SyBIT TechDay Update 20110525x - wiki.systemx.ch - SystemsX ...

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4 Οκτ 2013 (πριν από 3 χρόνια και 6 μήνες)

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News / Planning

Tech Day May 25 2011

Continuation is safe

SystemsX.ch

and
SyBIT

will continue with
the same level of funding until the end of
2016

Formal approval by parliament needed,

for 2012 now in October 2011,

for 2013
-
16 in October 2012

SyBIT

has to provide a
plan

May 25, 2011

2

Tech Day

Making
SyBIT

part of the
SystemsX.ch

eval
. process

Problem: Many misunderstandings about

What
SyBIT

provides

What
SyBIT

does not provide

NEW
:
SystemsX.ch

guidelines are updated that:

SystemsX.ch

proposals
must
describe and
request funding for computational work:

1.
Bioinformatics research and development

2.
Algorithm development, modeling

3.
Tooling and Standards

4.
IT resources, additional HW

May 25, 2011

3

Tech Day

Making
SyBIT

part of the
SystemsX.ch

eval
. process

Problem: Many misunderstandings about

What
SyBIT

provides

What
SyBIT

does not provide

NEW
:
SystemsX.ch

guidelines are updated that:

SystemsX.ch

proposals
must
describe and
request funding for computational work:

1.
Bioinformatics research and development

2.
Algorithm development, modeling

3.
Tooling and Standards

4.
IT resources,
additional HW

May 25, 2011

4

Tech Day

Project Funding

SyBIT

Scoping
SyBIT

How to explain to others what
SyBIT

is

Essential for ‘the Plan’

May 25, 2011

5

Tech Day

Challenge : Scale Up

High Throughput Instruments

Much larger
data

volumes

Increased
data

complexity


Large Collaborations

More people

More experiments and measurements


May 25, 2011

6

Tech Day

Actors

May 25, 2011

7

Tech Day

Researchers

IT Resource
providers

Data Intensive
Systems Biology
Research

Platforms

SyBIT

: Integrator

May 25, 2011

8

Tech Day

Researchers

IT Resource
providers

Data Intensive
Systems Biology
Research

Platforms

SyBIT

SyBIT

Scope

May 25, 2011

Tech Day

9

SyBIT

IT Resource
providers

Researchers

Support
C
ollaborate

Define requirements for


team up with

Tools

Bioinformatics Services

Data Management

Standards, Integration

Software engineering

Legacy support

Documentation

Education

Collaboration support

Setup, Configuration

Versioning

Commercial
software

provide

Platforms


Enable

Strengthen

Scope
wrt

research

May 25, 2011

Tech Day

10

Research Data
Analysis

Modeling

Bioinf
. Software
Engineering

Data Management
Automation

Algorithms and
New Tools, Scripts

Standards,
Software
Modules,
Reusable Services

Bioinformatics Research

SyBIT

Updated Organization

May 25, 2011

11

Tech Day

SEB

Management

Core Team @ CISD, Vital
-
IT, FGCZ



Platforms, Core Facilities


EPFL:BBCF


ETH:LMC, BSSE:DSU


UniBas:ResearchIT


FMI:Bioinformatics

Platform


..




Research
Laboratories


ETHZ


Biozentrum


EPFL


..

Embedded Teams

Embedded Teams

Embedded Teams

Tech Days

Tutorials

Hands
-
On
Education

Simplified Organization

Drop

Management Board

User Forum

Communities

Coordination
Team


now ‘Management’

Follow RTD model for management

PI and Co
-
PIs: Platform managers

Reporting directly to the SEB

Follow SIB model for embedded teams in research labs

Line manager remains outside of the group

Make use of unlimited duration SIB contracts

Blurred line between bioinformatics tooling and research…

May 25, 2011

12

Tech Day

Also in the Plan for 2012
-
2016

Development*

Focused projects with empowered, embedded teams

Always in tight cooperation with researchers

Don’t develop anything that is not used immediately

Rotate people through projects to spread knowledge

Support effort is growing**

Approx. 20% of the effort by developers

Needs dedicated people for systems management: installations,
configurations, first line support

Much more education

How to use the tools we provide

How to use the processes we set up

May 25, 2011

13

Tech Day

* Development Projects

Interaction with research labs essential

But we are few, they are many

Make use of embedded SIB model

Embed developers for a limited duration to work tightly with the
labs

Understand requirements

Specify the project scope such that it is reasonable (max 3 months,
renewable


but prioritization of projects up to
mgmt
)

Implement what was agreed on together with the local team

Developers are responsible for the whole process


Just stick to the basic project guidelines on documentation and communication

SyBIT

Management responsible to bring projects in,
assignments and for priorities between projects

