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Bioinformatics Resource
Description
The RPCI Bioinformatics Core Facility offers collaborative research and services in the areas of bioinformatics. The staff has experience and expertise in bioinformatics software/database development, customized data analysis, and providing bioinformatics infrastructure and training. Our specialties include but are not limited to: development of bioinformatics software and databases, analysis of high throughput data (e.g.: gene expression, array CGH, SNPs, large sequencing data, genome wide methylation), identification of transcriptional regulatory elements, mapping of pathways, gene annotation, identification of alternative splicing forms, etc. A list of examples for the types of projects we support is available here. Also, we are developing a tight partnership with the University of Buffalo, particular the Center of Computational Research (CCR), in coordinating the effort of providing bioinformatics service/support to the local biomedical research community.
Location
Buffalo Life Science Complex (BLSC) Rm# L2-231 (east end on the 2nd floor of the BLSC Roswell Wing, located at corner of Virginia St and ELM St).
Facility Personnel
Ping Liang, PhD, Director
Tel: 845-1556
Fax: 845-1698
Email: Ping.Liang@roswellpark.org
Jianmin Wang, PhD, Bioinformatics Scientist, Assistant Director
Tel: 845-8897
Fax: 845-1698
Email: Jianmin.Wang@roswellpark.org
Maochun Qin, MCs, Bioinformatics Programmer
Tel: 845-8897
Fax: 845-1698
Email: Maochun.Qin@roswellpark.org
Equipment
- Bioinformatics server (Beowulf cluster); Dell Workstations
- Access to the high performance computing facility at the Center of Computer Research (CCR) at University of Buffalo.
- Bioinformatics software and databases:
- In-house built or public resources: AutoPubMed, Vector NTI, GenePattern, geWorkbench, KaryoReader, digiNorthern, aCGHViewer, TRANSFAC, dbRIP, UCSC genome browser, BLAST server
- Commercial subscriptions (available to RPCI users only): GeneSifter (controlled web access), Spotfire, Methyl Primer Express, SDS 2_3, Chromas (all these 4 tools are accessible only from RPCI computers at here), TRANSFAC Professional V11.
Operating Schedule
Monday to Friday: 9am - 5pm
Services
The Bioinformatics Resource provides assistance in: 1) analysis of high throughput biological data (including but not limited to DNA sequences, gene expression, and array CGH data); 2) development of customized bioinformatics software, databases, and data analysis pipeline; 3) in silico analysis of existing public and/or in house data for gene discovery or feasibility testing; 4) access to high performance computation; 5) training for use of bioinformatics software/database; 6) providing write-up for the bioinformatics sections in manuscripts and grant proposals. A list of examples for the types of projects we support is available here.
Scheduling
All users please submit your job request through our online submission site. In the case of job overload, priority is given to funded projects and projects associated with immediate grant applications or manuscript submission.
Billing Procedure
The investigator’s grant is charged for services upon completion of all requested tasks except for services listed as free (see below for details) and projects providing salary support to the core staff members via grants. The light service fee (below 20% of the actual cost) is designed to help the facility to improve services by being able to pay for the cost of computer supplies, software and database subscriptions. Due to the low percentage of cost we are charging, we consider all support activities in which significant scientific input is provided as collaborations.
The fee scheme is based on the amount of time spent on the specific project (applying to all projects except for service listed as free and projects which provide salary support to the staff members at this core).
- A $50 setup fee covering up to a half day (4 hours) of work.
- $30 for additional half day of work.
- $200 for additional 1 week of work.
- $600 for additional one month of work.
The above fee scheme is for RCPI CCSG members and serves only as a guideline as the actual exact cost will be determined based on the specific needs of projects. For non-CCSG members and outside users different rates may apply. In addition to these fee-based collaborations and services, we also offer a variety of free services to our inside users. These free services include but are not limited to: 1) quick feasibility check and consultation, 2) simple sequence extraction, and 3) manuscript and grant writing. A bill of zero amount may also be sent to users for these free and grant paid services to allow us to keep a good record of services we provide.
Examples of bioinformatics projects
Click here to see a detailed list of examples for projects we support and click here to see of list of publications we contributed to.
