Lab Software

Contents

1. Data Processing & Analysis
2. Plasmids, PCR and Cloning
3. Writing Papers

1. Data Processing & Analysis

• ImageJ (dead link) - a free, open-source NIH-funded image processing software. ImageJ is written in Java and is extended through a variety of plugins. It is the software of choice for processing microscopy images.
  • Fiji - an extended version of ImageJ with a set of additional plugins. Fiji includes a Python interpreter that allows python scripting of ImageJ.
  • ImageJ 2 - ImageJ 2.0 development promises to improve an already great package
• Matlab - powerful mathematics suite for data analysis
• Python - a very easy-to-use programming language with a full suite of numerical methods and science packages. Great, free alternative to writing MatLab code.

2. Plasmids, PCR and Cloning

• ApE - a free, cross-platform plasmid editor. Maintained out of University of Utah
• Online tools:
  • NEB Primer Tm Calculator PDF - recommended for doing PCR with NEB polymerases
  • Primer3Plus - very powerful PCR and sequencing primer design tool
  • NIH DNAWorks PDF - Oligo design for gene synthesis.

3. Writing Papers

• Microsoft Word - I write all manuscripts in MS Word.
• EndNote - Citation manager for manuscripts written in Word.
• OriginLab PDF - Creates publication-quality graphs.
• PyMol - Publication-quality protein structures.
• Adobe Illustrator - Publication-quality illustrations and figure layouts.