Tools & Technology Seminar series

NCIBI holds a weekly seminar each Thursday, at 12 noon EST, highlighting a tool or technology that is under development or currently being used by NCIBI researchers. These seminars are streamed live using Adobe Connect and are also are archived and made available on the list below for future viewing via Flash video streaming.

The aim of the NCIBI Tools & Technology Seminar Series is to have open and interactive discussions about the software tools and technologies being used in NCIBI led by the people doing the work. Participation is strictly voluntary and based on interest. Collaborators and other interested parties are welcome to attend.

Date	Presenter	Seminar Title
5-2-2013	Mallory Freeberg	A novel pipeline for identifying transcriptome-wide binding sites of RNA-binding protein from PAR-CLIP sequencing data
4-25-2013	Jeremy Hallum	Services for Computations and storage for researchers in the Medical School: Update for 2013
4-18-2013	Guido Scarabelli	Dynamical network analysis of kinesin motor domain
4-11-2013	Dongxiao Zhu	RNA-seq to Capture Transcriptome Landscape - Methods, Algorithms, and ComputationalTools
4-4-2013	Jianyi Yang	BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions
3-28-13	Hui Jiang	Analyzing RNA-Seq data using rSeq
3-21-2013	Michelle Wynn	Using parameter free logic models to investigate network dynamics
3-14-2013	Terry Weymouth	Grails a framework for Web-Based application
3-7-2013	George Michailidis	Pathway enrichment tools: statistical models and methodological issues
2-28-2013	Vasudeva Mahavisno	Developing Mobile applications for bioinformatics
2-21-2013	Yanxiao Zhang	PePr: a Peak-calling and Prioritization pipeline to test group differences in ChIP-Seq data
2-14-2013	Nickolay Khazanov	Analysis of 3,000 Cancer Exomes to Identify Novel Cancer Drivers and Therapeutic Opportunities
2-7-2013	Rich McEachin	The Tuxedo RNA-Seq Analysis Suite
1-31-2013	Terry Weymouth and Alex Ade	Tools for software development: Git, the GitHub archive, and Jenkins
1-24-2013	Ashwini Bhasi and Zach Wright	Winnow: A tool to filter and prioritize NGS datasets to extract user-specific results
1-17-2013	Mark Reppell	Incorporating faster than exponential population growth into the coalescent using FTEC
12-20-2012	Hyun Min Kang	Genomes on the Cloud: A scalable pipeline from raw sequence data to complex disease mapping
12-13-2012	Chao-Yie Yang	Evaluation and identification of potential small molecule binding sites at protein-protein interaction interface
12-6-2012	Stephen Smith	Next generation phylogenetics: emerging technologies and techniques for non model organisms
11-29-2012	Willy Wriggers	Situs and Sculptor: Next Generation Tools for the Computational Interpretation of 3D Electron Microscopy and Tomography Data
11-16-2012	Bob Lyons	How to Keep Up in Genomics
10-25-2012	Ulysses Balis	Ephemeral Images, Indelible Data: The Promises and Challenges of Digital Imaging as Applied to Pathology
10-18-2012	Cody Sheik	Application of meta'omics to understand the microbiology of the deep-sea
9-27-2012	Gang Su	Tools for Network Analysis Roundup
9-20-2012	Terry Weymouth, Brian Athey	tranSMART
9-13-2012	Alla Karnovsky	Connecting metabolites to diseases
9-6-2012	Matthew Iyer	High-throughput RNA sequencing to comprehensively annotate the human cancer transcriptome
