Notes from 1st PG&P Bioinformatics workshop - NERC

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1

of
4

Notes from
1
st

PG&P Bi
oinformatics workshop


30 Sept 2005 at CEH Oxford.


Present:


Nathan Haig
h
, David Westhead, Anil Wipat, Rachel Rusholme, Da
wn Field,
Fernando Ortega, Lucia
ne
Mello
, Bela Tiwari, Stewart Houten, Joe Wood,
Norman Morrison, Dave Hancock,

Tim Booth.



The meeting started at 10.30

with presentations from four of the PG&P research
groups starting with Nathan Haigh from Professor Kunin’s group.


Nathan presented an overview of the database that he has created for use within
the group, and emp
hasized that this was still under development, but could be
used by other groups if they wished.


Anil Wipat, from the Ian Joint group, outlined Metashark, Access Grid and
Taverna technology that their group were currently using for data mining. They
are
currently building a large condor grid cluster of up to 2000 machines.


Rachel Rusholme, from an EG research group, represented the Tamas Dalmay
group and presented information on sequence analysis handling. The group does
not have a dedicated
bioinformati
cian
, but a research assistant has produced two
JAVA programs that reduce the manual handling times during analysis. They are
also working with David Studholme at the JIC Sainsbury Lab

with regard to
database

support.


The last
PG&P
presentation was from F
ernando Ortega of the Kevin Chipman
group. Fernando described the research they were undertaking with regard to
Stickleback and Flounder pattern recognition analysis. Their project uses genetic
algorithms

to predict/classify the location a fish sample came

from.



After lunch, the NEBC team gave a brief outline of projects within the centre.


Joe Wood reviewed the NERC Data Policy and its implications for the PG&P
groups. Copies of the policy are available from the NEBC website. Joe also
discussed the MIAM
E/Env project
and its use within EG groups.



Tim Booth gave an overview of the EnvBase data catalogue and its use within
the EG groups. Tim also reviewed progress of the Barcode project that the Ian
Joint/Kevin Chipman groups will be testing shortly.



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Da
ve Hancock reviewed the maxd project and with regard to meta
-
data capture
and analysis.


Norman Morrison gave an overview of Data Standards and the work being
undertaken within the FuGE and FuGO groups, with particular mention of the re
-
structuring of work

on the Mged standards project.


Bela Tiwari concluded this session with an overview of the NEBC, Bio
-
Linux and
the Bio
-
Linux documentation project.



Anil
Wipat
and Dawn

Field

gave
an
overview of

the

Microbial Metagenomics
p
roject and their f
unctional an
notation
of
data using Blast routines.
They
suggested that we c
ould use a central repository (maybe NEBC).

Data can be
collected from
the
repository and then updated.


Barcoding
was mentioned
for M
icrobial
M
etagenomics

via
NEBC
.

Progress will
be presente
d in December’s PG&P workshop by Tim. Booth.


Anil mentioned adding
the Taverna

package to

Bio
-
Linux
, Bela
will look into this
and may ask Newcastle group for sample workflows.



A general discussion followed along the lines of the agenda with the followin
g
topics covered.


PG&P
Wiki.

A wiki has been made available for the bioinformaticians group to use. This will
be a notice board for ongoing projects (e.g. barcoding), as well as a potential site
to publish software scripts that other groups may find usefu
l.


Nathan
agreed

to place his scripts on the
PG&P
Wiki.
Rachel and David thought
a Wiki
a good idea. Rachel’s RNA program may go up on Wiki?

Dave

suggested a c
oding helpdesk would be useful.


Everyone

said
ok to have a ma
iling list. Dawn would like
the
EG

b
ioinformaticians
to be added to the

mailing list.

It was suggested that we r
emove
the
envgen
-
dev
mailing list, and
also maybe envgen
-
announce and replace with
a new

mailing
list.


Today’s
presentations
will be available
from
the Wiki.


Dawn
required a st
atement added to the
Wiki

that announced
bioinformatics

support for

all projects (EG / PG&P)


Software Distribution

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Bela
s
uggested

that
Bio
-
Linux
would be a good platform
for circulating n
ew
software from the team/group, as Bio
-
Linux packages are updated e
ach night.


Bela continued with a general question;
What do
EG and PG&P
people want?


David
said he would

review
any
software that could be ready for dispersal to
oth
er teams via Bio
-
Linux. Bela to
check/test metashark for David to review.


Norman and Dav
e proposed “experts” for each group for support purposes, for
example

Joe
’s role with the Chipman group re
garding

annotation support.



Training

Bela
mentioned

training needs within the group.


N
athan
replied that he
has lots of data to input f
r
o
m field
su
rveys, and

would

like
training for transcriptomics
, data standards, omics, structures of data
bases.
Discussion and visits to
users

of specific programs

would

also
be of use.


Fernando suggested a course on arrays or stats.
This was not supported due to
the

length of time such a course would require to give anyone a reasonable
understanding of statistics.


Dawn
will

review/confirm funding arrangements for courses.




Andy Brass Lab runs a
microarray course
.

3 month train
ing course by distance
learning.

Peop
le should check his website for details.


David could use assistance

with quality control on stats package/data quality
(confirm the image before stats used

etc
!).


LuciAne mentioned NIBHI (North West Institute for Bio
-
Health Informatics), and
confirmed tr
aining available in microarrays in Liverpool, also Bioinformatics,
Linux, Bio
-
Linux (Wolfson lab), Basic Linux, Blast and Database
Structures/alignments to 3
rd

level structures.

This training was mainly for
molecular Biologists for a taste of bioinformatic
s.

A
Sept
-
Dec course is o
pen
and
free to Liverpool residents.



Fernando

highlighted that

MIT offer free online trai
ning courses


Lectures on
line form their website.




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David
suggested that a

focus group training day

would be useful
. People
can
present w
hat they know/do
. Open to awardees? (1 day only or maybe 2 for
p
ostdocs?)


Bela outlined the Genespring courses available, 2

beginner and
2

Intermediate
Genespring courses available

from Agilent as part of

the
new license. Courses
start from
January

200
6
a
ccording

to the agreement.


Posters regarding courses to be
made
available at the PGP workshop meeting in
December.



PGP Workshop,
12
-
13
December

We will provide posters for training courses. A room
has been
allocated for
use
by N
EBC and PG&P Bioinformati
cians.
This would be a good time to review the
notes and actions from the meeting today while everyone is together.



Key Points from the meeting

Meeting frequency


short review meeting
at the PGP workshop in December
(use room allocated to NEBC).

Then a
review/strategy planning meeting shou
ld
be arranged for Jan/Feb 2006. NEBC will organise this.


Mailing list
-

arrange as outlined above.

Wiki
-

continue use, add more material.

Training material
/slides
-

to be discussed at next meeting, ideas/proposals
r
equired.

Focus groups
-

decide
topics to be covered
, then look for candidate tutors etc.



The meeting closed at 16.30


Actions:


1.

Tim/NEBC to present barcoding process at PG&P
group

meeting in
December.

2.

Bela to look into myGrid/Taverna for Bio
-
Linux

3.

Bela/A
shley to re
-
organize scripts section on Wiki and alert others when
this is done.

4.

Mailing list to be created.

5.

Ashley/Bela to put presentations on Wiki site.

6.

Ashley/Bela to add statement to Wiki highlighting support for both EG and
PG&P projects.

7.

Bela to pac
kage Metashark for Bio
-
Linux.

8.

Bela to arrange microarray data quality workshop.