Computer Programming for Biologists Class 9 Dec 4 th, 2014 Karsten Hokamp .
Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information...
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Transcript of Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information...
![Page 1: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/1.jpg)
IntroductionSample ProjectsResourcesSummaryFuture Plans Bioinformatics Support
Information Session
Karsten Hokamp
TCD
3rd October, 2007
![Page 2: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/2.jpg)
Introduction:backgroundjob description
Sample ProjectsResources SummaryFuture Plans
IntroductionBackground
![Page 3: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/3.jpg)
Introduction:backgroundjob description
Sample ProjectsResources SummaryFuture 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
IntroductionBackground
![Page 4: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/4.jpg)
Introduction:backgroundjob description
Sample ProjectsResources Summary Future Plans
Data
IntroductionJob Description
Biochemistry Genetics Microbiology Physiology
Bioinformatics
Applications
![Page 5: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/5.jpg)
IntroductionSample Projects
Resources SummaryFuture Plans
Sample Projects
![Page 6: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/6.jpg)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample ProjectsThe 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
![Page 7: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/7.jpg)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample ProjectsPrediction of miRNA targets
Loscher et al., Genome Biology (accepted for publication)
experiments
miRandaSanger miRDB
4 microRNAs
predictedtargets
retina-specificgenes
ESTlibraries
![Page 8: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/8.jpg)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample ProjectsCASBAH: The CAspase Substrate dataBAse
http://www.casbah.ie
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IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample ProjectsCASBAH: The CAspase Substrate dataBAse
Luthi and Martin (2007) Cell Death Differ 14, 641-650
![Page 10: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/10.jpg)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsspeed up programs through parallelisation
LDhatcomplete
stoppedafter
six weeks
finished within two days
single CPUvs
TCHPC IITAC(up to 356 CPUs)
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
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IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsmiscellaneous activities
microarray data analysis (ArrayPipe, BioConductor)
![Page 12: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/12.jpg)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsmiscellaneous activities
microarray data analysis
programming help
(Perl, C, Java)
![Page 13: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/13.jpg)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsmiscellaneous activities
microarray data analysis
programming help
local installation of programs
(clustalw, BLAST, hmmpfam)
![Page 14: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/14.jpg)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsmiscellaneous activities
microarray data analysis
programming help
local installation of programs
advise on experimental design
(microarray experiments)
![Page 15: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/15.jpg)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsmiscellaneous activities
microarray data analysis
programming help
local installation of programs
advise on experimental design
help with grant applications
![Page 16: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/16.jpg)
IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resourceshardware
local servers:
bioinf.gen.tcd.iegen152061.gen.tcd.iegen152063.gen.tcd.iegen152064.gen.tcd.ie
external HTTP and SSH access
2 x dual core G58 GB RAM1 TB disk space
2 x 1 TBbackup
shared home directoriesgigabit connection
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IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resourceshardware
hosted server:
genserver.tchpc.tcd.ie
2 x dual core AMD Opteron8 GB RAM1.5 TB disk space
linked via Infiniband to IITAC
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IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resourcesonline
http://bioinf.gen.tcd.ie
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IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resourcesbioinf.gen.tcd.ie
links to locally installed programs
PubCrawler: It goes to the library. You go to the pub
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IntroductionSample Project:Resources
hardwareonline
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
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IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resources bioinf.gen.tcd.ie
links to locally installed programs
course material
mailing list
![Page 22: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/22.jpg)
IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resources bioinf.gen.tcd.ie
links to locally installed programs
course material
mailing list
contact information
![Page 23: Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007.](https://reader035.fdocuments.in/reader035/viewer/2022062408/56649f135503460f94c26cd5/html5/thumbnails/23.jpg)
IntroductionSample Project:ResourcesSummary
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 toa 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?
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IntroductionSample Project:ResourcesSummaryFuture Plans
Future Plans
tutorial: interactive web graphics
survey
backups
downstream microarray data analyses (network visualisations, GO enrichment)
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IntroductionSample Project:ResourcesSummaryFuture Plans
End