May 25, 2011

14

Tech Day

Also in the Plan for 2012
-
2016

Development*

Focused projects with empowered, embedded teams

Always in tight cooperation with researchers

Don’t develop anything that is not used immediately

Rotate people through projects to spread knowledge

Support effort is growing**

Approx. 20% of the effort by developers

Needs dedicated people for systems management: installations,
configurations, first line support

Much more education

How to use the tools we provide

How to use the processes we set up

May 25, 2011

15

Tech Day

** Growing Toolset

Data
Management

openBIS

Metadata catalog

and file management

10+

installations in production

Several TB of data, over 100 users

Most RTDs

GenRep

Genomic

data repository

Lausanne

Automation
and Workflows

Bein

Tool to build analysis pipelines

Lausanne

iBRAIN2

Automated

analysis of HCS
-
HTS

3 Installations

Zurich and Basel

Web

Interfaces

GDV

Genomic

Data Browser

Lausanne

P
-
GRADE

Proteomics analysis portal

Zurich

CRK Web

Protein

Crystal Structure analysis

PSI

Tools and
Libraries

HTSstation

Processing tools for HTS

Lausanne

BioDB

Distribution of external Databases

Zurich,

Basel

XuvTools

Image Stitching tool

Basel

MorphoGraphX

3D visualization

of confocal images

Bern

Collaboration

Wiki,
Sympa

ELN
-
Wiki, SVN

SLIMS,
webvanta

In daily

use by many groups and projects

Most RTDs

May 25, 2011

16

Tech Day

Also in the Plan for 2012
-
2016

Development*

Focused projects with empowered, embedded teams

Always in tight cooperation with researchers

Don’t develop anything that is not used immediately

Rotate people through projects to spread knowledge

Support effort is growing**

Approx. 20% of the effort by developers

Needs dedicated people for systems management: installations,
configurations, first line support

Better documentation***, more education

How to use the tools we provide

How to use the processes we set up

May 25, 2011

17

Tech Day

***Improve Documentation

Documentation for users and developers

Make use of the Wiki

Code documentation, versioning, packaging

Installation instructions and scripts

Training videos where it makes sense

Do not forget: Publications

Make tools available on
Expasy
,
SyBIT.net

May 25, 2011

18

Tech Day

***Improve Documentation

Documentation for users and developers

Make use of the Wiki

Code documentation, versioning, packaging

Installation instructions and scripts

Training videos where it makes sense

Do not forget: Publications

Make tools available on
Expasy
,
SyBIT.net

May 25, 2011

19

Tech Day

I need some volunteers to work out the details in a

‘Documentation Guidelines Project’


How to document, where


Usage of
S
ourceforge
,
GitHub
,
G
oogle code


How to write user doc



End of July


To be used for all
SyBIT

projects


Be compatible with local processes

User Education

Joint projects: daily interaction

Workshops, hands
-
on events

Presentations in groups

May 25, 2011

20

Tech Day

Industry Interactions I

Pharma


No reaction from Novartis

Roche: one visit, no interest shown

Sanofi
-
Aventis: HCS deployment of
openBIS

Agios
:
openBIS

server


May 25, 2011

21

Tech Day

Industry Interactions II

Standards, Tools and Software

ToolPoint

and
SiLA

Standards for instruments, image formats
etc

CloudBroker

GmbH


ETH Spinoff

IBM and
CloudBroker
, 250’000 CPU hours in the
IBM Cloud for protein structure simulations (ETH)

Data Intensive computing in the cloud: new project
with FGCZ

May 25, 2011

22

Tech Day

Industry Interactions III

GeneData


Offers 1FTE for
exclusive

marketing rights of
openBIS

in HCS context

50
-
50 share in revenues


May 25, 2011

23

Tech Day

May 25, 2011

Tech Day

24

3
. Infrastructure Providers

Not a buyers market

Works very well in Arc
Lémanique

Not so well in Zurich, Basel

Reason: LS
-
specific resource planning through Vital
-
IT


Emulate Vital
-
IT model, adapt it

Channeling of common requests for central
infrastructure to the top

Organized planning of local and central resources
by all involved groups,
SyBIT

as catalyst

May 25, 2011

25

Tech Day

3
. Infrastructure Providers

Not a buyers market

Works very well in Arc
Lémanique

Not so well in Zurich, Basel

Reason: LS
-
specific resource planning through Vital
-
IT


Emulate Vital
-
IT model, adapt it

Channeling of common requests for central
infrastructure to the top

Organized planning of local and central resources
by all involved groups,
SyBIT

as catalyst

May 25, 2011

26

Tech Day

Goal
:

WE need to be able to DEFINE what the
infrastructure will be for Life Science

Receive funding from researchers to invest

Coordinate also across institutions for better deals