Somethings Biotech
Follow
Find
1.1K views | +0 today
Somethings Biotech
Observations of the world of biotechnology
Curated by chrisjo
Your new post is loading...
Your new post is loading...
Scooped by chrisjo
Scoop.it!

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction | Somethings Biotech | Scoop.it
Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

VAMPS: a website for visualization and analysis of microbial population structures

The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 105-108 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing.
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

Synchronized Speeds on the Straightaway

Synchronized Speeds on the Straightaway | Somethings Biotech | Scoop.it
A group at the Weizmann Institute recently looked at a chaotic system and found a surprising underlying order that helps determine the movement on a tiny, busy “road.”
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

SPAdes Genome Assembler | Algorithmic Biology Lab

SPAdes Genome Assembler | Algorithmic Biology Lab | Somethings Biotech | Scoop.it
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

That "$1000 genome" is going to cost you $72M

That "$1000 genome" is going to cost you $72M | Somethings Biotech | Scoop.it
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

UniProt release 2014_01 < Service news < News < About us < EMBL-EBI

UniProt release 2014_01 < Service news < News < About us < EMBL-EBI | Somethings Biotech | Scoop.it
UniProt 2014_01 is out. Get your 52,159,208 protein records! Headline article 'Mouse attacks!' and latest news at http://bit.ly/1dvRo7m
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

EMSL: User Access

EMSL: User Access | Somethings Biotech | Scoop.it
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

Streaming Data with Plotly

Streaming Data with Plotly | Somethings Biotech | Scoop.it
Plotly provides a free platform for makers to stream data to the cloud, where they can graph and analyze their data, discover other makers, and share and comment on these data streams.
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

gsGator: an integrated web platform for cross-species gene set analysis

Gene set analysis (GSA) is useful in deducing biological significance of gene lists using a priori defined gene sets such as gene ontology (GO) or pathways.
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

How I published a fake paper, and why it is the fault of our education system | smritiweb.com

more...
No comment yet.
Scooped by chrisjo
Scoop.it!

Ensembl has Migrated to Git

Ensembl has Migrated to Git | Somethings Biotech | Scoop.it
Today I am happy to announce Ensembl's migration away from CVS as our primary version control system (VCS) to Git. This migration sees the end of nearly a year's worth of work to ensure that our Gi...
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

RCSB Protein Data Bank - New Release!

RCSB Protein Data Bank - New Release! | Somethings Biotech | Scoop.it
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise.
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

Comparison of genotype clustering tools with rare variants

Along with the improvement of high throughput sequencing technologies, the genetics community
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

ParaFrap - Online Application System

ParaFrap - Online Application System | Somethings Biotech | Scoop.it
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

HostDB

chrisjo's insight:

This pre-release version of HostDB is available for early community review. Please explore the site and contact us with your feedback. Note that any saved strategies in the beta sites will be lost once the sites are fully released. Some of our sites remain under active development during their Beta release which might require occasional site outages or data re-analysis.

more...
No comment yet.
Scooped by chrisjo
Scoop.it!

The Pistoia Alliance

The Pistoia Alliance | Somethings Biotech | Scoop.it
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

How to ditch Word

How to ditch Word | Somethings Biotech | Scoop.it
I spent an hour this morning polishing up a proposal. This mostly involved running spell-checks, cleaning up tables, and making sure I added in all the right references. That’s when I realized something.
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

Quilt Plots: A Simple Tool for the Visualisation of Large Epidemiological Data

Quilt Plots: A Simple Tool for the Visualisation of Large Epidemiological Data | Somethings Biotech | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations

more...
No comment yet.
Scooped by chrisjo
Scoop.it!

Scientists use DNA sequencing to identify marine animals from only seawater | Center for Ocean Solutions

Scientists use DNA sequencing to identify marine animals from only seawater | Center for Ocean Solutions | Somethings Biotech | Scoop.it
“There are plenty of fish in the sea.” But which kinds of fish are where, and when? It’s a big question that scientists are now one step closer to answering.
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

RNAMatchMaker

RNAMatchMaker | Somethings Biotech | Scoop.it
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

Resuscitating investment in neglected tropical diseases

Resuscitating investment in neglected tropical diseases | Somethings Biotech | Scoop.it
While investment in diseases like malaria is growing, funding for NTD cures is drying up. Collaboration between researchers and industry will be key to bucking the trend
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

ELIXIR launches as legal entity | ELIXIR

ELIXIR launches as legal entity | ELIXIR | Somethings Biotech | Scoop.it
more...
No comment yet.
Scooped by chrisjo
Scoop.it!

Design Informatic

Design Informatic | Somethings Biotech | Scoop.it

Design Informatic

more...
No comment yet.