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Name: Oskar Lindsjö
Type: User
Company: SLU
Bio: Researcher at SLU
Location: Uppsala
Name: Oskar Lindsjö
Type: User
Company: SLU
Bio: Researcher at SLU
Location: Uppsala
MAG analysis for AMB group, GATC sequencing summer 2018
Workshop tutorials for the 2017 Benthic Invertebrates, Metagenomics, and Bioinformatics Workshop in Corpus Christi, Tx (January 9-13, 2017)
Scripts for analysis of Campylobacter from Illumina WGS sequencing
An R docker with DADA2 preinstalled. Can be run as a Rstudio server.
Analysis of E.Hirae WGS sequencing data
Minimalist alternatives to "best practices" paper
Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.
Nextflow basic tutorial for newbie users
Learning Git... Way to late but still
:rocket: A sequencing simulator
Testing building a phylogeny based on Mash distance as in https://www.biorxiv.org/content/10.1101/119420v1.full.pdf
The operating temperature strongly affects biogas yield, process stability and prospect for process optimization. Yet, many questions remains on how changed temperature influences on microbial communities and how to optimally manage the process in association to such changes. A long-term anaerobic digestion experiment was conducted to determine temperature-related questions raised by operative full-scale biogas plants and to evaluate optimization potentials and links to microbial community structure and responses. Four digesters fed household and slaughterhouse waste were operated in sets of two, at 37°C or 52°C, followed by a gradual increase or decrease in temperature in one digester in each set. Stability and flexibility of the digesters were then assessed by step-wise increases in organic loading rate (OLR) from 3 to 7 g VS/L/day, concurrently with decreased hydraulic retention time from 33-40 days to 14-17 days. The digester that had altered from thermophilic to mesophilic conditions failed at 6 g VS/L/day, whereas the digesters with constant temperature and the mesophilic-to-thermophilic digester remained stable at all OLR investigated. Amplicon sequencing showed divergent grouping of the mesophilic communities, whereas the thermophilic communities were nearly identical after the temperature change. Both biological and chemical parameters indicated that lagging in resilience of the acetate and propionate-degrading populations inherited from the community shaped by the initial operation at thermophilic conditions caused the thermophilic-to-mesophilic process less resistant to stress and counteracted process optimization. Overall, these results are valuable in the development of guidelines for process monitoring and strategies during changed temperature conditions with the prospect to optimize performances.
De novo assembly of nanopore reads using nextflow
Plotting scripts for nanopore sequencing data
Create statistic summary of an Oxford Nanopore read dataset
A tutorial on up-to-date methods of 16S analysis with QIIME
functions to analyse sanger sequencing reads in R
:notebook_with_decorative_cover: Various bioinformatics tutorials
Tutorials for basics bioinformatics courses
A docker for VAPiD
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.