NML Bioinformatics Service Program FactSheet


Oct 1, 2013 (3 years and 6 months ago)


NML Bioinformatics ServiceNML Bioinformatics ServiceNML Bioinformatics ServiceNML Bioinformatics Service
Bioinformatics Tools
We license and provide free access to a comprehensive collection of
state-of-the-art bioinformatics software to USC faculty, staff and
Literature Search & Study
Quickly locate relevant literature
as well as expert-curated findings
on genes, proteins, diseases, drugs,
etc.  Nextbio
 Ingenuity Pathway Analysis
Public Genomic Data Mining
Explore and mine huge collections
of pre-analyzed public genomic
data to help hypothesis
formulation, experimental design
and results interpretation.
 NextBio
 Oncomine
 Genevestigator Advanced
Making Sense of Gene Lists—
Downstream functional
Find the most relevant molecular
functions, canonical pathways,
diseases, and interactive networks
for gene lists.  Ingenuity Pathway Analysis
 NextBio
 GenomeTrax (BIOBASE)
NGS Data Analysis
Analyze raw and aligned NGS
data (RNA-seq, ChIP-seq, DNA-
seq, etc.) with open source and
proprietary bioinformatics and
biostatistics methods.  Partek Flow
 Galaxy
 Partek Genomics Suite
Microarray Data Analysis
Analyze all types of microarray
data (gene/exon expression,
SNP/CNV, methylation,
microRNA, etc.) with these user-
friendly tools.  Partek Genomics Suite
 Golden Helix SNP and
Variation Suite (SVS)
 Microarray Я US
Making Sense of Gene Lists—
Upstream regulation analysis
Find the transcription regulators
(transcription factors, microRNA
etc.) affecting the observed gene
expression patterns in a list of
genes.  Ingenuity Pathway Analysis
 ExPlain (BIOBASE)
About Our Service
The Norris Medical Library
(NML) Bioinformatics
Service helps USC faculty,
staff and students with their
bioinformatics needs and
facilitates interdisciplinary
collaboration on ’omics
Get Your Access
All software and resources
are available to USC users at
no cost. You can find access
request forms on our
Both in-house developed
and vendor training
workshops are offered.
Tutorials, materials and
recording of previous
training workshops can be
found on the individual
software page.
Computing Resources
To meet the computational demand of the analysis of large ’omics
data set (such as NGS), we purchased high-performance computer
workstations and teamed up with USC’s high performance
computation facility, and offer USC users with the following
bioinformatics computing resources at no cost.
On-demand Service
For your specific research
questions, we offer:  Individual and group
consultation on
bioinformatics resources
and applications
 Instruction and training on
using our licensed
bioinformatics software
 Collaborations on
bioinformatics analysis of
’omics data
Stay informed
Keep informed about the
latest training and offerings,
email us to join our listserv:
High-performance servers in a custom condo within USC
High Performance Computing and Communications (HPCC)
To address the computational needs of NGS studies, we established a
custom condo and implemented powerful tools for NGS data analysis,
including Galaxy and Partek Flow on USC’s computer clusters HPCC
Computer Workstations at the NML Bioinformatics
Computation and Consulting Center
 Don’t have a computer or a
fast-enough computer to
analyze your data?
 Don’t want to bother with the
installation of bioinformatics
You can walk in the library and
use the dedicated workstations
pre-installed with key
bioinformatics software.
