Resources

Useful links for research

• KEGG: Metabolic pathways & genes
• BRENDA: Enzyme database
• NCBI: National Center for Biotechnology Information – BLAST, Pubmed, Genbank, and more!
• EcoCyc: Encyclopedia of E. coli genes and metabolism
• Phobius: A combined transmembrane topology and signal peptide predictor
• MIBiG: Minimum Information about a Biosynthetic Gene cluster
• antiSMASH: Prediction of BGCs from genomic information
• UniProt: protein information repository
• PDB: protein structure-related information repository
• Protocol Exchange: an NPG preprint repository where new protocols are published
• STAR Protocols: a Cell Press repository where new protocols are published
• AlphaFold Protein Structure Database
• BaseBuddy: a codon optimization tool developed from Jay Keasling’s lab
• KBase: a web-based platform for data analysis, sharing & publication (e.g., genome assembly, metabolic modelling, comparative genomics)
• SWISS-MODEL: a web-based protein structure homology modelling server

Useful links for paper writing

• CAS Source Index (CASSI): Journal abbreviations
• Quillbot: AI-based paraphrasing tool
• Biorender: Bio-related figure components (raster files)
• Inkscape: Open-source figure drawing SW (vector files) – see tutorial
• GIMP: Open-source figure drawing SW (raster images)
• Blender: Open-source 3D figure drawing SW
• Lightworks / DaVinci Resolve: video editing SW
• Tutorial for Adobe Illustrator
• Bioicon: open-source illustrator files related to biology/biotechnology