MinION is a portable device for molecular analyses that is driven by nanopore technology. It is adaptable for the analysis of DNA, RNA, proteins or small molecules with a straightforward workflow.
The MinION can be run for minutes or days according to the experimental need. Users can adjust settings like the speed that the DNA passes through the nanopore. PromethION, which will soon be released into early access, is designed to be fully scalable so that users can operate between one or 48 flow cells at any one time.
Long read lengths
The Oxford Nanopore system processes the reads that are presented to it rather than generating specific read lengths. The longest read reported by a MinION user to date is more than 200Kb, but it can process the spectrum of read lengths.
Population genetics is the study of the distribution and change in frequency of alleles within populations, and as such it sits firmly within the field of evolutionary biology.
The main processes of evolution are natural selection, genetic drift, gene flow, mutation, and genetic recombination and they form an integral part of the theory that underpins population genetics.
Studies in this branch of biology examine such phenomena as adaptation, speciation, population subdivision, and population structure.
Population stratification refers to differences in allele frequencies between cases and controls due to systematic differences in ancestry rather than association of genes with disease.
It would be caused by systematic differences in the ancestry of cases and controls.
Diploid genome refers to a genome that contains a balanced set of chromosomes derived equally from maternal and paternal sources.
Coalescent theory is a retrospective stochastic model of population genetics that relates genetic diversity in a sample to demographic history of the population from which it was taken.
That is, it is a model of the effect of genetic drift, viewed backwards in time, on the genealogy of antecedents.
A repository is usually used to organize a single project. Repositories can contain folders and files, images, videos, spreadsheets, and data sets – anything your project needs. We recommend including a README, or a file with information about your project. GitHub makes it easy to add one at the same time you create your new repository. It also offers other common options such as a license file.
Branching is the way to work on different versions of a repository at one time.
By default your repository has one branch named master which is considered to be the definitive branch. We use branches to experiment and make edits before committing them to master.
On GitHub, saved changes are called commits.
When you open a pull request, you’re proposing your changes and requesting that someone review and pull in your contribution and merge them into their branch. Pull requests show diffs, or differences, of the content from both branches. The changes, additions, and subtractions are shown in green and red.
GitHub Pages are public webpages hosted and published through our site.
You can create and publish GitHub Pages online using the Automatic Page Generator. If you prefer to work locally, you can use the GitHub Desktop or the command line.
Pages are served over HTTP, not HTTPS, so you shouldn’t use them for sensitive transactions, like sending passwords or credit card numbers.
3. Strawberry Perl
1. daemon tool lites
Benoit Mandelbrot: (20 November 1924 – 14 October 2010)
TED title: Fractals and the roughness
Introduction: Benoit Mandelbrot was a Polish-born, French and American mathematician. He is recognized for his contribution to the field of fractal geometry, which included coining the word “fractal” as well as for developing a “theory of roughness” and “self-similarity” in nature.
TED title: A 3D atlas of the universe
Introduction: It is a standalone 4-dimensional space visualization application built on the programmable Partiview data visualization engine designed by Stuart Levy of the National Center for Supercomputing Applications (NCSA) as an adjunct of the NCSA’s Virtual Director virtual choreography project. The Virtual Universe Atlas project was launched by the American Museum of Natural History’s Hayden Planetarium with significant programming support from the National Aeronautics and Space Administration as well as Stuart Levy. The database draws on the National Virtual Observatory.
TED title: The riddle of experience vs. memory.
Introduction: (Hebrew: דניאל כהנמן, born March 5, 1934) is an Israeli-American psychologist notable for his work on the psychology of judgment and decision-making, as well as behavioral economics, for which he was awarded the 2002 Nobel Memorial Prize in Economic Sciences (shared with Vernon L. Smith). His empirical findings challenge the assumption of human rationality prevailing in modern economic theory.
- one of the most prevalent pathogens in swine causing a range of disease syndromes including arthritis (关节炎), meningitis (脑膜炎), pneumonia (肺炎), septicemia (败血症) and endocarditis (心内膜炎), etc. 
- an zoonotic agent able to induce meningitis, endocarditis, and streptococcal toxic shock-like syndrome in humans. 
- Thirty three S. Suis serotypes identified on the basis of antigenic differences in their CPS (Capsule Polysacharides). 
- S. suis 2 mainly infects people who have direct contact with carrier pigs, sick pigs, or raw pork via wounds on the skin, or the mucosa of the mouth, or nasal cavity. 
