evolving all we are: Installing libsequence and analysis tools on OSX

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FlowingData

Swooping vote margins - The New York Times used swooping arrows to show vote swings left and… *Tags:* election, margin, New York Times
3 小时前
Nothing in biology makes sense!

FizzBurn – opinie, efekty, działanie, skład, cena i gdzie kupić? - W dzisiejszych czasach, gdy odchudzanie staje się coraz trudniejszym wyzwaniem, kluczem do sukcesu jest znalezienie odpowiedniego wsparcia. Jeśli szukasz...
4 小时前
Discover Blogs

Feeling Stressed? You May be More Likely to Believe in Spooky Phenomena - People who feel they have less control over their lives are more likely to embrace the paranormal.
17 小时前
Jabberwocky Ecology

We’re hiring a computer vision developer! - Interested in using computer vision to help understand, manage, and conserve nature? We hiring for a new position to join our team working on models, softw...
1 天前
Getting Genetics Done

Build a Python CLI with Click+Cookiecutter (repost) - *Reposted from the original at https://blog.stephenturner.us/p/python-cli-click-cookiecutter. * *---* In the spirit of Learning in Public, I wanted an e...
5 天前
Phylogenetic Tools for Comparative Biology

Fitting a discrete or hidden character multi-rate continuous trait evolution model using the discrete approximation in phytools - For a few months, *phytools* has had a function called fitmultiBM which uses the discrete approximation of Boucher & Démery (2016) to jointly model the ...
1 周前
Abhishek Tiwari

Input vs Output Privacy - Privacy in data systems has traditionally focused on protecting sensitive information as it enters a system - what we call input privacy. However, as syste...
1 周前
The Molecular Ecologist

Coming to PAG 32 this January? Join the first-ever Molecular Ecology workshop - Posted on behalf of Loren Rieseburg and Shawn Narum, workshop organizers. We are pleased to announce the inaugural workshop for Molecular Ecology at the Pl...
2 周前
Shige's Research Blog

TidierData and dplyr - TidierData is a Julia implementation of the dplyr R package. This post is very informative.
2 周前
iPhylo

Internet Archive as a single point of failure - How to cite: *Page, R. (2024). Internet Archive as a single point of failure https://doi.org/10.59350/1r3m1-c5e22* Just a placeholder to mark the ongoing i...
2 周前
PubMed New and Noteworthy

Filters Interface Improvements - The PubMed filters interface on the search results page has been updated to provide a more intuitive, user-friendly experience.
3 周前
Anole Annals

Etymologies of All Anoles - Collecting reptile names is one thing, but it’s a different thing to figure out what these names actually mean. At the Reptile Database we have collected t...
3 周前
The Tree of Life

Talk on Sequencing and Microbes ... - I recently gave a talk where I combined what are normally two distinct topics - the Evolution of DNA Sequencing, and the use of Sequencing to Study Micro...
3 周前
Living in an Ivory Basement

Why Rust is an increasingly beloved part of my programming toolbox - Rust is nice!
4 周前
Econometric Sense

Master of Science in Agriculture - Agricultural Statistics - As defined by R.A. Fisher *“Biometry, the active pursuit of biological knowledge by quantitative methods”* is the application of statistical and quantita...
4 周前
theBioBucket*

QGIS3: Aggregate Over Layer with Expression Builder Using a Filter - array_sum( array_foreach( generate_series(0, layer_property('MY_LAYER', 'feature_count'), 1), if(attribute(get_feature_by_id('MY_LAYER', @element), 'M...
2 个月前
Quantum Forest

Time for correlations - A few posts ago I was talking about heritabilities (like here) and it’s time to say something about genetic correlations. This is how I explain correlation...
2 个月前
Modern Toolmaking

This blog has moved! - https://www.ai-insight-solutions.com/blog/
2 个月前
ENMTools

Bug fix: plots for RTS-style tests - In the midst of doing some modeling work I discovered that the plots for the RTS-style tests were incorrect - the training AUC was used for the vertical ...
3 个月前
Darren Wilkinson's research blog

Using optimised BLAS and LAPACK libraries with Scala Breeze - Breeze is the standard scientific and numerical library for Scala. For linear algebra operations, it builds on top of the Java library, netlib. This prov...
4 个月前
What You're Doing Is Rather Desperate

Pattern recognition in Google Maps - Headline: Second farm in the Hawkesbury region confirmed to have bird flu as biosecurity zone widened. Quite rightly, the news organisation chooses not to ...
4 个月前
Statistics, R, Graphics and Fun

