City of Hope’s Bioinformatics Core (BIC) facility provides researchers with high-throughput biological data analysis tools, data management, unified cyber-infrastructure, training, as well as trained staff working within multidisciplinary teams to facilitate experimental design, information management, data integration, annotation, dissemination and visualization. Our goal is to foster collaborations and provide high-performance parallel computational support for principle investigators and develop modern computational techniques and methods for their basic and translational research.
Image Analysis Resources
BIC will support CPU/memory intensive parallel computation for Smith-Waterman alignment algorithm on GPU using CUDA sequence alignment, BLAST/BLAT/BioMart database search, MEM motif prediction, MFOLD RNA folding, and sequence contig assembly analysis etc. Invitrogen Labshare Oracle based data management is provided for Vector NTI sequence analysis, MacVector, GeneCode Sequencher, CLC Bio Workbench, TRANSFAC gene transcription factor database, as well as open source NCBI BLAST, BLAT services, Oligo design, UCSC local mirror site with human and mouse database, Broad IGV, and Mathwork Matlab statistical and bioinformatics tool kits.
BIC will support statistical and computational analysis for image preprocessing, base calling, sequence alignment, and down-stream analysis of DNA-Seq, ChIP-seq, Methyl-seq, mRNA-seq, smRNA-seq, targeted resequencing, RNA-seq. BIC currently hosts commercial Illumina Solexa GA II pipeline and CASAVA, Roche 454 , vendor based NGS analysis software from SoftGenetics NextGENe, and Partek Genomics Suite, as well as several academic open source software products such as local mirror site of UCSC Genome browser, Blat, SOAP, MAQ, BWA, Bowtie, Novoalign, Samtools, R/Bioconductor, LIMS such as SeqWare and CBIS. BIC also developed accelerated Smith-Waterman alignment algorithm on GPU using CUDA for supporting efficient Solexa genome-wide alignment which will accommodate large indels and abundant structural variations, as well as SeqGene for Exome and transcritomic open source NGS analysis. BIC also provides training workshops for Partek, NextGENe, NCBI, Ensemble, BioMart, UCSC genome browser, and Broad IGV etc.
Genomic Analysis Resources
BIC will support statistical and computational programs for microarray image preprocessing, generating differential expression profiling for biomarkers, down-stream analysis for expression, copy number, miRNA, ChIP-ChIP analysis, as well as integrated genomic analysis. BIC currently hosts comprehensive commercial microarray software from Affymetrix, Agilent, NimbleGen, Exiqon, BioDiscovery, Nexus, Partek Genomics Suite, Agilent GeneSpring, Ingenuity as well as many academic open source software such as local mirror site of UCSC Genome browser, Blat, Biobase TRANSFAC, Gene Cluster, and R/Bioconductor, etc. We also provide user training workshops for Partek, GenSpring, NCBI, Ensemble, BioMart, and UCSC genome browser etc.
Computer-Assisted Molecular Design Resources
BIC can provide a structure based virtual ligand screening (VLS) approach to identify potential leads against the X-ray crystal structure and/or homology models of potential ligand binding sites that were predicted. BIC can provide the qualitative assessment for virtual mutagenesis experiments to predict the structural activity relationships and then compare with bioassay results. BIC offers molecular dynamic simulation of these protein-ligand complex structures as well as their association constants as confirmation of the docking strategy. BIC can also design a highly diverse HTS compound library available for robotic screening based on approximately 15 million compounds downloaded from NCBI PubChem, as well as several thousand natural compound libraries. BIC can correlate binding affinity and IC50 of potential ligands to perform CoMFA and QSAR analysis to assist medicinal chemistry to optimize potential leads. BIC can also perform ADMET analysis for the prediction of toxicity and metabolomic predictions to develop drugable compounds for clinical trials. BIC currently hosts comprehensive commercial modeling software from Tripos, Schrodinger, SimulationPlus, Chemiinovation, academic software AMBER, Charmm, MOPAC, as well as compound libraries from NCBI, UCSF ZINC, and several pharmaceutical companies such as Chambridge, ChemDiv, etc. User training workshops are conducted for NCBI, TRIPOS, Schrodinger, Ensemble.