This is a sandbox where DigiSal members can learn to use the SEEK.
Tutorial document: http://tinyurl.com/seek-ds17
The SEEK is a web interface to a database of research "assets" organised in a hierarchical "ISA structure" (investigation-study-assay) .
These are further organised into projects and programmes.
* Programme = Overarching research theme (The Digital Salmon)
* Project = Research grant (DigiSal, GenoSysFat)
* Investigation = a particular biological process, phenomenon or thing
We are modelling ROS management and mitochondrial dysfunction. Mitochondria produce both energy and reactive oxygen species (ROS), and suffer from ROS. Experimental data from University Milan-Bicocca.
Pesticides, plastics, cosmetics, electrical transformers and many other products contain Endocrine disruptors (EDCs). EDCs interfere with natural hormone functions and may cause the disease.
The SilicoTryp project aims at the creation of a “Silicon Trypanosome”, a comprehensive, experiment-based, multi-scale mathematical model of trypanosome physiology.
Trypanosomes are blood-stream parasites transmitted by tsetse flies; they cause African sleeping sickness in humans and livestock. Currently available drugs have severe side effects, and the parasites are rapidly developing resistance.
In this project, we collect a wide range of new experimental data on the parasite in its various
Global metabolic switching in Streptomyces coelicolor
Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.
Public web page: https://www.wsbc.warwick.ac.uk/groups/sysmopublic/
Within the e:Bio - Innovationswettbewerb Systembiologie (Federal Ministry of Education and Research (BMBF)), the SulfoSYSBIOTECH consortium (10 partners), aim to unravel the complexity and regulation of the carbon metabolic network of the thermoacidophilic archaeon Sulfolobus solfataricus (optimal growth at 80°C and pH 3) in order to provide new catalysts ‘extremozymes’ for utilization in White Biotechnology.
Based on the available S. solfataricus genome scale metabolic model (Ulas et al., 2012)
"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling
Biomining is a biotechnological process carried out in many parts of the world that exploits acid loving microorganisms to extract metals from sulphide minerals. One industrial biomining method is called ‘heap bioleaching’ where typically copper containing minerals are piled into very large heaps, acid and microorganisms are added to the top and the soluble metal is collected at the heap base.
The role of the different types of microbes in the process is to speed up metal solubilisation by oxidising
The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
* facilitates and maximises the potential for data exchange between SysMO research groups;
* maximises the ‘shelf life’ and
There is an urgent need for novel antibiotics to fight life-threatening infections and to counteract the increasing problem of propagating antibiotic resistance. Recently, new molecular genetic and biochemical tools have provided insight into the enormous unexploited genetic pool of environmental microbial biodiversity for new antibiotic compounds. New tools for more efficiently lifting this hidden treasure are needed to strengthen competitiveness of European industry, as well as for a cost-saving