All of the facilities, equipment, and software resources for molecular biology, tissue culture, histology, immunohistochemistry, bioinformatics, and modeling are available in the wet lab area, continuously available to the Institute faculty.
The Daniel Baugh Institute has 2200 square feet of wet lab space. The wet labs are divided into rooms or spaces suitable for tissue culture (dedicated room with incubators, hood, microscope, and storage), histology, microscopy – laser capture microdissection, molecular biology and neurophysiology. All of the equipment for tissue culture, molecular biology and gene expression profiling studies in the wet lab areas are dedicated to Institute researchers’ use. There is a full neurophysiology suite containing three complete electrophysiology/recording/analysis setups. The appropriate oscilloscopes, surgical microscopes, amplifiers, air tables, computers and analytical software etc. are in place. The laboratory has enough room for appropriate areas dedicated to animal surgery, brain slice preparation, solution preparation, electronics manufacturing, 3 full physiology stations, each with an air table and associated electronics racks, and counter space for electrode pullers, balances, and other equipment, 2 sinks, and a house distilled water line.
The computer lab (JAH 318) is 800 square feet containing 10 reconfigurable computer work areas and two conference areas used for bioinformatics and computational biology. This software lab contains a Sun Enterprise 4500 server w/ 6 CPUs; 14 GB contiguous RAM, 500 GB Disk, and a Dell 2900 server with 8 CPU cores, 16GB contiguous RAM, 6TB Disk.
Two computational servers (Dell R910), each with 32 Xeon X7560 CPU cores, 256GB RAM and 12TB raw storage, are housed at the Thomas Jefferson University Data Center and available over a private network at a 10Gbps bandwidth. There are ten high-end Dell Engineering Workstations, running Windows or Linux OS and a high end Mac Pro workstation with 8 CPU cores, 20GB RAM and 1.5TB Disk storage. All computers are on a Local Area Network (LAN) with 100Mbps switching connecting all computers. UNIX, LINUX, OSX and Windows operating systems are used. There are specialized in house and licensed software for modeling and simulation studies, statistical analyses, sequence analysis and for microarray analysis. We have software licenses for Transfac Pro, GeneSpring, Partek Genomic Analysis, Fluidigm Genetic Analysis Suite, and Matlab. We have our own in house bioinformatics tools such as the PAINT suite
The Daniel Baugh Institute is part of the Department of Pathology, Anatomy, and Cell Biology, with access to the clinical pathology services, especially Surgical Pathology for assistance in cell identification for laser capture microdissection.
Animal facilities are in the same building as the laboratories and offices at Thomas Jefferson University. They are AAALAC accredited, and overseen by a licensed veterinarian and staff.
There are six offices with a conference area and kitchen adjacent to the wet labs. In addition, there are several desks inside the wet lab space used by support personnel. In addition, the Computer Lab described above also serves as overflow office space when needed.
Thomas Jefferson University provides Core facility support for histology, DNA sequencing, and DNA synthesis. Several faculty of the Daniel Baugh Institute are members of the Program for Computational System Biology, a regional consortium of researchers promoting biomedical application of engineering and computational approaches, and members of the Greater Philadelphia Bioinformatics Alliance. This provides access to additional expertise in data analysis, bioinformatics, and modeling and simulation.
The Fluidigm BioMark high-throughput qRT-PCR system
The Institute has a BioMark system with MX 48.48, HX 96.96, ad RX 192.24 Controllers. The BioMark platform provides novel experimental design opportunities due to both high capacity and nanoliter reaction volumes. The ability to run over 2000-9000 reactions (up to 96 samples assayed for 96 amplicons in a typical single run) allows for statistically robust clinical sample cohorts. The small volume requirements allow for both RNA and DNA analyses from samples as small as a single cell.
Access to Next-generation Sequencing systems:
The next-generation sequencing systems that we have access to through regional core facilities offer sufficient throughput and cost effectiveness for the proposed work at Thomas Jefferson University (TJU), Penn Genome Frontiers Institute, the Wistar Institute and University of Delaware (UD).
Thomas Jefferson University Sequencing Core Facility:
The two AB SOLiD 5500XL sequencing systems at TJU can process a total of 24-48 samples at a time generating 100-250 millions of reads per sample. This enables an expected coverage of >80% of the transcriptome, even at typical 60-65% mappability. The SOLiD system at TJU can sequence 50 bases from the 3’ end and up to 35 bases from the 5’ end, giving us a read depth that when combined with the number of total reads is sufficient for transcriptomic analysis.
The University of Delaware DNA Sequencing & Genotyping Center:
This Center provides state of the art genetic analysis for University of Delaware research groups and outside users on a fee-for-service basis. The center has a Illumina HiSeq 2000 as well as a Pacific Biosciences RS Single-Molecule Sequencer. The HiSeq 2000 sequencing system offers unprecedented output and a breakthrough user experience. Leveraging Illumina's proven and widely-adopted, reversible terminator-based sequencing by synthesis chemistry in combination with innovative engineering, HiSeq 2000 delivers the industry's highest sequencing output and fastest data generation rate. Human interaction design features and the easiest sequencing workflow set a new standard for simplicity and user experience.
Penn Genome Frontiers Institute High-throughput Sequencing Facility:
In this facility, investigators have access to different types of HTS technology: Illumina’s HiSeq and Applied Biosystem’s SOLiD4 and 5500xl. With two HiSeqs, the facility can provide the latest innovation from Illumina featuring up to 3 billion paired-end reads (up to 100x100 bp reads) per flow cell, 8 lanes per flow cell and 2 flow cells per machine. With the SOLiD4, the facility can provide up to 1.4 billion reads per slide, 50 x 25 bp paired-end reads, up to 8 sectors per slide and 2 flow cells per machine. With the 5500xl, the facility can provide up to 180 Gb or more than 2.8 B reads per run. The 5500xl offers 75 bp fragment runs, 75x35 bp paired-end runs and up to 60 bp x 60 bp mate paired runs with the added bonus of pay-as-you-go sequencing. All platforms offer multiplexing capability. Currently Illumina offers 48 barcodes and Life Technologies offers 96 barcodes. The SOLiD 4 system provides greater than 99.94% accuracy due to 2-base encoding. The 5500xl offers up to 99.99% accuracy utilizing 2-base encoding and Exact Call Chemistry.
High-performance Computing at University of Delaware:
High-performance Computing at University of Delaware:
Drs. Schwaber and Vadigepalli are Adjunct Faculty in Chemical Engineering at University of Delaware and have access to access to the Mills cluster, a 5136-core, 200 SMP node, high performance cluster system. In addition to priority access to a compute node, we also have opportunistic access to any of the idle processors owned by others. The 64 TFlops (peak) cluster is based on 24/48-core AMD Opteron 6234 Interlagos processors, AMD’s newest chipset. It is complemented by a 40 Gbps QDR InfiniBand interconnect, a 288 (raw) TB Lustre-based filesystem, with an additional 200 TB of local node scratch. A rich software environment is being installed including Scientific Linux 6, Oracle Grid Engine job scheduler, application software development tools, compilers and scientific libraries, and a wide range of open-source and commercial software. This is the first in a series of community clusters UD is developing and supporting over the next 5 years.
Daniel Baugh Institute
- Computational modeling analysis of mitochondrial superoxide production under varying substrate conditions and upon inhibition of different segments of the electron transport chain
- Silence on the relevant literature and errors in implementation
- Multiscale model of dynamic neuromodulation integrating neuropeptide-induced signaling pathway activity with membrane electrophysiology
- Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modelling
- Identifying functional gene regulatory network phenotypes underlying single cell transcriptional variability