Bye, RStudio/Posit! - Who is down? Me. After more than 10 years at RStudio/Posit, the time has come for me to explore other opportunities. A little over two weeks ago, I was t...
10 个月前
Public Rambling

State of the lab 10 and 11 - the first years at ETH Zurich - [image: a lake by a mountain] *Yet another lake by a mountain in Switzerland*This blog post is part of a (nearly) yearly series on running a research grou...
1 年前
theoretical ecology

Time to leave “species richness” behind, as it serves no scientific purpose on x- or y-axis - A guest post by Carsten F. Dormann, University of Freiburg In “biodiversity science”, species richness takes a very prominent role. It is the most analysed...
1 年前
Gregor Gorjanc

Overload of the term "additive" in quantitative genetics - The following discussion came up on SLiM (https://messerlab.org/slim/) mailing list (https://groups.google.com/g/slim-discuss), which I think is highly ind...
1 年前
The OpenHelix Blog

Dynamics 365 Finance moderniza las operaciones financieras de tu empresa - Dynamics 365 Finance es un sistema ERP basado en la nube diseñado para optimizar los procesos comerciales. Al ofrecer una plataforma para todas las funci...
1 年前
Junk Charts

Losing the plot while stacking up the bars - Kaiser looks at an infographic about dirty American cities.
1 年前
microBEnet: The microbiology of the Built Environment network.

Join Indoor Air 2024’s Conference Countdown Challenge - (posting on behalf of Dr. Karen Dannemiller) The Indoor Air 2024 conference from the International Society for Indoor Air Quality and Climate (ISAIQ) wil...
1 年前
crazyhottommy's blog

10 tips for learning git - 1/ Several basic commands will serve you a long way: git clone git add git commit -m git push Those are enough to get you started. To be honest, those a...
1 年前
Fabio Marroni’s Blog

An R function to compute Tumor Mutational Burden (TMB) - Tumor mutational (or mutation) burden, TMB, is considered a useful estimation of tumor neoantigenic load (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336...
1 年前
the mind wobbles

Summer Update: busy days behind us, busy times ahead - As August looms, and most of academia in Europe slows down as researchers take leave to escape the heat, there’s a few things I’d like to draw your attenti...
2 年前
One Tip Per Day

some Vi shortcuts - Copy and paste one line With the cursor at your desired line press yy. Press p wherever you like and the line will be pasted below the line you are on. ...
2 年前
The Genome Factory

How to perform a fresh Bioconda installation - Introduction Conda has been revolutionary for scientific software. For developers it has made it simpler to package their tools. HPC users have been empo...
2 年前
The Geek Stuff

PaloAlto init-cfg.txt Bootstrap Config file Layout with Examples - When you install and configure the PaloAlto firewall, when the firewall boots up for the first time, it does the bootstrapping process. PaloAlto uses the s...
2 年前
bayesianbiologist

Colouring book self-supervised learning - Recently at home with my mom and sister and I was explaining a bit about the work I’m going to be doing in AI for digital pathology. We got talking about h...
2 年前
Seqonomics

Favorite books 2021 - I've been reading mostly fiction this year. Rather than go over my favorite books, this year year I'm recommending three authors whose books I find consi...
2 年前
派的无理性

MES、ERP企业管理系统开发视频课程 - 极简模式开发MES、ERP企业管理系统的视频课程
2 年前
Archaeological Network Analysis

GIS and networks for archaeology: spring school for PhD students - There’s a cool Brussels spring school coming up on GIS and networks for archaeology. I’m giving the networks keynote, yay 🙂 The program looks very detaile...
3 年前
My Weblog on Bioinformatics, Genome Science, Next Generation Sequencing

HGVS nomenclature - Was recently asked about HGVS nomenclature reporting. The fun thing about biology is that there's going to be exceptions to the rule or some shenanigans...
3 年前
Struggling Through Problems

Can we have anti-lambdas please? - Aren’t you tired of flattening your code to avoid repeated computation: val x = longComputation() ls map { y => (x, y)} when you’d rather write ls map...
3 年前
Dienekes’ Anthropology Blog

Happy New Year 2021 - Health and Happiness to all.
3 年前
MYRMECOS

The 9th Annual Holiday Print Sale - I am excited to announce the return of the Holiday Insect Print Sale, now in its 9th year! I have selected 35-ish photographs that will be available at 70%...
3 年前
Linux Commando