- 1642 cases of S. suis human infection had been reported worldwide until Dec. 31, 2013. 
. Zhang, Y., Ding, D., Liu, M., Yang, X., Zong, B., Wang, X., Chen, H., Bei, W., and Tan, C. (2016). Effect of the glycosyltransferases on the capsular polysaccharide synthesis of Streptococcus suis serotype 2. Microbiological research.
- The incomplete CPS resulting from deletion of the cps genes in S.suis 2 SC19;
- Interplay between S.suis 2 SC19 and different cell lines in vitro changed by these
cps2E, cps2G, cps2J and cps2L
- More deposition on the mutant strains of complement C3 in porcine serum
than on WT
- Essential role of the cps genes in viability of SC19 in a murine model
Zhang, Y., Ding, D., Liu, M., Yang, X., Zong, B., Wang, X., Chen, H., Bei, W., and Tan, C. (2016). Effect of the glycosyltransferases on the capsular polysaccharide synthesis of Streptococcus suis serotype 2. Microbiological research.
在KEGG中，分子水平上的功能保存在KO（KEGG Orthology）数据库中。这些功能与直系同源组联系在一起，以此来使得一个特殊物种的实验数据可以被扩展到其他物种。KEGG中的基因组注释是直系同源注释，其方式为，为GENES数据库中的每个基因制定KO identifiers (K numbers) 。对于原始数据，像由RefSeq或者GenBank给出的基因名和描述，即使他们和KO的分配不一致，KEGG也不会做任何修改。
将KO的条目与功能表征的序列数据的实验证据联系在一起的工作，已经开始了，并且现在已经展示在REFERENCE下的SEQUENCE子域中。而且，基因组层面的“KEGG GENES”（http://www.genome.jp/kegg/genes.html）集合已经被扩展，使其可以将蛋白数据也包含在附录中。最终KO数据库将覆盖所有的功能表征蛋白序列信息（另见“KEGG Enzyme”（http://www.genome.jp/kegg/annotation/enzyme.html））。
In KEGG, molecular-level functions are stored in the KO (KEGG Orthology) database and associated with ortholog groups in order to enable extension of experimental evidence in a specific organism to other organisms. Genome annotation in KEGG is ortholog annotaion, assigning KO identifiers (K numbers) to individual genes in the GENES database. No updates are made to original data, such as gene names and descriptions given by RefSeq or GenBank, even if they are inconsistent with the KO assignment.
Major efforts have been initated to associate each KO entry with experimental evidence of functionally characterized sequence data, now shown in the SEQUENCE subfield of the REFERENCE field. Furthermore, the genome-based collection of KEGG GENES has been expanded to allow individual protein data to be included in the addendum category. Eventually the KO database will cover all knowledge on functionally characterized protein sequences (see also KEGG Enzyme).
一般来说，KO对功能直系同源的划分是定义在KEGG分子网络的语境中（KEGG pathway maps, BRITE hierarchies and KEGG modules）。KEGG分子网络实际上是由K numbers标识的网络节点表示的。KOs和相应的分子网络的关系呗存储在下面这个系统中。
KEGG Orthology （KO）
将功能信息和直系同源组关联在一起这个功能是KEGG资源的一个独特的功能。基于有限总量的实验数据生成的对序列相似性的预测被预先定义好在KEGG中。如同在BlastKOALA和其他工具中实现的那样，对KEGG GENES的序列相似性搜索是针对K numbers的。一旦一个K numbers被指定给基因组中的基因，KEGG pathways maps, Brite hierarchies,和KEGG modules都会自动重建。如此一来，就能对较高水平的功能有一个生物学上的科学的诠释。
In general KO grouping of functional orthologs is defined in the context of KEGG molecular networks (KEGG pathway maps, BRITE hierarchies and KEGG modules), which are in fact represented as networks of nodes identified by K numbers. The relationships between KOs and corresponding molecular networks are represented in the following KO system.
KEGG Orthology (KO)The fact that functional information is associated with ortholog groups is a unique aspect of the KEGG resource. The sequence similarity based inference as a generalization of limited amount of experimental evidence is predefined in KEGG. As implemented in BlastKOALA and other tools, the sequence similarity search against KEGG GENES is a search for most appropriate K numbers. Once K numbers are assigned to genes in the genome, the KEGG pathways maps, Brite hierarchies, and KEGG modules are automatically reconstructed, enabling biological interpretation of high-level functions.