5-10-12	Patrick Schloss	Next generation sequencing and microbial ecology
5-3-12	Curt Bagne	Causality Assessment with Multiple Time Series Data (slides in PDF) (final annotated slides in PDF)
4-26-12	Yongsheng Bai	SNPAAMapper: an efficient genome-wide SNP variant analysis pipeline for next-generation sequencing data
3-22-2012	Alfred Hero	Biomarker discovery for predicting health and disease
3-15-2012	Jeremy Hallum	Flux: a computational tool for research at the University of Michigan
3-8-2012	Barry Grant	The Bio3D package for comparative analysis of protein sequence, structure and dynamics
3-1-2012	Ryan Welch	ChipEnrich: gene set enrichment for ChIP-seq data
2-23-2012	Sira Sarntivijai	Cell Line Ontology and the collaboration to move towards translational informatics
2-16-2012	Datta Mellacheruvu and Zach Wright	Building and Using Contaminant Repositories for Scoring Protein-Protein Interactions
2-9-2012	Julie (Jung) Kim	LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types
2-2-2012	Yuanfang Guan	Exploring on-line functional networks
12-15-2011	Patrick Nelson	Translating Glucose Variability Metrics into the Clinic via a Continuous Glucose Monitoring Graphical User Interface for Diabetes Evaluation (CGM-GUIDE)
12-8-2011	Hui Jiang	Read alignment for the next generation
11-17-2011	Lior Shamir	Bioimage Informatics: An emerging area of BioEngineering
11-10-2011	David Hanauer	Issues and Approaches for using Time and Motion Methods to Study Workflow in Health IT
10-27-2011	Christoph Jacob	Validation of Gene Ontology mapping results
10-20-2011	Srayanta Mukherjee	TACOS: Template based assembly of complex structures
10-13-2011	Manhong Dai	The MBNI Cloud+: Secure high performance biomedical computing through a cost effective co-op model
10-6-2011	Ye Li	Structure-based search for small molecules in biomedical research
8-25-2011	Jim Cavalcoli, Yongsheng Bai, Yu-Hsuan Lin	ISMB 2011 - Recap
6-9-2011	Marci Brandenburg	Exploring bioDBnet: A Database for Converting Between Database Identifiers
6-2-2011	Aaron Bookvich and Zach Wright	Building Websites and Custom Applications in Drupal
5-26-2011	Susan Dombrowski	Uncovering the Biology in Your Data with Genomatix Software
3-31-2011	Debprakash Patnaik	Discovering Excitatory Networks from Discrete Event Streams with Applications to Neuronal Spike Train Analysis
1-20-2011	Sebastian Martini	Functional genomic based hypothesis generation through combination of transcriptional modeling and pathway analysis in diabetic nephropathy
1-13-2011	Gil Omenn	The Emerging Global Human Proteome Project (HPP)
11-18-2010	Alex Ade, Glenn Tarcea, and Zach Wright	NCIBI Web Services - The Next Generation
11-11-2010	Eric Shah	A Synergistic Collaboration Between MiMI Molecular Interactions and Drug Path Oncology Pharma Pipeline Database
10-28-2010	Alla Karnovsky, Terry Weymouth, Tim Hull, Glenn Tarcea	Linking Genes and Metabolites with Metscape 2.0
09-30-2010	Zhenjun Hu	Integration of VisANT and NCIBI Tools
09-23-2010	Raphael Isokpehi	Functional Annotation Analytics of Gene Families
09-16-2010	Yongsheng Bai	Illumina Genome Analyzer Pipeline & CASAVA
09-10-2010	Rich McEachin	Chip-Seq assessment of Growth Hormone Response via STAT and BCL transcription factor binding
06-10-10	Jen Steiner-Tonks	What Can Usability Tell Us About Interdisciplinarity?