Useful command-line date utilities - My earlier post, Fun with Date Arithmetic shows how to use the *date* command to compute a future or past date that is a certain number of days ahead or ...
4 年前
The UNIX School

Linux Shell - What is IFS? - IFS stands for internal field separator. This is the delimiter used when words are split. The man page of bash tells : *IFS The Internal Field Separat...
4 年前
PLoS Blogs Network

PLOS Stands with the National Academies on Continuing WHO Funding - Yesterday, the presidents of the National Academies of Sciences, Engineering, and Medicine released a statement warning that interrupting funding for Wor...
4 年前
Yixf's blog

无题 - 无题万言不入秦王耳，南花魂游丞相园。六月雪飞君莫笑，一秋更比一秋寒。
5 年前
geolabs

Map of an meadow orchard (Streuobst) - A few months ago I rented a meadow with orchards (ca. 8000m²). Some of the 70 trees (mainly cherry trees) are over 40 years old. The age, however, has no i...
5 年前
HubLog

Converting PDF to PNG or JPEG - What are the best tools or services for converting a page of a PDF file to an image? The first thing that usually shows up for converting PDF to PNG or J...
5 年前
Biospherica

Phased antenna array design using Hamiltonian Monte Carlo - Phased antenna arrays allow a radio or microwave beam to be steered electronically. They are of increasing practical importance. Array optimisation problem...
5 年前
Vijay Barve

India has 100k records on iNaturalist - Biodiversity citizen scientists use iNaturalist to post their observations with photographs. The observations are then curated there by crowd-sourcing the ...
5 年前
Next-Gen Sequencing

Some tips to optimize bacterial genome assembly - I just finished a revised genome assembly for a collaborating lab. We do de novo sequencing of bacterial genomes all the time, sometimes in batches of 50 ...
6 年前
nzprimarysectortrade

Introducing the New Zealand Trade Intelligence Dashboard - I’d like to introduce to you the New Zealand Trade Intelligence Dashboard. This is one of the New Zealand government shiny web apps that should have been m...
6 年前
Keep on Fighting!

优秀到无法被忽视 - 看了一篇《优秀到无法被忽视》的总结，有几个观点有所共鸣： 1. 激情是一种稀缺的特质，尤其是职业激情。在《穷查理宝典》读书笔记中谈芒格的第六个人生道理时，我曾说多数人都缺乏对某件事的强烈兴趣。在对秦旭的采访中，我也曾说有稳定热情的人相对少见。激情已经够少见，职业激情就更少见了。...
6 年前
Sharp Statistics

EasyER Version 1.2 - Version 1.2 of EasyER has now been released. The main change is the addition of a chart builder interface for interactively creating charts. The chart bu...
6 年前
The MolBio Hut

A “bottoms-up” approach to scientific publishing - A few days ago, a piece was posted at ASAPbio which reminded me of an idea I had a long time ago about a new model for publishing and peer review. I descri...
6 年前
Tr8dr

Blog Moved - After a long hiatus, have started writing again., however have moved the blog to GitHub. The new URL is: https://tr8dr.github.io Advertisements
7 年前
The Spittoon

23andMe Adds New Genetic Health Risk Reports - 23andMe released two new genetic health risk reports for customers for Age-Related Macular Degeneration and Hereditary Hemochromatosis. The post 23andMe ...
7 年前
Research tips

Monash Rmarkdown templates on github - My Rmarkdown templates for staff and students in my department are now available as github repositories. MonashThesis: For PhD theses. MonashBeamer: For be...
7 年前
Timely Portfolio

Picking the Top - In Shorting With Reckless Abandon I expressed my views. I have now started documenting my journey at Picking The Top for anyone who wants to see my foolish...
7 年前
CoreGenomics

CoreGenomics has moved - *Follow this link to Enseqlopedia/coregenomics...* "CoreGenomics is dead...long live CoreGenomics"...the CoreGenomics blog has moved to its new home: http...
7 年前
YOKOFAKUN

Creating a custom GATK Walker (GATK 3.6) : my notebook - This is my notebook for creating a custom engine in GATK. Description I want to read a VCF file and to get a table of category/count. Something like this: ...
7 年前
Portfolio Probe

US market portrait 2016 final - US large cap market returns. Fine print The data are from Yahoo The S&P 500 stocks are used (as implied by Wikipedia on 2016 January 16) that still survive...
7 年前
Ewan's Blog; bioinformatician at large

