Potential-Client Scenarios

If you see yourself in one of these situations, we would suggest you have a lot to gain by contacting BioInformatics Services.

• You have lots of data with time plotted on the horizontal axis. You have a working hypothesis and you want to know if your data support your theory.
• You are studying the secretory pathway in a cultured cell line. Your experimental protocol is fundamentally a classical pulse-chase, but you are exploring the mechanism of action of a supposedly Golgi-specific drug by changing the cell medium to one containing the drug after 15 minutes of chase. It's obvious from your data that the drug induces a transient, and you are not sure whether your ³⁵S-methionine tracer data can be analyzed in this non-steady state.
• You are studying regulation of the cell cycle. You have measured the kinetics of cells as they move from G₁ to S to G₂ to M. You also have time series data on the expression of several cyclins and cdks, as well as a new protein inhibitor of cdk2-cyclinA. You want to determine whether your favorite mechanism can actually account for your kinetic data.
• You have a beta-test version of a new oligo array detection system. You've collected expression data on an enormous number of gene products in response to various estrogen and retinol derivatives. You want to quantitate the effects of these physiological and pharmacological perturbations, taking account of the highly interconnected nature of the expression control system.
• You have performed a primed-infusion of d3-leucine in a group of children diagnosed with one of several closely related inherited diseases. You want to determine the fractional catabolic rates and production rates for several key enzymes present in blood plasma.
• You have been working with the fluorescent Ca²⁺ indicator, Fura 2, and have measured Ca_i transients in response to several receptor agonists. In addition you have measured InsP₃ concentration time courses and you would like to compare the predictions of a recently published theory to your experimental results. If possible you would also like to analyze simultaneously your data on ER calcium content in response to InsP₃.
• You are a pharmacokineticist responsible for a drug candidate whose plasma kinetics suggest a very slowly turning over compartment. You know that protracted low dose exposure could be associated with undesirable side effects, so it's critical that you extract as much information as possible from the available experimental data.
• You have recently discovered a third signaling cascade that is a powerful modulator of the transcriptional response you are measuring. In response to your physiological perturbation, you now have time course measurements for 7 signaling molecules in these three cascades and you need to quantitate the relative importance of each pathway.
• Using the Biacore® device or similar protocol, you have recorded extraordinarily complex on- and off-kinetics for the binding of a novel peptide ligand of an established transcription factor. You want to incorporate these findings in a working model of combinatorial control and promoter specificity.
• You have measured the time course of mRNA and protein concentrations for six genes that are turned on by PDGF. You want to sort out cause and effect, and to test your current hypothesis concerning this regulatory cascade.
• You have a group of 10 - 30 investigators and students who want to learn how to use the SAAM II software for the formulation and testing of biological models based on detailed analysis of their own experimental data. You are looking for a workshop leader with extensive experience and outstanding presentation skills.

These scenarios have a common theme. Each investigator has important mechanistic questions about a biological system. Each has collected data with time on the horizontal axis. Some call these data a time series, some describe it as a time course, others say they are measuring the kinetics or dynamics of the response.

All have the intuitive knowledge that dynamic measurements often yield pivotal mechanistic information, and all need access to the powerful integrative tools of modern computational biology. Some may want to bring these computational tools into their laboratories, others will want to conserve their time and personnel resources to concentrate on what they do best. BioInformatics Services aims to help both groups.

We can help you learn to apply these tools to your own research problems; we can get you up to speed and productive. We call this, in the current business parlance, "partnering." For those who see the potential of computational approaches, but who wish to concentrate on their existing core skills, we can take full responsibility for the computational aspects of a project and keep you abreast with well-written, cogent and compelling project reports. The current phrase for this arrangement is "outsourcing." Again, if you see your own situation reflected in those outlined above, you owe it to yourself to explore the possibilities with BioInformatics Services.

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