06-03-10	Jing Zhang	Tracing Provenance of MiMI Data
05-27-10	Anna Shaverdian	Algebra basis for biological network analysis
05-20-10	Sirarat Sarntivijai	NCIBI tools to translate clinical data to bioinformatics practice: a case study of Influenza vaccine adverse events
05-13-10	Marcio Mourao	MIKANA: Method for the Inference of Kinetics And Network Architecture
04-29-10	Andrew Hodges	Edge Clipper: A Computational Algorithm For Bayesian Consensus Network Refinement
04-08-10	Gang Su	Identification of Significant Metabolic Fingerprints in NCI-60 Dataset
03-26-10	Arzucan Ozgur	Biomedical Information Extraction and Literature-based Discovery
03-18-10	Glenn Tarcea	MiMI Data Pipeline Load, merge & display Gene, Interactions & Metabolomics data at NCIBI
03-04-10	Beth Kirschner	Biositemaps - the CIRWP Explorer and the Editor
02-25-10	Rich McEachin	Lithium in Bipolar Disorder
02-04-10	Alex Ade	Using Web Services to Access NCIBI Data
01-21-10	Tolulola Oyeleye	Automatic classification of bioinformatics abstract text
12-10-09	Chris Maher	Analysis of Next Generation transcriptome sequencing to detect chimeric transcripts
11-11-09	Weijian Xuan	PubAnatomy: Integrated Exploration of Biomedical Literature and Data in the Context of Mouse Brain Anatomy
11-05-09	Josh Buckner	"A gpu enabled package for the R statistical environment"
10-08-09	Matt Huyck	"An Overview of VisANT and a Peek Inside"
10-01-09	Tolulola Oyeleye	Bioinformatics Tools Categorizer
09-17-09	Alla Karnovsky	Overview of the Tools for Visualization and Analysis of Biological Networks Containing Experimental Data
08-27-09	Aaron Bookvich	The NCIBI Portal: Highlights and Features
08-20-09	Jing Zhang	Tracing Provenance of MiMI Data
08-13-09	Yuehua Cui	Identifying novel pathway regulators in eQTL mapping: a systems biology approach Identifying novel pathway regulators in eQTL mapping: a systems biology approac
07-23-09	Anna Shaverdian	A Network Based Pattern Matching Approach to Protein Function Prediction
06-18-09	Abhik Shah	"anyCloud: python library to run code on a variety of grids and cloud computing platforms"
06-11-09	Sirarat Sarntivijai	"Ontology Integration in the Framework of Translational Informatics"
06-04-09	Haiming Chen	Functional analysis of gene expression data in bipolar disorder
05-21-09	Gang Su	Robust Estimation of Correlation between Metabolomics and Transcriptomics data
05-07-09	Jim Cavalcoli	Genomic Resequencing using Illumina Technology Genomic Resequencing using Illumina Technology (Next-Gen Sequencing)
04-16-09	Arzucan Ozgur	Biomedical Information Extraction using Text Mining and Network Analysis Methods
04-09-09	Beth Kirschner	"Biositemaps: what, why and how to use them"
04-02-09	Ben Keller	Molecular Psychiatry: It's not all downhill (Conference Report)
03-19-09	Kay Robbins	Browsing large scale microarray data sets
03-12-09	Xiaosong Wang, Maureen Sartor	M-score statistics
03-05-09	Yongsheng Bai	Uncovering Genetic Factors Contributing to Type 2 Diabetes an Diabetic Nephropathy
02-26-09	Weijian Xuan	Cross Internet Application Integration
01-22-09	Rich McEachin	Comorbid Bipolar Disorder with Nicotine Addiction
12-04-08	Mor Peleg	Using the BioWorkflow model to represent and reason with biological systems
11-20-08	Marci Brandenburg	Life and Times of the Laptop Librarian
11-05-08	Maureen Sartor, Vasu Mahavishnu	Conceptgen: A concept mapping and gene annotation tool
10-30-08	Qiang Tian	Loss of N-myc downstream-regulated gene 1 (NDRG1) increases prostate cancer cell invasion by upregulating CCL5
