BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

An essential prerequisite for any systems-level understanding of cellular functions is to correctly uncover and annotate all functional interactions among proteins in the cell. Toward this goal, remarkable progress has been made in recent years, both in terms of experimental measurements and computational prediction techniques. However, public efforts to collect and present protein interaction information have struggled to keep up with the pace of interaction discovery, partly because protein-protein interaction information can be error-prone and require considerable effort to annotate. Here, we present an update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING); it provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information. Interactions in STRING are provided with a confidence score, and accessory information such as protein domains and 3D structures is made available, all within a stable and consistent identifier space. New features in STRING include an interactive network viewer that can cluster networks on demand, updated on-screen previews of structural information including homology models, extensive data updates and strongly improved connectivity and integration with third-party resources. Version 9.0 of STRING covers more than 1100 completely sequenced organisms; the resource can be reached at http://string-db.org.

https://www.zora.uzh.ch/id/eprint/41629/4/21045058_V.pdf

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network. This primer covers the theoretical basis of the approach, several practical examples and a software toolbox for performing the calculations.

/pdf/what-is-flux-balance-analysis-4wuuwjci7s.pdf

What is flux balance analysis

Motivation: Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods.

Results: Here, we present COPASI, a platform-independent and user-friendly biochemical simulator that offers several unique features. We discuss numerical issues with these features; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic--stochastic methods, and the importance of random number generator numerical resolution in stochastic simulation.

Availability: The complete software is available in binary (executable) for MS Windows, OS X, Linux (Intel) and Sun Solaris (SPARC), as well as the full source code under an open source license from http://www.copasi.org.

Contact: mendes@vbi.vt.edu

/pdf/copasi-a-complex-pathway-simulator-320i5gmr5f.pdf

COPASI---a COmplex PAthway SImulator

Application of a multiple
 Escherichia coli
 reporter strain to study population heterogeneity in a novel two‐compartment bioreactor

The gram-negative bacterium Pseudomonas putida is of increasing interest for industrial applications due to its intrinsic resistance to a broad range of stresses, its metabolic versatility, and the availability of genetic tools. Our group aims to introduce new metabolic pathways by genetic engineering to further expand the metabolic spectrum of this microorganism. Here, we summarize the process of engineering a sucrose consuming strain of P. putida, the obstacles found on the way, and how they were overcome to achieve a stable phenotype.

/pdf/friss-oder-stirb-erweiterung-des-substratspektrums-von-p-3huypz51fh.pdf

Andreas Kremling

Papers

Application of a multiple Escherichia coli reporter strain to study population heterogeneity in a novel two‐compartment bioreactor

Friss oder stirb! Erweiterung des Substratspektrums von P. putida

A counting-strategy together with a spatial structured model describes RNA polymerase and ribosome availability in Escherichia coli.