but not providing mash
-
ups. They will test the system with several of their in
-
house
researchers in the Zoology department. Any system

has to have a positive gain for researchers or they will
not use it.


Norman gave a brief overview of the Habitat Ontology that he is working on. He said that “flicker”, the
website service for displaying photographs, may be useful for distributing data?


Allyson Lister then gave a presentation on the CISBAN project, and how they are implementing the FuGE
milestone 3 object model. It is Java based. Uses POJO’s


Giles Velarde gave a talk about the Streptobase project that his group at Manchester University

are working
on. It uses maxdbrowse code, has web access.


Dave and Giles updated the group on the omixed.org website and project. Dave’s Generic Experiment Model
is almost done. It has no documentation and is rough round the edges. This is for the generi
c version of
maxdload2.


Omixed has a website, and has a Flash version of a possible user based web access form. The Flash version
is a test/play version for Giles.


A follow up action is to see what was in the Sabre proposal that can be used for omixed.


A general discussion followed regarding MAGE
-
MEMO, MyExperiment.


The Monday session closed at 5pm.


Tuesday 20
th

.


Bela began with an overview of the Excel spreadsheets that NEBC have created for annotating data for
maxdload2.


Philippe presented his dat
a on the Excel spreadsheet based IDF file system (MGED Format), for multi omic
experiments. MAGE
-
Tab. Check the PRIDE harvester website at EBI. MAGE
-
TAB does not produce XML.


Can we use Google spreadsheets?

Action on Ashley to see if NEBC spreadsheets ca
n be made available on Google spreadsheets so that they
are available on
-
line. (Even though they already on a website).


Tim gave a demo of EnvBase and Handlebar. Reviewed data entries and showed the options available to
users of Handlebar. EnvBase has no
unique persistent ID. Can we get EnvBase entry by webpage?


DF.


Tim discussed the meeting he and Dawn had with Renzo and Wolfgang from the Max Planck Institute,
Bremen regarding their request to use Handlebar. Security of system was an issue. Spreadsheet

validation of
data and validation on upload to database was also an issue. Check out MEGX.


Andy Jones gave a FuGE presentation on the project history, background. The FuGE model, UML to XML.
AndromeDA. More complex than Maxd. FuGE v1 due by April 2007.
Accepted by MSI and PSI.

Action on Dawn to email andy re GSC input to FuGE.