protocol-book
  • Salis Lab Protocol Book
  • Getting Started
  • Modeling & Algorithms
    • Linux
      • Install
      • Using Bash
      • CRUD Files & Directories
      • Text Editors
      • Git
    • Server Computing
      • ssh
      • High Performance Computing
      • Cloud Computing
    • Dev
      • How to be a Pythonista
      • Developing Python Packages
      • Setting up a repo
    • Bioinformatics Tools
      • BLAST
      • BWA-mem
      • kallisto
      • mfold
      • OligoAnalyzer
      • OligoCalc
      • ViennaRNA
    • DNA Sequence Editors
      • A Plasmid Editor
      • Benchling
    • Online Resources
      • Addgene
      • CGSC
      • EcoCyc
      • Genbank (NCBI)
      • RegulonDB
  • Molecular Biology
    • Microbiology Lab
      • Personal Protective Equipment
      • Aseptic Technique
      • Media & Recipes
      • Growing Bacteria
      • Enumerating Bacteria
      • Storing Bacteria
      • Bacteriophages
    • Lab Equipment
      • Shaker Incubators
      • Genetic QPix2 Colony Picker
      • NanoDrop
      • Thermal Cyclers
      • Microplate Reader
      • Microplate Incubator
  • Design Genetic Systems
    • Models and Design Algorithms
      • Getting started
      • RBS Calculator
      • RBS Library Calculator
      • Riboswitch Calculator
      • Operon Calculator
      • Non-Repetitive Parts Calculator
      • Synthesis Success Calculator
      • PyVRNA
      • RNAdynamics
      • Dependencies
      • Glossary
      • UIPAC Code
      • Jupyter tutorials
  • Build Genetic Systems
    • Plan and Execute Your DOE
    • DNA
      • Ordering DNA
      • DNA Assembly
      • Anneal Oligonucleotides
      • PCR
      • PCR Cleanup
      • PCR Assembly
      • Gel Extraction
      • Plasmid Extraction
      • Genomic Library Preparation
    • Restriction Cloning
      • Restriction Enzyme Digestion
      • Ligation with T4 DNA Ligase
    • Multi-Fragment Assembly
      • Golden Gate
      • LCR
      • Gibson Assembly
      • TA Cloning
    • Genome Editing
      • Lambda Red Recombination
      • MAGE
      • pORTMAGE
      • CRISPR/Cas9
    • Transformation and Integration
      • E. coli Electroporation
      • E. coli Heat Shock
      • B. subtilis
  • Test
    • DNA
      • Gel Electrophoresis
      • Sanger Sequencing
      • Illumina
      • LCR-Seq
    • Protein
      • Flow Cytometry
      • Fluorescence Activated Cell Sorting
      • Gram's Iodine Stain
      • LacZ (beta-gal)
      • Microplate Fluoresence
      • Neurosporene
      • SDS-PAGE
      • TX-TL Crude Cell Extract Prep
      • Transcription-Translation (TX-TL)
    • RNA
      • Spin Column-Based Extraction
      • Phenol-Chloroform Extraction
      • Reverse Transcriptase (RT)
      • qPCR with TaqMan
      • qPCR with SYBR Green
      • Targeted RNA-Seq
      • Transcriptome RNA-Seq
      • T7 HiScribe Kit RNA Synthesis
      • T7 RNAP Reaction Clean-Up
    • Metabolite
      • HPLC
      • LC-MS
    • Other
      • TCSPC
      • MinION
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Salis Lab Protocol Book

A protocol book by the people, for the people!

NextGetting Started

Last updated 1 year ago

This introduces skills in computational biology and experimental microbiology required in the Salis Lab. First, you'll be introduced to popular bioinformatics tools, our best practices for software development, and a how-to-guide for using the DNA Compiler (DNAc). With these tools, you'll be well equipped to design and study synthetic genetic systems. Secondly, you'll be introduced to conceptual workflows, basic lab techniques, and experimental protocols to build and test your designed genetic systems. Continue reading for more details on the contents of this protocol book and how to get started in the Salis lab.

We're under construction! There are a number of pages that are incomplete or empty! Please help out. The best way to contribute is to directly edit the pages in the . You will need your GitHub login. If you don't have edit access to the GitHub repo, then please contact Howard Salis at salis@psu.edu.

Contributing Authors

Thanks to the following individuals for contributing to this git-protocol-book: Alex Reis, Sean Halper, Grace Vezeau, Daniel Cetnar, Ayaan Hossain, Chiam Yu Ng, and Howard Salis. If you are a new contributor, please add your name to the authors list.

Git Protocol Book
here
GitHub Repo