Resources & Research Tools

Liner Scholar

An AI-powered academic search and research assistant that helps users discover scholarly papers, summarize findings, and quickly understand complex research topics.

Anara

An AI tool for literature reviews that simplifies reading, extracts key insights, enhances writing, and guides you through complex topics with ease.

ScienceOpen

A free search engine for research papers with citation metrics, altmetrics, and a user-friendly design for exploring scholarly works.

Semantic Scholar

An AI-powered platform for discovering and analyzing academic papers, offering deep insights into scholarly literature.

SciSpace

A research tool with 270+ million papers and an AI assistant, Copilot, providing summaries, explanations, and answers to aid comprehension.

PICO Portal

An AI tool designed to streamline systematic reviews by predicting the most relevant articles based on your criteria, reducing the number of studies you need to screen.

Elicit

An AI research assistant that helps in literature review by finding relevant papers, summarizing findings, and extracting key information to answer specific research questions.

Research Rabbit

A tool that allows researchers to create collections of papers and visualize the connections between them, aiding in the discovery of related work and the development of comprehensive literature reviews.

Consensus

An AI-powered search engine that finds and summarizes research papers, helping users quickly understand the consensus in scientific literature on a given topic.

A Complete Guide to the Key Components of a Research Article By Wiley Researcher Academy

Write and Publish a Research Paper: Complete Guide By Adam Academy

Fundamentals of Manuscript Preparation By Elsevier Research Academy

Writing Skills By Elsevier Research Academy

Fundamentals of Publishing By Elsevier Research Academy

JANE (Journal/Article Name Estimator)

A tool that helps you find the most relevant journals for your research based on article titles or abstracts.

Clarivate Master Journal List

A comprehensive list of journals indexed by Clarivate, offering essential information for journal selection.

Scopus Journal Comparison

Allows you to compare journals indexed in Scopus based on various metrics like impact factor and citation counts.

Jot (Journal Targeter)

A tool to help you identify the best journals for submitting your manuscript based on keywords or topics.

Elsevier Journal Finder

Helps you find Elsevier journals that match your research topics and manuscript.

Taylor & Francis Journal Suggester

This tool suggests journals from Taylor & Francis based on the title and abstract of your manuscript.

Think. Check. Submit

A resource to help you evaluate the trustworthiness of journals and avoid predatory publishers.

Wiley Journal Finder

A tool that helps you find Wiley journals by matching your manuscript with relevant journals.

Cabell's

Provides a directory of journals and their evaluation metrics, helping you find suitable journals for your research.

Journal Evaluation Tool

A tool for evaluating journals based on multiple performance metrics and journal reputation.

Sage Journal Recommender

Suggests Sage journals that are a good fit for your research topic using your manuscript title and abstract.

dplyr

A package for data manipulation, offering functions like filtering, selecting, and summarizing data. Part of the tidyverse.

tidyr

Focuses on tidying data, such as reshaping and separating columns. Works well with other tidyverse packages.

Tidyverse

A collection of R packages (e.g., ggplot2, dplyr, tidyr, purrr) for consistent data analysis and visualization.

gtsummary & gt

Used for creating customizable summary tables for data frames and statistical models.

ggplot2

A powerful visualization package implementing the "grammar of graphics" to create complex plots.

hrbrthemes

Enhances ggplot2 plots with additional themes, color palettes, and customization options.

RColorBrewer & viridis

Provide color palettes for data visualization, ideal for maps and charts.

Heatmaply

Creates interactive heatmaps with customization options.

Introduction to R for Life Scientist By Proteintech

Introduction to Programming with R By CodeSignal

R Programming for Data Science By Alison

Regression Analysis Using R By Great Learning

Data Visualization with ggplot2 By CodeSignal

NumPy

Foundation for scientific computing, offering support for multidimensional arrays and mathematical operations.

Pandas

Simplifies data wrangling and analysis, providing powerful tools for handling structured data.

Matplotlib

Used for creating static, basic data visualizations.

Seaborn

Enhances Matplotlib with advanced statistical visualizations and attractive aesthetics.

Plotly

Enables interactive and dynamic data visualizations.

researchpy

Data and performs statistical tests efficiently.

Dask

Handles big data analysis with parallel computing support.

scikit-learn

A versatile library for machine learning, offering tools for classification, regression, and clustering.

scikit-image

Provides tools for image manipulation, especially useful in life sciences.

Python By Kaggle

Introduction to Python for Biologists By Proteintech

Programming Foundations with Python By CodeSignal

Machine Learning with Python By freeCodeCamp

AI for Medicine Specialization By DeepLearning.AI

NCBI Databases

Provides genomic, transcript, and protein sequences for multiple organisms.

BLAST

Identifies similar DNA, RNA, or protein sequences to predict function and evolutionary relationships.

EMBOSS Stretcher

Performs pairwise sequence alignment using dynamic programming.

Clustal Omega

Multiple sequence alignment for evolutionary and functional studies.

MAFFT

High-speed, scalable multiple sequence alignment tool.

PROSITE

Identifies protein motifs and conserved functional domains.

Pfam

Detects protein families and conserved domains using HMMs.

BWA

Aligns short DNA reads to a reference genome.

Bowtie2

High-speed short-read aligner for large genomes.

SPAdes

De novo genome assembler for bacteria and small eukaryotic genomes.

Velvet

De novo short-read genome assembler using de Bruijn graphs.

Prokka

Automated prokaryotic genome annotation.

AUGUSTUS

Gene prediction in eukaryotic genomes.

