Resources & Tools

A Research Toolkit

Research tools first - bench planning, sequence analysis, structural work, and high-throughput data. Study and application material for students follows below.

Showing 59 resources.

Research toolbox

The tools I actually use - bench planning, sequence analysis, structural work, and high-throughput data.

Molecular Biology Tools

6

Molecular Biology Tools

Primer-BLAST

Designs PCR primers while checking specificity, combining Primer3 with NCBI BLAST.

Molecular Biology Tools

Primer3

Highly trusted primer design software for PCR, qPCR, and sequencing projects.

Molecular Biology Tools

Benchling

Cloud-based molecular biology and lab platform for sequence analysis, cloning, and collaboration.

Molecular Biology Tools

SnapGene Viewer

Visualises plasmids, cloning workflows, and DNA constructs - popular with researchers.

Molecular Biology Tools

PyMOL

Professional molecular visualisation for publication-quality protein structure figures.

Molecular Biology Tools

ChimeraX

Advanced visualisation for structural analysis and interactive molecular rendering.

Basic Bioinformatics

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Basic Bioinformatics

NCBI BLAST

Sequence similarity search for identifying homologous DNA, RNA, and protein sequences. Essential for comparative genomics.

Basic Bioinformatics

EMBL-EBI Tools

Comprehensive suite for sequence analysis, alignment, phylogenetics, and database access.

Basic Bioinformatics

Clustal Omega

Widely used multiple sequence alignment for DNA and protein, suited to evolutionary studies.

Basic Bioinformatics

MAFFT

Fast, highly accurate multiple sequence alignment popular for large genomic and proteomic datasets.

Basic Bioinformatics

UniProt

Comprehensive protein sequence and functional annotation database with curated structure and function.

Basic Bioinformatics

Ensembl

Genome browser for vertebrate and model organisms supporting comparative genomics and variation analysis.

Basic Bioinformatics

RCSB Protein Data Bank (PDB)

Primary repository of experimentally determined protein structures, essential for structural biology and drug design.

Basic Bioinformatics

KEGG

Integrated database for pathways, diseases, and molecular interactions used in systems biology.

Drug Design

8

AlphaFold Database

AI-predicted protein structures for millions of proteins, transforming structural biology and target ID.

SWISS-MODEL

Automated homology modelling that builds reliable 3D protein models from sequence.

AutoDock Vina

Popular molecular docking software for ligand–protein studies and virtual screening.

CB-Dock2

Blind docking server with automatic cavity detection that simplifies docking workflows.

HDOCK

Protein–protein and protein–ligand docking combining template-based and ab initio approaches.

GROMACS

High-performance molecular dynamics for biomolecular stability and interaction studies.

SwissADME

Predicts pharmacokinetics, drug-likeness, and medicinal chemistry properties for lead optimisation.

ADMETlab 3.0

Advanced ADMET prediction evaluating absorption, distribution, metabolism, toxicity, and excretion.

Vaccine Design

6

IEDB

Comprehensive immune epitope database and analysis resource, central to immunoinformatics.

NetMHCpan

Predicts peptide binding to MHC molecules - critical for T-cell epitope identification.

ABCpred

Machine-learning B-cell epitope prediction server useful for vaccine candidate selection.

VaxiJen

Alignment-independent antigenicity prediction widely used in reverse vaccinology.

AllerTOP

Predicts allergenic potential of proteins and peptides to improve vaccine safety.

C-ImmSim

Immune simulation platform modelling adaptive and innate responses to evaluate vaccines.

High Throughput Data Analysis

5

High Throughput Data Analysis

Galaxy

Web platform for reproducible analyses supporting NGS, RNA-seq, proteomics, and workflow automation.

High Throughput Data Analysis

DESeq2

Gold-standard R package for differential gene expression analysis in RNA-seq studies.

High Throughput Data Analysis

Seurat

Powerful single-cell RNA-seq toolkit for clustering, integration, and visualisation.

High Throughput Data Analysis

GATK

Industry-standard toolkit for variant discovery and genotyping from the Broad Institute.

High Throughput Data Analysis

IGV

Interactive genome visualisation for exploring sequencing and genomic datasets.

For students

Material I point mentees toward: language testing, funded study, application writing, and general study resources.

IELTS Resources

4

IELTS Resources

IELTS Official

Official source for IELTS information, sample tests, and registration details.

IELTS Resources

British Council IELTS

Official preparation materials, practice resources, and test booking.

IELTS Resources

IELTS Liz

Trusted free IELTS site with lessons, strategies, and practice materials.

IELTS Resources

IELTS Advantage

Comprehensive preparation focused on score-improvement strategies and tutorials.

Free Courses

4

Coursera

University-level courses from top institutions worldwide; many can be audited free.

edX

Online courses from leading universities - excellent for STEM and professional development.

MIT OpenCourseWare

Free access to MIT course materials and lectures, ideal for self-paced learning.

DeepLearning.AI

Industry-leading AI and machine learning education created by field experts.

PhD Scholarships, SOP & CV

5

PhD Scholarships, SOP & CV

FindAPhD

Largest database of PhD opportunities worldwide, including funded positions and scholarships.

PhD Scholarships, SOP & CV

EURAXESS

European research careers and funding portal - great for international PhD opportunities.

PhD Scholarships, SOP & CV

DAAD

Major scholarship platform for Germany with funding for international students.

PhD Scholarships, SOP & CV

Overleaf CV Templates

Professional LaTeX CV and academic resume templates widely used in academia.

PhD Scholarships, SOP & CV

The Professor Is In

Expert guidance on academic careers, SOPs, and interview preparation.

AI Tools for Research & Education

7

AI Tools for Research & Education

ChatGPT

AI assistant for writing, coding, brainstorming, and research support.

AI Tools for Research & Education

Claude

Advanced AI assistant with long-context reasoning, great for manuscript review and writing.

AI Tools for Research & Education

Perplexity

AI search engine with source citations, ideal for literature exploration and fact-checking.

AI Tools for Research & Education

Elicit

Research assistant for scientific literature that automates evidence gathering and discovery.

AI Tools for Research & Education

Consensus

Search engine extracting evidence directly from scientific papers, built for researchers.

AI Tools for Research & Education

SciSpace

AI platform for reading and understanding papers, explaining complex scientific concepts.

AI Tools for Research & Education

Zotero

Reference manager that organises citations, PDFs, and bibliographies efficiently.

Explore at Least Once in a Lifetime

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Explore at Least Once in a Lifetime

NASA Eyes

Interactive visualisation of the solar system and space missions in real time.

Explore at Least Once in a Lifetime

Human Cell Atlas

Global effort to map every human cell type - a landmark in modern biology.

Explore at Least Once in a Lifetime

Allen Brain Atlas

Comprehensive atlas of human and mouse brain explored through interactive datasets.

Explore at Least Once in a Lifetime

Our World in Data

Data-driven insights into global health, science, economics, and society.

Explore at Least Once in a Lifetime

Foldit

Protein-folding game contributing to real science - anyone can join biological discovery.

Explore at Least Once in a Lifetime

Zooniverse

World's largest citizen-science platform contributing to genuine research projects.