We are tearing apart a next generation sequencing machine to scavenge parts for use in our home built automated microscopes. Follow our progress on the Illumina GAIIx teardown blog.      Click on the thumbnail above to see evidence for multiple high temperature sensing mechanisms in plants. The plant in the top movie was heated at 37 degrees, the one on the bottom was heated at 40 degrees. Note the differences in the timing and location of the responses. This work is described in Kast et al., 2013


Here are some of the web sites that our lab uses regularly:

Swarthmore links
Confocal sign up
Lab Wiki (requires log in)
Moodle (requires log in)

Arabidopsis links
TAIR - Order stocks, find publications associated with your genes, get the latest Arabidopsis news
Genevestigator - Microarray data and analysis
Ensemble genome browser - Browse the Arabidopsis genome
BAR - Microarray analysis tools including the eFP browser, clustering, and promoter analysis tools
T-DNA express - Find and order T-DNA insertions and cDNA clones
ATTED - Arabidopsis trans-factor and cis-element prediction database and co-expressed genes
How to grow Arabidopsis from Purdue University
POLYMORPH Polymorphism data for Arabidopsis accessions and marker design tools
Marker Tracker More CAPS marker design tools
Thermotolerance phenotyping of seeds and seedlings

Illumina GAIIx tear down - Reusing GAIIx parts to build microscopes
iBiology Microscopy Course - an excellent online course on light microscopy
ImageJ - Image processing and analysis software
- Calibration information for lab Tucsen cameras
- Scale bars with ImageJ
- .lif reader for ImageJ - Manipulate Leica .lif files in ImageJ
- LAS software - Leica software download (Windows only)
Micro-Manager microscopy automation software
Plant image analysis software database
MircoscopyU - Microscopy information and tutorials
Capturing light - a blog from QSI about scientific imaging
Digital photography basics - good information about digital imaging including noise, dynamic range, and depth of field
A computational image analysis glossary for biologists

Other tools and information
Practicing Safe Science - Lab safety training video
MSDS database - MSDS chemical safety information
CoGe - Comparative genomics platform
BLAST - Basic Local Alignment Search Tools at NCBI
BioEdit - Local BLAST with custom databases, sequence alignment, trace viewing, restriction mapping, plasmid drawing and many more tools (Windows only)
Pubmed - Literature searches
Primer3 - Primer design
Essentials of Real Time PCR
How to give an academic talk
practice images for making figures