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UP Bioinformatics and Computational BiologyUnit
Fourie Joubert
Bioinformatics and Computational Biology UnitUniversity of Pretoria
March 25, 2011
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Introduction
Where does the Unit fit in?
Started in 2003
A unit in the Faculty of Natural and Agricultural Sciences,resorting under the Department of Biochemistry
An ACGT facility
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Who are we?
Prof Fourie Joubert Associate Professor
Prof Oleg Reva Associate Professor
Mr Oliver Bezuidt Senior Lecturer
Mr Jeanre Smit Software Developer
Currently appointing additional lecturer and developer
Fourie Joubert UP Bioinformatics and Computational Biology Unit
What do we do?
Undergraduate lectures
Postgraduate lectures
Short courses
Support services
Research
Fourie Joubert UP Bioinformatics and Computational Biology Unit
What research are we involved in?
Malaria target and drug discovery
Genome linguistics, gene Islands and metagenomics
Computational Immunology
Genomics and next-generation sequencing
Fourie Joubert UP Bioinformatics and Computational Biology Unit
What research are we involved in?
Malaria target and drug discovery
Genome linguistics, gene Islands and metagenomics
Computational Immunology
Genomics and next-generation sequencing
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Equipment
What equipment do we have?
Multiprocessor systems
Parallel systems
Storage
Backup
Training
GRID computing
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Multiprocessor
1 x Dell R 900 with 24 cores and 256GB of RAM
1 x Dell R 910 with 24 cores and 512GB of RAM
Various other systems with 8 cores
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Parallel systems
1 x IBM BladeCentre with 14x 8-core nodes 48GB RAM pernode
112 cores in total
Infiniband 40Gbps interconnect
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Storage
1 x VTrak m500f with 10TB storage
1 x IBM DS3400 with 20TB storage
1 x Dell MD3200 with 30TB storage
Local storage on servers
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Backup
1 x L180 LTO1 with 12 TB backup
2 x IBM TS3200 LTO4 with 80TB backup each
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Training
Training lab with 28 quad-core PCs 4GB RAM running Linux/ Windows
Fourie Joubert UP Bioinformatics and Computational Biology Unit
GRID computing
We are an SAGRID site
Various sequence analysis tools and structural biologyapplications on the GRID
SAGRID currently has over 1,000 cores set up
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Software and databases
Commercial software
Accelrys Discovery Studio and Materials Studio
12 tokens for UP use
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Genome Assembly
Velvet
Oases
Abyss
etc.
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Genome Annotation
Maker
Pfam and HMMer
InterProScan
RSA-tools
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Microarrays
BioConductor
SSHscreen
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Databases
BLAST
GenBank
EMBL
SwissProt
InterPro
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Skills and expertise
Skills and expertise
Genome assembly and annotation
Genome linguistics and metagenomics
Trancriptomics
Microarrays
Protein modeling and docking
Pipelines and workflows
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Short courses
Past short courses at the unit
General bioinformatics
Genome annotation
Infectious diseases bioinformatics
Phylogenomics
Phylogeny (Inqaba / FABI)
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Planned new short courses
NGS assembly and annotation
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Interaction models
Collaboration
Approach us in advance in the planning phase
Provide a student to be involved, or help fund abioinformatics student
Co-supervise
Co-publish
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Part-time work
Fund a needy student to work part-time on a project
Fourie Joubert UP Bioinformatics and Computational Biology Unit
Contact information
Contact information
Fourie Joubert
http://www.bi.up.ac.za
Fourie Joubert UP Bioinformatics and Computational Biology Unit