YouTube Channel
Software Tools
Fellowships
Blogs

 

The Kunjapur Lab Academy YT Channel:

Watch the videos below on our YT Channel to access our recommended playlists.
https://www.youtube.com/@KunjapurLabAcademy/featured

Collectively, these videos strive to help educate undergraduate and early graduate student audiences on topics such as:

• Biotechnology
• Synthetic biology
• Preparation for graduate school
• Careers in research and academia
• Science highlights from our lab
• Biochemical pathway engineering
• Theory of ideal reactor design

We believe this information should be widely available and is easier to digest through videos than text.

1. The SynBio Transcript - a series of short videos for online audiences interested in synbio

2. CHEG621 - Metabolic Engineering & Synthetic Biology - sample of course videos from SP20

3. CHEG332 - Chemical Engineering Kinetics & Reactor Design - sample of course videos from F20
(upgraded videos from F22 coming soon)

4. (Coming Soon) CHEG420 - Intro to Biochemical Engineering - sample of course videos (SP23)

 

​Selected Software Tools for Synbio Research:
   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
• Crystal Structures - Protein Data Bank
• Homology Modeling - SWISSMODEL or I-TASSER
• Visualization - PyMOL or Chimera
• Ligand Docking - AutoDock Vina
• Computational Protein Design - PyRosetta
• Protein Similarity Networks - EFI-EST

   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)​

 

Fellowship Opportunities (US Centric):

• 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)
  • Ford Foundation Fellowship (geared towards under-represented minorities)
  • Johns Hopkins Database of Graduate Fellowships
• Post-Doctoral
  • ​NIH F32
  • USDA
  • Intelligence Community Fellowship
  • ​Life Sciences Research Foundation
  • L'Oreal USA for Women in Science
  • Helen Hay Whitney Foundation
  • Arnold Beckman Postdoctoral Fellowship
• Postdocs' Guide to Gaining Independence​

 

Our Blog Posts & Perspectives:

• An Introduction to Synthetic Biology Start-Ups

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