SOPs
What is a SOP?Filters
Standard Operating Procedure describing the process and software used in generating a Genome Scale Metabolic model of M. hyopneumoniae. Used software: Pathway tools PathLogic Cobrapy the Cobra Toolbox libSBML
Creator: Niels Zondervan
Submitter: Niels Zondervan
We have adapted the definitions of terms in [ISA best practice][1] and [programmes and projects][2]:
Programme = Overarching research theme (The Digital Salmon) Project = Research grant (DigiSal, GenoSysFat) Investigation = a particular biological process, phenomenon or thing (typically corresponds to [plans for] one or more closely related papers) Study = experiment whose design reflects a specific biological research question Assay = standardized measurement or diagnostic experiment using a ...
Creators: Jon Olav Vik, Natalie Stanford
Submitter: Jon Olav Vik
Describes the cultivation-, washing- and electroporation-steps required in order to transform bacterial cells with DNA.
Creator: Maximilian Bahls
Submitter: Maximilian Bahls
Describes the steps required in order to run an error-prone PCR (epPCR) for the creation of DNA libraries of a given template gene.
Creator: Maximilian Bahls
Submitter: Maximilian Bahls
Oxygen gradients were developed as a quick and easy way to simultaneously adapt (recombinant) strains to decreasing levels of oxygen and monitor their progress over multiple days. This SOP can be used for o/n checks or for adaptation experiments spanning over multiple days. For the latter, a time-lapse camera setup is recommended. This SOP can also be applied to check the oxygen requirements of unknown strains.
Creators: Linde Kampers, Fons Stams
Submitter: Linde Kampers
Initial configuration and parameters of the Bioleaching
Creator: Stephan Christel
Submitter: Stephan Christel
This README file describes how the s-core / s-core+ analysis perl script is to be executed together with data files.
Creators: Eivind Almaas, Marius Eidsaa
Submitter: Eivind Almaas
Metabolic networks with gene expression are researched under very different banners with different techniques. For example, there are the dynamic enzyme-cost Flux Balance Analysis (deFBA) [1], conditional Flux Balance Analysis [2], Metabolism and Expression models (ME models) [3], Resource Balance Analysis [4], etc. At their core, these methods can all understood as Resource Allocation Models (RAM) and while investigating their potential and their results, we encountered the problem of sharing ...
Creators: Henning Lindhorst, Alexandra-M. Reimers
Submitter: Henning Lindhorst
Method extraction of intracellular metabolites in Lactococcus lactis
Creator: Martijn Bekker
Submitter: The JERM Harvester
Method extraction of intracellular metabolites in Lactococcus lactis
Creator: Martijn Bekker
Submitter: The JERM Harvester
Method for transformation of plasmids into Lactococcus lactis
Creator: Martijn Bekker
Submitter: The JERM Harvester
Method for synthesis of LAB-medium sued for the SYSMO-LAB project
Creator: Martijn Bekker
Submitter: The JERM Harvester
Method for analysis of various organic acids in the medium
Creator: Martijn Bekker
Submitter: The JERM Harvester
Creators: Theresa Kouril, Andreas Albersmeier, CeBiTech, University Bielefeld, Germany; Jörn Kalinowski, CeBiTech, University Bielefeld;
Submitter: Theresa Kouril
Protein extraction, iTRAQ labeling, peptides separation, mass spectrometry and data analysis
Creators: Theresa Kouril, Phil Wright, Trong Khoa Pham
Submitter: Theresa Kouril
Creator: Tomas Fiedler
Submitter: Tomas Fiedler
Creator: Tomas Fiedler
Submitter: Tomas Fiedler
Protocol for applying a glucose perturbation in Streptococcus pyogenes.
Creator: Martijn Bekker
Submitter: Martijn Bekker
Perturbation of starved cells with glucose. Concentrations of intra- and extracellular metabolites are followed in time.
Creator: Martijn Bekker
Submitter: Martijn Bekker
Creator: Martijn Bekker
Submitter: The JERM Harvester
This HPLC method uses a isocratic method and a RI detector to identify and quantify almost all excreted catabolic metabolites.
Creator: Martijn Bekker
Submitter: Martijn Bekker
A protocol for acidic quenching of lactic acid bacteria used for analyses of intracellular metabolites.
Creator: Martijn Bekker
Submitter: Martijn Bekker
This protocol for applying glucose perturbations works for Lactococcus lactis and Enterococcus faecalis
Creator: Martijn Bekker
Submitter: Martijn Bekker
Creator: Martijn Bekker
Submitter: The JERM Harvester
Creator: Martijn Bekker
Submitter: The JERM Harvester
Creator: Martijn Bekker
Submitter: The JERM Harvester
Creator: Martijn Bekker
Submitter: The JERM Harvester
Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236).
Creator: Natalie Stanford
Submitter: Natalie Stanford
Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236) for OptKnock.
Creator: Natalie Stanford
Submitter: Natalie Stanford
Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236) for RobustKnock.
Creator: Natalie Stanford
Submitter: Natalie Stanford