10-23-08	Sharon Lewis	Molecular Genetic Analysis of COMT in Bipolar Disorder
10-16-08	Wayne Wilson	Storage trends and Medical School Information Systems response
08-28-08	Manhong Dai, Tyler Brubaker, Walter Meixner	High performance computing with the Depression Center-NCIBI cluster
08-22-08	Jim Cavalcoli	Technology Basics: Nucleic Acid Hybridization and Sequencing Methods
06-25-08	Lisa Allred, David Hanauer	The Electronic Medical Record Search Engine (EMERSE)
06-05-08	Santiago Schnell	XPP/AUTO: A tool for solving differential equations in computational biology
05-29-08	Jean Song, Marisa Conte	MiSearch Evaluation: Pilot Usability Test
05-22-08	Vince Chmielewski	Enhancing the NCIBI Development Process with JIRA: Bug tracking, issue tracking and project management software
03-14-08	Mark Iwen	Scalable Rule-Based Gene Expression Data Classification
03-06-08	Manhong Dai, Justin Wilson	CPU and Storage Clustering for Common Bioinformatics Problems
02-28-08	David States	MiMI R2
02-21-08	Jim Cavalcoli	MBI-NextGen: Data Warehouse for NCIBI
02-07-08	Terry Weymouth	NCIBI Tools: Overall Architecture
01-31-08	Alex Ade	NLP with Pubmed Central and Full Text Databases
01-17-08	Glenn Tarcea	MiMI Data Build and Merge Process
12-20-07	Molly Kleinman	Copyright Essentials for NCIBI
12-13-07	Jun Li	Next Generation Sequencing: Principle, Application and Challenge
11-29-07	Jing Gao	Cytoscape MiMI Plugin
11-15-07	Elvis Jakupovic	Comparative Analysis of Abstracts from the Society for Neuroscience Meetings and Medline: Trends and Fun Facts
11-08-07	Dave Strenski	Supercomputing using FPGA
10-25-07	Fan Meng	In silico evaluation of Knowledge-based data analysis results
10-18-07	Steve Qin	Literature-based distance measure reflects relationship among genes
10-11-07	Fan Meng	FunctionScore: a flexible frame work for knowledge-based high throughput data analysis
10-04-07	Abhik Shah	Bubble and Bayesian Networks in Biology
09-27-07	Maureen Sartor	Improvements in genome-wide Microarray analysis and an application to ChIP-chip (chromatin immunoprecipitation on chip) data
09-20-07	Ben Keller	Revisiting Genetic Influences
09-13-07	Axel Mosig	Reading the Genome between the Lines: Homology Search based non-coding RNA gene finding
09-06-07	Naren Ramakrishnan	Compositional Mining of Multi-Relational Biological Datasets
08-23-07	Tim Wiggin, Kelli Sullivan	Mouse Models of Diabetic Complications
08-16-07	Tim Wiggin, Kelli Sullivan	Microarray Analysis of a Large Tissue Bank of Human Sural Nerves
08-09-07	Jim Cavalcoli	Recap of 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)
07-26-07	Sandeep Tata	Periscope/SQ: Declarative Querying on Biological Sequence Databases
07-19-07	Jignesh Patel	SAGA and TALE update: NCIBI Graph Analysis Tools
07-12-07	Andrea Califano	Cancer DBP Presentations NCIBI and MAGNET
07-05-07	Rich McEachin	Prioritizing Disease Genes by Analysis of Common Elements (PDG-ACE)
06-28-07	Steve Qin	Flexible model-based clustering of gene expression microarray data using Chinese restaurant process
06-21-07	Oliver He	Web-based bioinformatics systems for study of pathogen-host interactions
05-24-07	Ben Keller	Recommendation within the Resourceome
05-17-07	Jim Cavalcoli	Survey of External Tools and Databases for use with NCIBI
05-10-07	Terry Weymouth, Tim Wiggin	GenePattern applications and integration in NCIBI
04-26-07	Kai Zheng	User Interface Optimization for an Electronic Medical Record System
