Bioinformatics Services Computational Tools for Biological Complexity

BioInformatics Services (BIS) is a biotechnology consulting firm specializing in applying the power of computational biology to build solutions to complex biological and data analysis problems faced by scientists in public and private research institutes, biotechnology companies, and universities. BIS is operated by Robert D. Phair, Ph.D.

What's New ?

KinMet2008 - We cordially invite you to attend KinMet2008, an unofficial satellite meeting of the AHA/ATVB meeting. This year we are meeting on April 15 at the Omni Hotel in Atlanta. All investigators interested in kinetic analysis of lipid, lipoprotein and sterol metabolism are welcome. Details and current schedule of talks are on the KinMet2008 page.

MABS Study Section - A new NIH study section devoted to modeling an analysis of biological systems has been formed. It is managed by Malgorzata Klosek who is very aware of the issues surrounding modeling grants and whom you might want to know. This new study section is chaired by Les Loew from NRCAM. Drs. Malgorzata and Loew have recruited an impressive roster of biological modeling expertise. Definitely worth looking into.

Science Reprint on kinetic analysis of RNA Pol I dynamics in vivo

Nature Reprint on COPI and Arf1 dynamics in Golgi membrane transport

IntegrativeBioInformatics.com - BioInformatics Services is partnering with Integrative BioInformatics, Inc. (Los Altos, CA) to develop database support for the modeling process. If your interest lies in mechanistic analysis of large-scale biological systems, you might enjoy exploring our partner's newest software tool, ProcessDB. ProcessDB will be in beta testing February- June, 2006. Check us out and consider joining our group of smart, thoughtful early adopters for this beta test. We've been thinking about the problems faced by modelers for decades and we think we've solved some of the most important problems you all face.

Kinetic Modeling Approaches to Live Cell Imaging - Reprints available of this review published in the December 2001 issue of Nature Reviews Molecular Cell Biology

Nature Reprint on Kinetics of Protein Movement in the Mammalian Nucleus

NIGMS Grant Supplements for the Study of Complex Systems

Reprint on Nonlinear Modeling in Molecular Cell Biology

Modeling and Computational Biology Services - Integrative Bioinformatics

We find that some potential clients want to maintain a detailed understanding of all the computational steps taken in data analysis and model formulation and testing. These clients are interested in, and have time for, their own hands-on involvement in the computational biology. Our service to such clients includes the education and training necessary to establish integrative bioinformatics and advanced modeling techniques among their laboratory's core competencies.

We have years of award-winning experience in teaching these skills, enabling us to render a service that goes well beyond the solutions we provide to current problems. For larger research groups, we also offer 2-day private workshops on Kinetic Modeling of Biological Systems. Here is a sample workshop program.

Other clients prefer to stay focused on experimental work or on whatever else is their core skill. They see the power of computational tools, but cannot spare the time required to become expert in the methods of modern computational biology. Neither can they afford to hire a full-time staff person with expertise in this area. Such clients often choose complete outsourcing of their modeling and integrative bioinformatics work, relying on detailed project reports or BIS-written technical sections of their papers submitted for publication for documentation of the approach we take and the solutions we reach.

BIS supports the entire spectrum from hands-on partnering to outsourcing entire projects. If you are unsure how much you can or should do yourselves, contact us at BioInformatics Services.

Our selling points are:

• Rapid project completion
• We have the skill and experience to work at all levels of biological organization from molecular to physiological
• We speak the language of biomedicine fluently
• We know, from long experience, the difficulties of experimental biology and clinical research
• We can help formulate the big picture
• We support the transition from genomics to cell biology and physiology
• We are data-centered and discipline-aware

We can add significant, measurable value to your research enterprise. Give us a call (1.301.315.8114) or send us e-mail (info@bioinformaticsservices.com). If your need is not immediate, and you are eligible for an NIGMS supplement to your existing NIH investigator-initiated research grant, you may want to consider the recent NIGMS Program Announcement as a mechanism to fund a collaboration with BioInformatics Services. If this interests you, please read how BIS can help you take advantage of the new NIGMS initiative.

What does BioInformatics Services do that would benefit me? A series of specific scenarios describing problems we can help solve.

Free Resources for Modeling and Computational Biology

• Bob Phair's CyberTextbook: Integrative Bioinformatics: Practical Kinetic Modeling of Biological Systems (the version of this book on the IBI website is the one being actively maintained)

About the Author

Contents A Step-by-step Procedure for Model Development and Testing

Chapter 1 The Rationale for Kinetic Modeling

Chapter 2 Assembling Your Experimental Data

Chapter 3 Drawing a Rigorous Symbol and Arrow Diagram for Your System

Chapter 4 Converting Your System Diagram to Mathematics: The Central Importance of Rate Laws

Rate Laws for the Three Major Classes of Biological Processes:

Chapter 5 Writing Rate Laws for Molecular Interactions: Binding

Chapter 6 Writing Rate Laws for Chemical Reactions: Transformation

Chapter 7 Writing Rate Laws for Transport Processes: Translocation

• Computational Biology FAQ (Frequently Asked Questions) A small but growing collection of answers to questions often asked of kineticists, modelers, and other computational biologists. I've written many questions, but only a few answers are complete. If you would like to see other questions added, or if you would like me to push one of the unanswered questions toward the top of my to-do list, or if you want to comment on my answers, send me a message.
• Other Useful Sites on the World Wide Web Come browse!
• Free Workshops on Kinetic Modeling and Computation in Biomedicine