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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

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  • Contact
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