04-19-07	Xiaosong Wang	From identification of a novel urine marker for bladder cancer to construction of human potential cancer targets database
04-12-07	Barry Smith	The OBO Foundry: Towards Gold Standard Terminology Resources in the Biomedical Domain
04-05-07	Manhong Dai, Justin Wilson, Elvis Jakupovic	Supercomputing with Toys
03-29-07	Weijian Xuan	PubViz: A Graphic Search Engine of Medline Database
03-22-07	Beth Kirschner	NCIBI Portal Workshop
03-15-07	Ben Keller	Strategies for Finding Genetic Interactions in Complex Disease
03-08-07	Elvis Jakupovic, Bohua Yu	A RDF database for community-wide biomedical knowledge capture, integration and mining
03-01-07	Michael Reich	GenePattern 3.0 Preview
02-22-07	Robert Murphy	Image Data Integration
02-15-07	Sirarat Sarntivijai	An Ontology Describing Cell Lines
02-08-07	You Jung Kim	Follow up and next generation MiBLAST
02-01-07	Junguk Hur	Defining Reactive Oxidant Genes
01-25-07	Doug Hockstad	Overview of Technology Transfer
01-18-07	Bohua Yu, Cong Yu	Database Schema Summarization
01-11-07	Abhik Shah	Bayesian Networks
01-04-07	Terry Weymouth	MiMI
12-14-06	Celine Berthier	Gene Expression Regulation in Renal Disease
12-07-06	Carlos Santos	NLP Resources at the NCIBI - Data Resources and Corpus Summarization
11-30-06	Jim Ottaviani	Deep Blue
11-16-06	Chris Mungall	Chado Database
11-09-06	Alex Ade	Semantic Integration of NLP
10-26-06	David States	Pathways and Microarrays GSEA <> ExpBlast
10-19-06	Manhong Dai	Web-based GeneChip Analysis System
10-12-06	Damian Fermin	Whole genome proteomics
10-05-06	Anthony Fader	Language processing, information retrieval, and summarization using clairlib
09-28-06	Beth Kirschner	The Sakai Product, A Collaboration and Learning Environment
09-07-06	Arvind Rao	Computational Tools for Understanding Transcriptional Regulation
07-13-06	Terry Weymouth	The Design of a geWorkbench Module
07-05-06	Barbara Mirel	Interactive Visualizations, Re-envisioning Users' Exploratory Analysis
06-29-06	Terry Weymouth	Building a module in GenePattern
06-22-06	Anne Jackson	Potential uses of SNP annotation in the analysis of genome-wide association data from the FUSION type 2 diabetes study
06-15-06	Aaron Bookvich	An Introduction to Plone & The NCIBI Collaboration Sites
05-25-06	Andy Caird	A brief introduction to the Center for Advanced Computing
05-18-06	Mark Musen	Biomedical Ontology
05-11-06	Michael Reich	Genomic Analysis and Reproducible Research with GenePattern
05-04-06	Damian Fermin	Genome Search for Novel ORFs Using the HUPO PPP Data
04-20-06	Aris Floratos	geWorkbench
04-13-06	Rich McEachin	Understanding Genetic Influences on Susceptibility to Bipolar Disorder
04-06-06	You Jung Kim	miBLAST, Scalable evaluation of a batch of nucleotide sequence queries with BLAST
03-30-06	Rich McEachin	GeneGo
03-23-06	Inna Dubchak	VISTA
03-16-06	Glenn Tarcea	MiMI, A Biological Data Warehouse on a native-XML Database
03-09-06	David States	NCBI, OMIM and web resources for bioinformatics
02-16-06	Aaron Elkiss	Extensible Information Retrieval with Apache Nutch
02-09-06	Dragomir Radev	NLP/IR Tools Developed at the CLAIR Lab
02-02-06	Weijian Xuan	Automated Extraction of Genetic Marker Information from Biomedical Literature
01-26-06	Carlos Santos	NLP in Biomedicine
01-19-06	Yuanyuan Tian	SAGA, A fast and flexible graph matching tool
12-15-05	Terry Weymouth	Kepler Workflow System
12-08-05	Sirarat Sarntivijai	Gene Pattern
12-01-05	Jeremy Phillips	Molecular Biology Integration Database
01-12-05	Dan Rhodes	Oncomine