My blog has moved! - As you may already be aware, I have moved my blog over to WordPress for practical reasons. I've enjoyed Blogger for its simplicity, but the experience on ...
7 年前
Quantitative Ecology

Recursively search for text in R scripts. - Often I find myself needing to search for .R or or .Rmd files in which I have used a specific function. There are a variety of searches that you can do; ho...
7 年前
The Praise of Insects

Cook Islands Insect Expedition: Black Twig Borer - The black twig borer *Xylosandrus compactus* (Eichhoff, 1875). Image courtesy of Ken Walker via PaDIL. Licence: CC: BY. A timely interview on Radio New Z...
7 年前
librestats

Comparing Symmetric Eigenvalue Performance - Lazy reader’s guide: skip to the pretty pictures, skim the conclusions section, ignore the rest. Background I think a lot about eigenvalue and singular ...
8 年前
bioCS

My knitr LaTeX template: manuscript and supplement interleaved in one source file - Most of the time between starting manuscript and having it accepted after peer-review is spent writing, re-writing and re-arranging content. In Word, keepi...
8 年前
Genome Toolbox

R Function to Calculate Confidence Interval from Odds Ratio and P-value - Every once in a while I need a confidence interval from a published estimate that only reports the estimated odds ratio and respective p-value. With a litt...
8 年前
me nugget

RSpectra::svds function now default method for sinkr::dineof - The summary blog post describing the RSpectra (formerly rARPACK) package made a convincing case for the improved decomposition speed of the "svds" function...
8 年前
Bigcomputing

Setting up the Twitter R package for text analytics - The Twitter R package by Jeff Gentry is a great way to get started in Text Analytics. This tutorial is about how to get setup to pull twitter data into R s...
8 年前
IDV User Experience

That's All - I started blogging at IDV in April of 2007. Over the years it has become a terribly important venue for me, where I've shared surprisingly personal events ...
9 年前
Oscillatory Thoughts

New Voytek Lab paper by Richard Gao! - Voytek Lab Cognitive Science PhD student, Richard Gao, wrote a detailed piece about his new paper, "Interpreting the Electrophysiological Power Spectrum,” ...
9 年前
Stochastic Nonsense

Splitting Audio with ffmpeg - Here’s a quick utility to use a set list and ffmpeg to split single audio files into multiple tracks. It splits audio files via a setlist then sets the s...
9 年前
We think therefore we R

The curious case of ARIMA modelling using R - I recently made an interesting observation that I thought is worth sharing. During a data expedition process while trying to fit an ARIMA (auto-regressi...
9 年前
Biochemistry, Molecular, Cellular & Developmental Biology

Night Vision Without the Goggles - The human eye consists of focusing elements and photoreceptors. Images are formed when light is projected onto the retina, which houses photoreceptors call...
9 年前
Systematic Investor

New Home of Systematic Investor Blog - Please visit the New Home of Systematic Investor Blog at SystematicInvestor.GitHub.io
9 年前
Left Censored

R and MPI on Ohio Supercomputer Center’s Oakley cluster - A few years ago, I wrote a short guide to Using R and snow on the Ohio Supercomputer Center’s Glenn cluster. Several things have changed in the world of R ...
9 年前
Statistic on aiR

Adjustment for Multiple Comparison Tests with R: Resources on the web - *1. Bonferroni correction* p.adjust(p, method = "bonferroni") Read: http://en.wikipedia.org/wiki/ *2. Sidak (Dunn-Sidak) correction* Read: http://en.wiki...
9 年前
Carnival of Evolution

Carnival of Evolution #78 - the Short-Arse edition - Finally, the 78rd edition is up. Not too much has happened in the evolution blogosphere to my knowledge, so this edition is really short but good. Like sho...
9 年前
MycorWeb Fungal Genomics

1000 Fungal Genome (1KFG) project: Graduate Student-Postdoc Challenge (2014) - The 1000 Fungal Genome (1KFG) project is a large-scale community sequencing project supported by the Joint Genome Institute (JGI). The goal of 1KFG is to ...
10 年前
Matt's Stats n stuff

Shading between two lines – ggplot - First one to say geom_ribbon loses. I was plotting some data for a colleague, had two lines (repeated experiment) per person (time on the x axis) facetted ...
10 年前
The Ubuntu R Blog

c2d4u and RRutter Ubuntu PPA Updates - On January 27, 2014 Raring Ringtail (13.04) reached end of life. I have been slowly removing the Raring repositories from the RRutter PPA, c2d4u PPA, and...
10 年前
anrprogrammer

