Resources - Kunjapur Lab

Contents:

Blog Posts
Useful Online Tools / Software
Sources of DNA / Strains
Fellowships

Blog Posts:

http://blogs.plos.org/synbio/2015/09/08/an-introduction-to-start-ups-in-synthetic-biology/

Useful Online Tools / Software:
DNA

DNA/Plasmid Editing - Benchling
Codon Optimization - IDT
Sequence Identification - BLAST
Sequence Alignment - Clustal Omega
Phylogenetic Tree Generation - Phylogeny

Metabolism

Metabolic Pathway Database - KEGG
Database of Pathway/Genome Relationships - BioCyc or EcoCyc
Constraint-Based Metabolic Modeling - COBRAPy
Genome-Scale Metabolic Models - BiGG
Genome Mining for Biosynthetic Genes - antiSMASH

Genome Engineering

MAGE Oligo Design Tool - MODEST
CRISPR-Cas9 Guide RNA Design Tool - ATUM
Genome Sequencing - Millstone

Protein Engineering

Enzyme Database - BRENDA
Homolog Identification - PaperBLAST
Protein Families - Pfam or UniProt
Protein Crystal Structures - Protein Data Bank
Protein Visualization - PyMOL
Computational Protein Design - PyRosetta
Protein Mutagenesis (First-Pass) - HotSpot Wizard

General

Python Scripting - Jupyter/iPython Notebook
Molecular Interaction/Pathway Visualization - Cytoscape
Reference Management - Mendeley
Data Visualization - Origin (license required)
Chemical/Biochemical Reaction Drawing - ChemBio Draw (license required)
Graphic Design - Adobe Illustrator (license required)
Numerical Scripting and Kinetic Modeling - MATLAB (license required)

Sources of DNA / Strains:

U.S. Research-Oriented Scholarships & Fellowships:

Undergraduate
- Goldwater - for sophomores or juniors interested in research careers
- Amgen Scholars - for sophomores or juniors interested in summer research at 1 of 11 institutions
- National Science Foundation GRFP - for seniors going to graduate school
- Hertz Fellowship - for seniors going to graduate school
- DOE Computational Science Graduate Fellowship - for seniors going to graduate school
- National Defense Science & Engineering Graduate Fellowship - for seniors going to graduate school
Graduate
- National Science Foundation GRFP
- Hertz Fellowship
- DOE Computational Science Graduate Fellowship
- National Defense Science & Engineering Graduate Fellowship
- NIH F31 (geared towards students from under-represented backgrounds)
Post-Doctoral
Postdocs' Guide to Gaining Independence