SOPs

What is a SOP?
363 SOPs visible to you, out of a total of 670

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

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 ...

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

This README file describes how the s-core / s-core+ analysis perl script is to be executed together with data files.

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 ...

Method extraction of intracellular metabolites in Lactococcus lactis

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

No description specified
No description specified

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

A protocol for acidic quenching of lactic acid bacteria used for analyses of intracellular metabolites.

This protocol for applying glucose perturbations works for Lactococcus lactis and Enterococcus faecalis

No description specified
No description specified

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).

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.

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.

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