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Dates:  August 31  –  September 2, 2018

Location: ILSB Auditorium

Open Source for Open Science (OSOS) 2018 is a free workshop aimed to familiarize participants with selected open source software and programing tools to be able to conduct quantitative analysis and statistical methods for scientific inquiry. This year we are excited to have six module instructors focusing on an introduction to R, graphics in R, intermediate R tools for data handling, multivariate analysis in R, ecological niche modeling, accessing data repositories, a phylogenetic pipeline tutorial and a WGCNA tutorial. This course is aimed at incoming EEB graduate students; however, you need not be in EEB or a graduate student to attend. In addition, you may receive 1 credit hour of EEBL 612 for this course in the Fall 2018 semester.

Registration form:  https://goo.gl/forms/aQZK9w5ta856W9Tb2

Instructors and R packages/software required

Danielle Walkup, TAMU

openxlsx
tidyverse
car
PerformanceAnalytics

Pierre Lesne, TAMU

ggplot2
gridExtra
scales
ade4

Adrian Castellanos, TAMU

 “Ideally for my modules, each attendee will open up the .R files and attempt to run every install.packages and library function (they are the very first things written). If there are any problems, they should contact me at acastellanos@tamu.edu WITH the error that they are receiving and the operating system they are using.”

Zach Hancock, TAMU

Zach isn’t using R, but everyone needs to download the following programs:

Text editor:

Windows: https://notepad-plus-plus.org
Mac: http://www.barebones.com/products/bbedit/

Programs:

Mesquite: https://www.mesquiteproject.org
PAUP*: https://paup.phylosolutions.com
BEAST2: http://www.beast2.org
TRACER: http://tree.bio.ed.ac.uk/software/tracer/
FigTree: http://tree.bio.ed.ac.uk/software/figtree/

Also, be sure you make an account on the CIPRES portal (https://www.phylo.org).

Please download these programs before the tutorial. The directions for each are relatively straightforward; if you have any difficulties, please let me know at zhancock@bio.tamu.edu or (903) 809-3625.

Pablo Delclos, TAMU

GO.db
impute
preprocessCore
edgeR
WGCNA
flashClust

To make everything easier, the following code below will do it all for you! Just copy and paste into R:

source (“https://bioconductor.org/biocLite.R“)
biocLite(“GO.db”)
biocLite(“impute”)
biocLite(“preprocessCore”)
biocLite(“edgeR”)
install.packages(“WGCNA”)
install.packages(“flashClust”)

Rick McMullen, TAMU – PowerPoint file (see below)

Schedule

Friday, August 31

Session 1 – Danielle Walkup
5:00 – 6:30 pm, Intro to R   [download files]
Session 2 – Danielle Walkup
6:45 – 8:00 pm, R Intro

Saturday, Sept 1

Session 1 – Pierre Lesne
9:00 – 10:30 am, Graphics in R
Session 2 – Pierre Lesne
10:45 am – 12:15 pm, Multivariate Analysis in R

Session 3 – Adrian Castellanos
2:00 – 3:30 pm, Accessing Data Repositories  [download files]
Session 4 – Adrian Castellanos
4:00 – 6:00 pm, Ecological Niche Modeling  [download files]

Sunday, Sept 2

Session 1 – Zach Hancock
9:00 – 10:30 am, Rousing the BEAST: A molecular phylogenetic pipeline tutorial   [download files]

Session 2 – Pablo Delclos
10:45 am – 12:15 pm, WGCNA tutorial: Incorporating interactions among genes into differential gene expression analysis   [download files]

Session 3 – Rick McMullen
1:30 – 3:00 pm, High-Performance Research Computing at TAMU   [download file]

OSOS Intro Flyer

OSOS 2018 Schedule flyer

Questions may be directed to Jason Martina (jason.marti993@gmail.com) or Anja Schulze (schulzea@tamu.edu).

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