OrthoFinder

Detects orthologous genes across multiple species.

UCSC Genome Browser

Interactive genome visualization with extensive annotation tracks.

Ensembl Genome Browser

Genome annotation, comparative genomics, and variation data.

IGV (Integrative Genomics Viewer)

Desktop tool for inspecting alignments and variants.

JBrowse

Web-based genome browser suitable for custom and local genomes.

FastQC

Quality control of raw sequencing reads.

featureCounts

Counts reads mapped to genes or genomic features.

HTSeq

Generates gene-level read counts for RNA-seq.

DESeq2

Identifies differentially expressed genes between conditions.

edgeR

Statistical analysis of RNA-seq count data.

RNAfold

Predicts RNA secondary structure using minimum free energy.

Seurat

R toolkit for single-cell RNA-seq analysis and visualization.

Scanpy

Python framework for large-scale single-cell analysis.

Cell Ranger

Processes raw single-cell sequencing data from 10x Genomics.

Monocle

Infers differentiation trajectories and pseudotime.

MODELLER

Builds 3D protein structures using homologous templates.

SWISS-MODEL

Automated homology-based protein modeling.

AlphaFold DB

AI-predicted protein 3D structures.

YASARA

Performs energy minimization and molecular simulations.

SAVES Server

Validates protein structure quality and stereochemistry.

SuperPose

Compares 3D structural alignments of proteins.

PyMOL

Visualizes, analyzes, and animates 3D molecular structures.

ChimeraX

Advanced visualization of proteins, complexes, and cryo-EM data.

BIOVIA Discovery Studio Visualizer

Analyzes protein–ligand interactions.

POCKDRUG

Predicts ligand-binding pockets and druggability.

fpocket

Detects potential binding pockets on proteins.

TRAPP Web Server

Analyzes pocket dynamics from simulations.

Marvin JS

Chemical structure drawing and editing.

LigandScout

Generates pharmacophore models for drug discovery.

ZINCPHARMER

Screens ligand libraries for pharmacophore matches.

AutoDock Vina

Performs ligand-protein docking simulations.

PyRx

Graphical interface for docking and virtual screening.

PatchDock

Docking based on geometric complementarity.

FireDock

Refines docking results using energy-based scoring.

GROMACS

High-performance molecular dynamics simulations.

VMD

Visualizes and analyzes MD trajectories.

Spartan

Performs quantum chemistry (DFT) calculations.

SwissADME

Predicts pharmacokinetics, solubility, and drug-likeness.

ADMETsar 2.0

Evaluates ADMET properties computationally.

RDKit

Cheminformatics toolkit for molecular modeling and drug design.

Cytoscape

Visualizes and analyzes biological networks such as protein–protein interactions.

STRING

Explores known and predicted protein–protein interactions.

KEGG

Links genes and proteins to metabolic and signaling pathways.

Reactome

Curated database of human biological pathways.

DAVID

Functional annotation and enrichment analysis of gene lists.

IEDB Tools

Predicts T-cell and B-cell epitopes for vaccines.

NetMHCpan

Predicts peptide binding to MHC class I molecules.

BepiPred

Predicts linear B-cell epitopes.

VaxiJen

Predicts protein antigenicity for vaccines.

C-ImmSim

Simulates immune responses to vaccine constructs.

SnapGene

Simulates DNA cloning, codon optimization, and plasmid construction.

SignalP

Predicts signal peptides for protein secretion.

How to analyze RNAseq Data for Absolute Beginners By NGS Learning Hub

Python Scripting for Biochemistry & Molecular Biology By 101 PDB

Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R By Wellcome Connecting Science and Future Learn

Bioinformatics for Biologists: Analysing and Interpreting Genomics Datasets By Wellcome Connecting Science and Future Learn

Diploma in Bioinformatics By Alison

WormBase

Central database for C. elegans genetics, genomics, phenotypes, and annotations.

WormBook

Open-access, peer-reviewed resource on C. elegans biology and research methods.

WormAtlas

Anatomical and structural reference with detailed imaging and connectivity maps.

Caenorhabditis elegans Natural Diversity Resource (CeNDR / CaeNDR)

Repository for wild isolates, natural variation, and genome-wide association mapping.

Caenorhabditis Genetics Center (CGC)

Provides C. elegans strains, stocks, and genetic resources.

OpenWorm

Computational project simulating C. elegans anatomy, connectome, and behavior.

Textpresso for C. elegans

Literature search engine for full-text publications on C. elegans.

C. elegans Connectome Datasets

Neural wiring and connectivity data for the full worm nervous system.

BioArt

Hosted by the National Institute of Allergy and Infectious Diseases (NIAID), BioArt provides over 2,000 science and medical visuals, including vectors, icons, and brushes, created by professional illustrators.

Bioicon

Bioicon offers a collection of high-quality biological icons and illustrations to enhance scientific presentations and educational materials.

BioRender

BioRender's scientific illustration software includes an activity sheet with editable lab icons, enabling users to create publication-quality figures using pre-made icons and templates.

SciDraw

SciDraw is a platform that offers a variety of scientific drawings, including vectors of cells, animals, and laboratory equipment, contributed by the scientific community.

Servier Medical Art (SMART)

It offers over 3,000 free, high-quality medical illustrations suitable for publications and presentations. The collection encompasses various medical specialties, including anatomy, cellular biology, and general medical items.

LabIcons

LabIcons offers free drawings of laboratory objects to improve knowledge communication in science and education, including clip arts of microcentrifuge tubes, plasticware, instruments, equipment, and glassware.