Resources

Internal

We are committed to open access scientific knowledge:

• Preprints: bioRxiv
• Software and source code: GitHub Repository
• Plasmid DNA: AddGene
• Protocols: Protocols.io
• Data and Media: FigShare

External

Software:

• Snakemake - reproducible and scalable data analyses
• Nextflow
• Tidyverse and R - RStudio Cheat Sheets
  • ggtree
  • ggseqlogo
• Alignment, MSA, Phylogeny tree generation:
  • BBtools - alignment
  • MAFFT - MSA
  • T-Coffee - MSA
  • FastTree - approximately-maximum-likelihood phylogenetic trees
• Protein/Molecular structure visualization and manipulation:
  • UCSF Chimera and UCSF ChimeraX
  • PyMol
  • Rosetta software suite
• Sequence manipulation and analysis:
  • starcode - paper
  • Enrich2 - paper
  • Edinburgh Genome Foundry repo - DnaChisel
  • bioawk
  • bioSyntax - paper
  • UMI-tools - paper
  • Miller
• CFU.ai

Online Tools:

• BLAST
• PaperBLAST
• EVolutionary Couplings and EVmutation
• Protein Repair One-Stop Shop - Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability - paper
• FuncLib - Automated Design of Efficient and Functionally Diverse Enzyme Repertoires - paper
• HotSpot Wizard - Automated design of mutations - paper
• ConSurf Server
• Dali - 3D protein structure comparison - paper
• FATCAT
• CASTp - paper

Databases:

• E. coli:
  • EcoCyc
  • The E. coli molecular phenotype under different growth conditions - genome-wide transcriptomics and proteomics dataset of E. coli grown under 34 different conditions
  • The quantitative and condition-dependent Escherichia coli proteome
  • Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability
  • Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
  • The binary protein-protein interaction landscape of Escherichia coli
  • Genomewide landscape of gene–metabolome associations in Escherichia coli
  • RegulonDB
• Proteins:
  • PDB
  • Pfam
  • InterPro
  • UniProt
  • Protein Contacts Atlas - paper
  • SWISS-MODEL Repository
  • ModBase
  • CATH
• MaveDB a public repo of MAVE, DMS, MPRA data sets.
• Therapeutic target database
• BRENDA
• KEGG
• Fluorescent Protein Database
• Fluorescent Biosensor Database

Data Visualisation and Graphics:

• Fundamental of data visualisation by Claus O. Wilke
• Visual vocabulary chart
• paletteer
• Python Graph Gallery
• Data Visualization Tools
• Circular Visualization in R
• Ten Simple Rules for Better Figures
• Scientific Journal and Sci-Fi Themed Color Palettes for ggplot2
• BBC Visual and Data Journalism cookbook for R graphics
• Comprehensive list of color palettes in r
• pals - a collection of color palettes and colormaps

Books, Courses, Blog posts:

• Modern Statistics for Modern Biology
• Readings in Applied Data Science
• HarvardX Biomedical Data Science Open Online Training
• initial steps toward reproducible research
• Common statistical tests are linear models
• Rosalind - a platform for learning bioinformatics and programming through problem solving

Sequencing:

• Next-Generation-Sequencing.v1.4.1 @albertvilella
• Illumina: Intro to Sequencing by Synthesis