• General Molecular Biology

1. Agarose Gel Electrophoresis to Analyze DNA Fragments

2. PCR primer design 

3. PCR amplification from gDNA or plasmid DNA 

4. Preparative Scale Restriction Digests of PCR products and Plasmids 

5. Ligation of Plasmid and Inserts Transformation of Chemically Competent Bacterial Cells 

6. Analytical Scale Restriction Digests of PCR products and Plasmids 

7. Commonly Used Sequencing Primers 

8. Plasmid Verification 

9. Archiving a Strain and/or Plasmid

• Specialized Cloning

1. Making ds DNA inserts from Oligonucleotides 

2. Site-Directed Mutagenesis of Plasmids 

3. Phusion Based Modification of Plasmids for Golden Gate Cloning 

4. Golden Gate Cloning 

5. Preparation of Electrocompetent Cells 

6. Transformation of Electrocompetent Bacterial Cells using Electroporation 

7. Doing 48 minipreps in parallel using the Qiagen Turbo Kit 

8. Genomic Deletions and Insertions with Lambda Red 

9. Single Colony PCR

• General Cell Biology

1. Cryopreservation of mammalian cells 

2. Thawing cells from liquid nitrogen 

3. Stem cells thaw, culture, split/passage, and cryofreezing. 

4. Bacterial cells thaw, culture, and cryofreezing.

• Protein Expression, Characterization and Purification

1. Strain selection 

2. Test induction 

3. Protein purification using HisTrap 

4. Periplasmic fractionation 

5. Cell lysis using the homogenizer 

6. Membrane fraction isolation 

7. SDS PAGE 

8. Immunoblotting

• Soft-lithography for microfabrication

• 3D Bioprinting: materials and procedures

• Sequencing

1. RNA-seq of stem cells

2. ATAC-seq

3. Joint mRNA + ATAC-seq

4. single-cell mRNA-seq

5. Linked single-cell mRNA+ATAC-seq by modified drop-seq

6.  16S sequencing of microbial samples

7. Sample preparation for PacBio sequencing

• more to add...

Dataset:

https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/

https://rdrr.io/cran/sybilSBML/ 

Data sources frequently used for metabolic reconstructions.

Name

Link

Comment

Genome Databases

Comprehensive Microbial Resource (CMR)

http://cmr.jcvi.org/cgi-bin/CMR/CmrHomePage.cgi. The

Genomes OnLine Database (GOLD)

http://www.genomesonline.org/

TIGR

http://www.tigr.org/db.shtml

NCBI Entrez Gene

http://www.ncbi.nlm.nih.gov/sites/entrez

SEED database32

theseed.uchicago.edu/FIG/index.cgi

Comparative genomics tool.

Biochemical Databases

KEGG41

www.genome.jp/kegg/

BRENDA42

www.brenda-enzymes.info/

Transport DB89

http://www.membranetransport.org/

PubChem86

http://pubchem.ncbi.nlm.nih.gov/

Transport Classification Database (TCDB)

http://www.tcdb.org/

TCDB is a curated database of factual information from over 10,000 published references.

pKa Plugin

http://www.chemaxon.com/product/pka.html

Free for academic users

pKa DB

http://www.acdlabs.com/products/phys_chem_lab/pka/

Commercial software package to determine acid-base ionization/dissociation constant, pKa.

Organism-specific databases

Ecocyc43

http://ecocyc.org/

Escherichia coli database

PyloriGene37

http://genolist.pasteur.fr/PyloriGene

Helicobacter pylori database

Gene Cards

www.genecards.org/

Human gene database

Protein Localization databases

PSORT47

http://www.psort.org/psortb/

Support vector machine (SVM) based.

PA-SUB48

http://www.cs.ualberta.ca/~bioinfo/PA/Sub/

Proteome Analyst Specialized Subcellular Localization Server (SVM based).

Bio-numbers

CyberCell Database (CCDB)88

http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi

B10NUMB3R5

http://bionumbers.hms.harvard.edu/

Available reconstruction software packages

Simpheny

http://www.genomatica.com/technology/technologySuite.html

Commercial software

COBRA simulation environments

CellNetAnalyzer90/FluxAnalyzer91

http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html

Matlab is required

COBRA Toolbox16

http://systemsbiology.ucsd.edu/Downloads/Cobra_Toolbox

Matlab is required

FluxExplorer92

MetaFluxNet93, 94

http://mbel.kaist.ac.kr/lab/mfn/