A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples.
Resource type: Jupyter notebook, PDF
Introductory image processing on biological images using python.https://github.com/dwaithe/model-training/https://tess.elixir-europe.org/materials/introductory-image-processing-on-biological-images-using-pythonA jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples.Dominic WaitheAnatole ChesselVolker BaeckerBioimage AnalystsImage AnalystsComputer Vision scientistsbioinformaticianscomputational scientistsBiophysicistsBiologistsMicroscopistsPython for BiologistsPhD students
Next generation sequencing (NGS) has become a commodity. With the commercialization of various affordable desktop sequencers, NGS will be of reach by more traditional wet-lab biologists . As seen in recent years, genome-wide scale computational analysis is increasingly being used as a backbone to...
Keywords: Bioinformatics, Next generation sequencing, Ngs
Next Generation Sequencing (NGS) wikibookhttps://www.mygoblet.org/training-portal/materials/next-generation-sequencing-ngs-wikibookhttps://tess.elixir-europe.org/materials/next-generation-sequencing-ngs-wikibookNext generation sequencing (NGS) has become a commodity. With the commercialization of various affordable desktop sequencers, NGS will be of reach by more traditional wet-lab biologists . As seen in recent years, genome-wide scale computational analysis is increasingly being used as a backbone to foster novel discovery in biomedical research. However, as the quantities of sequence data increase exponentially, the analysis bottle-neck is yet to be solved.
The current sources for NGS informatics are extremely fragmented. A novice could read review articles in various journals, follow discussion threads on forums such as Biostar or SEQanswers , or sign up for courses organized by various institutes. Finding a centralized synthesis is much more difficult. Books are available, but the development of the field is so fast that book chapters risk being obsoleted by the time they are even printed. Moreover, cost for a handful of authors to continually update their text would presumably take up a lot of their schedule.
Drawing from the obvious goodwill and community spirit displayed on discussion forums, and exploiting the collaborative tools made available by the Wikimedia foundation, we propose to initiate the editing of a collaborative WikiBook on NGS. Our plan is to collect a sufficient amount of text that people will be incentivized to contribute to it, essentially providing the same information as a forum but in a tidier form. Ultimately, our goal is to create a collective lab book that explains the key concepts and describes best practices in NGS.
Parnell LD, Lindenbaum P, Shameer K et al. BioStar: an online question & answer resource for the bioinformatics community, PLoS Comput Biol 2011;7:e1002216.
Li JW, Schmieder R, Ward RM et al. SEQanswers: an open access community for collaboratively decoding genomes, Bioinformatics 2012;28:1272-1273
Join this initiative now and contribute to further expand and improve the contents and case studies in the NGS wikibook!
Read about this initiative and the nine rules for NGS data analysis here: The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainabilityMaria Victoria ...Bioinformatics, Next generation sequencing, NgsBiologistsbioinformaticianscomputational scientists2013-07-152017-10-09