local installation of programs - SFI Bioinformatics Support Server

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Oct 2, 2013 (3 years and 10 months ago)

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Introduction

Sample Projects

Resources

Summary

Future Plans

Bioinformatics Support

Information Session

Karsten Hokamp

TCD

3rd October, 2007

Introduction:


background


job description


Sample Projects

Resources

Summary

Future Plans

Introduction

Background

Introduction:


background


job description


Sample Projects

Resources

Summary

Future Plans

1998:

M.Sc. equiv. in
Bioinformatics

2002:

Ph.D. in Genetics

Bielefeld University

2005:

current position

2002
-
2005:


Research Fellow,

SFU, B.C., Canada

Introduction

Background

Introduction:


background


job description


Sample Projects

Resources

Summary


Future Plans

Data

Introduction

Job Description

Biochemistry

Genetics

Microbiology

Physiology

Bioinformatics

Applications

Introduction

Sample Projects

Resources

Summary

Future Plans

Sample Projects


Introduction

Sample Project:


ext. LRRs


miRNA targets


The CASBAH


complete


misc


Resources

Summary

Future Plans

Sample Projects

The extracellular Leucine
-
Rich Repeat superfamily

Dolan et al,
BMC Genomics
. 2007 Sep 14;8(1):320

BLAST all vs all

TribeMCL clustering

selection for eLRR

manual curation

merging of isoforms

final list

IPI

human, mouse

MGC

human, mouse

Ensembl

fly, human,
mouse, worm

non
-
redundant
proteomes:

fly, human,
mouse, worm

architecture

hmmpfam with Pfam,
SMART

signal

TMHMM, HMMTOP,
TMPRED, SignalP

general

Ensembl, IPI, MGC
(gene ID, location, …)

Protein datasets

Annotation

Pipeline

Introduction

Sample Project:


ext. LRRs


miRNA targets


The CASBAH


complete


misc


Resources

Summary

Future Plans

Sample Projects

Prediction of miRNA targets

Loscher et al.,
Genome Biology

(accepted for publication)

experiments

miRanda

Sanger miRDB

4 microRNAs

predicted

targets

retina
-
specific

genes

EST

libraries

Introduction

Sample Project:


ext. LRRs


miRNA targets


The CASBAH


complete


misc


Resources

Summary

Future Plans

Sample Projects

CASBAH: The CAspase Substrate dataBAse

http://www.casbah.ie

Introduction

Sample Project:


ext. LRRs


miRNA targets


The CASBAH


complete


misc


Resources

Summary

Future Plans

Sample Projects

CASBAH: The CAspase Substrate dataBAse

Luthi and Martin (2007)
Cell Death Differ

14, 641
-
650

Introduction

Sample Project:


ext. LRRs


miRNA targets


The CASBAH


complete


misc


Resources

Summary

Future Plans

Sample Projects

speed up programs through parallelisation

LDhat

complete

stopped

after

six weeks

finished within


two days

single CPU

vs

TCHPC IITAC

(up to 356 CPUs)

LDhat

complete

LDhat

complete

LDhat

complete

LDhat

complete

LDhat

complete

LDhat

complete

LDhat

complete

LDhat

complete

LDhat

complete

Introduction

Sample Project:


ext. LRRs


miRNA targets


The CASBAH


complete


misc


Resources

Summary

Future Plans

Sample Projects

miscellaneous activities

microarray data analysis

(ArrayPipe, BioConductor)

Introduction

Sample Project:


ext. LRRs


miRNA targets


The CASBAH


complete


misc


Resources

Summary

Future Plans

Sample Projects

miscellaneous activities

microarray data analysis

programming help

(Perl, C, Java)

Introduction

Sample Project:


ext. LRRs


miRNA targets


The CASBAH


complete


misc


Resources

Summary

Future Plans

Sample Projects

miscellaneous activities

microarray data analysis

programming help

local installation of programs

(clustalw, BLAST, hmmpfam)

Introduction

Sample Project:


ext. LRRs


miRNA targets


The CASBAH


complete


misc


Resources

Summary

Future Plans

Sample Projects

miscellaneous activities

microarray data analysis

programming help

local installation of programs

advise on experimental design

(microarray experiments)

Introduction

Sample Project:


ext. LRRs


miRNA targets


The CASBAH


complete


misc


Resources

Summary

Future Plans

Sample Projects

miscellaneous activities

microarray data analysis

programming help

local installation of programs

advise on experimental design

help with grant applications

Introduction

Sample Project:

Resources


hardware


online


Summary


Future Plans

Resources

hardware

local servers:

bioinf.gen.tcd.ie

gen152061
.gen.tcd.ie

gen152063
.gen.tcd.ie

gen152064
.gen.tcd.ie

external HTTP

and SSH access

2 x dual core G5

8 GB RAM

1 TB disk space

2 x 1 TB

backup

shared home directories

gigabit connection

Introduction

Sample Project:

Resources


hardware


online


Summary


Future Plans

Resources

hardware

hosted server:

genserver.tchpc.tcd.ie

2 x dual core AMD Opteron

8 GB RAM

1.5 TB disk space

linked via Infiniband to IITAC

Introduction

Sample Project:

Resources


hardware


online



Summary


Future Plans

Resources

online

http://bioinf.gen.tcd.ie

Introduction

Sample Project:

Resources


hardware


online



Summary


Future Plans

Resources

bioinf.gen.tcd.ie

links to locally installed programs

PubCrawler: It goes to the library. You go to the pub


Introduction

Sample Project:

Resources


hardware


online



Summary


Future Plans

Resources


bioinf.gen.tcd.ie

links to locally installed programs

course material:

Computer programming for Biologists

Bioinformatics from the UNIX command line

Introduction

Sample Project:

Resources


hardware


online



Summary


Future Plans

Resources


bioinf.gen.tcd.ie

links to locally installed programs

course material

mailing list

Introduction

Sample Project:

Resources


hardware


online



Summary


Future Plans

Resources


bioinf.gen.tcd.ie

links to locally installed programs

course material

mailing list

contact info
rmation

Introduction

Sample Project:

Resources

Summary

Future Plans

Summary


I need help analysing my gene expression data!

Where can I store my data?

I’d like to learn how to program!

Which program can I use to do XXX?

I need access to

a powerful


UNIX computer!

How can I make this run faster?

I can only load up 20 sequences on the web!

What does this

parameter do?

I can’t get this program to run!

I wonder how Bioinformatics can boost this study?

Introduction

Sample Project:

Resources

Summary

Future Plans

Future Plans



tutorial: interactive web graphics


survey


backups


downstream microarray data analyses


(network visualisations, GO enrichment)

Introduction

Sample Project:

Resources

Summary

Future Plans

End