Database Reflection using dplyr - At work I write a ton of SQL, and I do most of my querying using R. The workflow goes: Create a string with the SQL in R Plug the string into fetchQuery (...
10 年前
Jack Zhu's Bioinfo

userstyles.org - Dictionary.com - permanent IPA pronounciation - Dictionary.com - permanent IPA pronounciation - Themes and Skins for Reference - userstyles.org
11 年前
Sacha Epskamp

A general Shiny app for reading data - A general Shiny app for reading data A general Shiny app for reading data I have been playing around a lot with making web-applications using shiny. What...
11 年前
mintgene

Reconstructing Principal Component Analysis Matrix - Edit: I’ve updated afterPCA function to work with input of any dimensions. Previously it only generated correct output for square matrices. PCA is widely u...
11 年前
Dodecad Ancestry Project

D-statistics on ADMIXTURE components - I have implemented the method of D-statistics as an R function. This will allow you to take your raw genotype data and calculate various D-statistics of th...
11 年前
genomeboy

Closing time - A note from PLOS Blogs Community Manager Victoria Costello: We’re sad to see Misha Angrist leave our blog roster but we’ve been honored to host the last tw...
12 年前
Quantitative Ecology

Blog Moving - Thanks to everyone who's visited this blog and provided encouragement and suggestions. My blog is moving to http://danieljhocking.wordpress.com/quantitativ...
12 年前
EvolvingSpaces

Sharing Data in Archaeology - ...I know it has been a long time since my last post and many, many things happened. Our CAA session on Uncertainty was great (many thanks to the contribu...
12 年前
Coffee and Econometrics in the Morning

Using apply() to create a unique id - Suppose you have a data set with two identifiers. For example, maybe you're studying the relationships among firms in an industry and you have a way to lin...
12 年前
Consistently Infrequent

R: A Quick Scrape of Top Grossing Films from boxofficemojo.com - Introduction I was looking at a list of the top grossing films of all time (available from boxofficemojo.com) and was wondering what kind of graphs I wou...
12 年前
Adventures in Statistical Computing

Portfolio Optimization in R, Part 4 Redeux - So where did we mess up? In the calculation of returns for the market cap weighted portfolio and the portfolio optimization portfolio, we simply took the...
12 年前
BMB's commonplace

Google Scholar (still) sucks - (This is a follow-up to my previous post on the topic.) I was encouraged by the appearance of *two* R-based Scholar-scrapers, within a week of each other. ...
13 年前
The Plant Informatics

Rod Page’s VIZBI 2011 annotated links - iPhylo is hands-down my favorite blog, whose author is Rod Page. In the blog post “Some VIZBI 2011 links”, Rod grabbed a list of visualization softwa...
13 年前
joint posterior

compiler and runiregGibbs (bayesm) - So everyone's excited about the new R 2.13 release because of the compiler package. Apparently it is easy to get a 3x speed increase by simply compiling a ...
13 年前
The Prince of Slides

Introduction to The Prince of Slides - In my everlasting search for the answer to every sports (among other topics) question imaginable, I decided to create this blog. While there are a number o...
15 年前
alexfarquhar's posterous

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Omnia sunt Communia!

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FinchTalk

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Biology-blog.com: The place for biology

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Data Jujitsu

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Blog | Wainwright Lab | University of California, Davis

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Jinlong Zhang's Homepage - Main

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R, Ruby, and Finance

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Treevolution: Biology through the evolutionary lens

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From the bottom of the heap

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The EEB & flow

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The Atavism

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Back Side Smack

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猴子的博客

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Cartesian Faith

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Carl Boettiger

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Zero Intelligence Agents

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Edwin Chen's Blog

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i'm a chordata! urochordata!

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Python for Bioinformatics

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OUseful.Info, the blog...

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怡然轩 | Yixuan's Blog

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格物堂

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数据科学与R语言

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All Things Tagxedo

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Sam Harris: Author, neuroscientist, philosopher.

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Bioinformatics Tutorials

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Haldane's Sieve

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PolStat Blog

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Mailund on the Internet

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AnthroGenetics' Blog

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Genomes Unzipped

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Pathogens: Genes and Genomes

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Graph of the Week

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EvoPhylo

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My Biased Coin

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Programming for Scientists

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JAGS News

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ExploringDataBlog

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evolving all we are

2012年5月26日星期六

Installing libsequence and analysis tools on OSX

Installing libsequence and analysis tools on OSX

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