NML Bioinformatics ServiceNML Bioinformatics ServiceNML Bioinformatics ServiceNML Bioinformatics Service
Website: www.usc.edu/bioinformatics
Location: NML Bioinformatics Computing and
Consultation Center,
Norris Medical Library RM203A/B
Contact: Yi-Bu Chen and Meng Li
o SNP analysis and association studies
o Linkage disequilibrium and haplotype analysis
o CNV identification and association studies
o Genome-wide associate studies (GWAS)
o Family-based SNP and CNV association studies
o Advanced linear and logistic regression
o Interactive visualization
Golden Helix SNP and Variation Suite
Powerful statistical and visualization solutions
for SNP/CNV/GWAS data analysis
o Recombinant cloning strategies and protocols
o PCR primer design and analysis
o Multiple DNA/protein sequence alignment
o DNA sequence assembly
o DNA/protein annotation and visualization
Vector NTI Advance
Comprehensive software package for DNA/
protein sequence analysis and manipulation
Vector NTI Advance®
o Various types of NGS data analysis
o SNP/WGA data analysis
o Direct retrieval of sequence files from major
genome repositories
o Manipulation of text and various sequence files
o Multiple regression and multivariate analysis
o Metagenomics analysis
Web-based platform with many cutting-edge
tools for genomic research, particularly NGS data
o Direct import of NGS raw reads from all major
o Pre- and post-alignment QA/QC, subsampling and
o Implementation of popular aligners TopHat,
TopHat2, BWA, Bowtie, Bowtie2, TMAP, SHRiMP2
o Proprietary differential expression modeling for
o Variant detection (SNP and indel)
o Fusion gene detection
Partek Flow
Web-based application for NGS data alignment,
QA/QC, gene expression and variant detection
o Data analysis of major microarray platforms with
popular Bioconductor packages (limma, maSigPro,
o Custom chip description files and probe re-
o Versatile gene list output utility tool that
automatically generates input files for over 20 most
widely used functional analysis software (GSEA,
NIH DAVID, GenMAPP, Onto-tools, etc.)
Microarray Я US
User friendly R and Bioconductor tools for
Microarray data analysis
o Complete data analysis workflows for all major types
of microarray and NGS, such as:
 Gene expression and exon arrays
 SNP and copy number arrays
 Methylation arrays and ChIP-chip
 RNA-seq, DNA-seq, ChIP-seq, microRNA-seq
o Direct data import from all major platforms
o Versatile visualizations (PCA plot, histogram,
heatmap, dot plot, etc.)
o Genomic data integration
Partek Genomics Suite
Advanced statistical analysis and visualization
tool for microarray and NGS data
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o Explore gene expression patterns using Meta-Profile
analysis tool
o Identify genes specifically expressed in given
experimental conditions for biomarker discovery
o Identify co-expressed genes under various
experimental conditions with bi-clustering analysis
o Find the most stably-expressed genes as qPCR
reference genes
Genevestigator Advanced
Multi-organism pre-analyzed microarray
database and gene expression meta-analysis tool
o Determine expression profiles of selected gene(s)
across 41 cancer types, tissues, perturbations,
treatments, or other clinical parameters
o Analyze your own sets of genes or signatures
against all Oncomine concepts (gene sets)
o Use Outlier-analysis for biomarkers discovery
o Use Meta-analysis to look for consistency across
independent experiments
Oncomine Research Premium
World’s largest cancer transcriptome profiles
database and data-mining platform
o PROTEOME: comprehensive protein knowledgebase
o TRANSFAC: largest eukaryotic gene transcriptional
regulation knowledgebase
o ExPlain: unique analysis workflow that integrates
functional classification and upstream transcription
regulator identification for large list of genes
o HGMD: human inherited disease mutation database
o GenomeTrax: variation and functional annotation of
human NGS data
Comprehensive biomolecule knowledgebase for
proteins, transcription factors, and mutations
o Identification of the most relevant signaling and
metabolic pathways, molecular networks, and
biological processes and their potential activities for
large lists of genes
o Interactive search and exploration of bio-molecule
interactions supported by manually curated
literature findings
o Publication-quality pathway graphics of customized
networks and pathways
o Toxicity and safety analysis
Ingenuity Pathway Analysis
Excellent literature-based pathway, network, and
functional analysis tool for gene lists
o Discovering gene behaviors with the largest pre-
analyzed high-throughput genomic study database
(gene expression, mutation, GWAS studies,
epigenetic studies)
o Meta-analysis of user-selected genomic studies
o Functional correlation study of user data and public
data, Gene Ontology, and MsigDB.
o Intuitive user interface and versatile analysis reports
Nextbio - Genomics
Large collection of curated and analyzed genomic
data for data-mining and meta-analysis
o Comprehensive abstract (PubMed), full text
literature (PubMed Central and Elsevier) and clinical
trials (ClinicalTrials.gov) search
o Easy results filtering and search refining
o Quick grasp of key concepts with ad-hoc keyword
extraction and tag cloud display
o Speed reading with matching sentences/paragraphs
search and section search
Nextbio - Literature
Advanced biomedical literature search and
study tool
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