Resources and Tools

Literature Review Tools

Unriddle.AI: 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.

Free Courses on Research Methods, Manuscript Writing, and Publishing

Understanding Research Methods By Coursera

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

Fundamentals of manuscript preparation By Elsvier Research Academy

Writing skills By Elsvier Research Academy

Fundamentals of Publishing by Elsevier Research Academy

Find Journer

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.

R Package for Data Analysis and Visualization

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.

Free Courses and Tutorials for R Programming

Data Analysis with R Programming By Coursera

Introduction to R Programming for Data Science By Coursera

Data Visualization & Dashboarding with R Specialization By Coursera

Expressway to Data Science: R Programming and Tidyverse Specialization By Coursera

Statistical Analysis with R for Public Health Specialization By Coursera

Mastering R for Research By CHIRAL Bangladesh [ In Bengali Language ]

Data Science Tools

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.

Free Courses and Tutorials for Data Science

Data Analysis with Python By Coursera

Python for Data Science, AI & Development By Coursera

Introduction to Artificial Intelligence (AI) By Coursera

Machine Learning Specialization By Coursera

AI in Healthcare Specialization By Coursera

Machine Learning for Bioinformatics By CHIRAL Bangladesh [ In Bengali Language ]

Bioinformatics Tools, Software, and Datasets

Sequence Retrieval and Analysis:

NCBI Database: Provides access to genomic and protein sequence data for various organisms.
EMBOSS Stretcher: Aligns nucleotide or protein sequences using dynamic programming.
PROSITE: Identifies protein motifs and conserved functional domains.

Homology Modeling:

Modeller v9.26: Constructs 3D protein structures based on homologous templates.
Swiss-Model: Automates template selection and homology-based structure modeling.

Model Evaluation and Energy Minimization:

YASARA: Performs energy minimization and molecular simulations.
SAVES: Assesses stereochemistry and structure validation of protein models.
Superpose: Compares 3D structural alignments of proteins.

Active Site Prediction:

POCKDRUG: Identifies and characterizes ligand-binding pockets.
Biovia Discovery Studio Visualizer: Analyzes and visualizes molecular interactions.

Ligand Design:

Marvin JS: Facilitates chemical structure drawing and editing.

Pharmacophore Modeling and Virtual Screening:

LigandScout: Generates pharmacophore models for drug discovery.
ZINCPHARMER: Screens ligand databases for potential drug candidates.

Pharmacodynamics and ADMET Analysis:

SwissADME: Predicts pharmacokinetics and drug-likeness of molecules.
ADMETSAR-2.0: Evaluates absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties.

Molecular Docking:

AutoDock Vina: Performs ligand-protein docking simulations.
PatchDock: Conducts molecular docking through geometric shape complementarity.
FireDock: Refines docking results with energy-based optimization.

Molecular Dynamics Simulation:

GROMACS: Runs high-performance molecular dynamics simulations.

Analysis of MD Trajectories:

VMD: Visualizes and analyzes molecular dynamics trajectories.

Pocket Dynamics Analysis:

TRAPP Web Server: Studies the dynamic behavior of binding pockets.

Density Functional Theory (DFT) Calculation:

Spartan 14: Computes electronic properties like HOMO/LUMO analysis.

Protein Annotation and Functional Prediction:

Pfam: Detects conserved protein families and domains.
SignalP: Predicts signal peptides for protein secretion.

Epitope Prediction and Vaccine Design:

IEDB Tools: Identifies MHC-binding and B-cell epitopes for vaccine design.

Codon Optimization and In-Silico Cloning:

SnapGene: Simulates in-silico DNA cloning and plasmid construction.

mRNA Structure Prediction:

RNAfold: Predicts secondary structures of RNA sequences.

C. elegans Databases & Resources

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.

Research & Scientific Databases

Genomics Databases

NCBI GenBank — A comprehensive nucleotide sequence database with annotated genetic information.
Ensembl Genome Browser — Provides genome data, annotations, and comparative genomics tools.
UCSC Genome Browser — Interactive genome visualization with integrated annotation tracks.
DDBJ — DNA Data Bank of Japan, part of the international nucleotide sequence collaboration.
1000 Genomes Project — A large-scale catalog of human genetic variation across populations.

Transcriptomics Databases

GEO — NCBI repository for functional genomics and transcriptomics datasets.
ArrayExpress — EMBL-EBI’s archive of functional genomics experiments and gene expression data.
SRA — Sequence Read Archive for high-throughput sequencing data storage.
Expression Atlas — Explores gene expression across tissues, conditions, and organisms.
GTEx — Genotype-Tissue Expression project linking genetic variation with tissue-specific expression.

Proteomic Databases

UniProt — Central hub for protein sequences and functional annotation.
PDB — Protein Data Bank containing 3D structural data of biomolecules.
Pfam — Database of protein families and domains with sequence alignments.
STRING — Protein–protein interaction networks from experiments and predictions.
PRIDE — Repository for proteomics mass spectrometry datasets.

Metabolomics Databases

HMDB — Human Metabolome Database for small-molecule metabolites.
MetaboLights — EBI resource for metabolomics experiments and studies.
KEGG Metabolomics — Pathway maps for metabolism and biochemical networks.
LipidMaps — Specialized database for lipid structures and pathways.
Reactome — Curated database of biological pathways and reactions.

Genetic Variation Databases

dbSNP — Archive of simple genetic variations such as SNPs.
ClinVar — Clinical relevance of genetic variants linked to diseases.
gnomAD — Genome Aggregation Database with allele frequency data.
COSMIC — Catalog of somatic mutations in human cancer.
dbVar — Database of large-scale genomic structural variations.

Cancer Databases

TCGA — The Cancer Genome Atlas, a molecular characterization of cancer.
ICGC — International Cancer Genome Consortium providing global cancer datasets.
cBioPortal — Interactive platform for exploring cancer genomics data.
Oncomine — Gene expression resource for oncology research.
COSMIC — Database of cancer mutations (also in variation databases).

Health & Biomedical Data

UK Biobank — Large-scale biomedical database with genetic and health data.
DHS Program — Demographic and Health Surveys for global population health.
World Values Survey (WVS) — Global survey on social, cultural, and health-related values.
GHDx — Global Health Data Exchange with worldwide health datasets.
MICS (UNICEF) — Multiple Indicator Cluster Surveys for child and maternal health.

Drug Discovery & Chemical Databases

ChEMBL — Bioactive drug-like compounds with activity data.
DrugBank — Drug and drug-target information database.
PubChem — Public database of chemicals and their biological activities.
BindingDB — Binding affinities for biomolecular interactions and drug discovery.

Plant Databases

TAIR — Arabidopsis thaliana genome and functional biology database.
Gramene — Comparative genomics resource for plants and crops.
PlantGDB — Plant genome resources and gene annotations.
Phytozome — Comparative platform for green plant genomics.
BAR — Bio-Analytic Resource for plant gene expression and visualization.

Microbiology & Virology Databases

ViPR — Virus Pathogen Resource with genome and analysis tools.
PATRIC — Pathosystems Resource for bacterial pathogens.
IMG/M — Integrated Microbial Genomes & Microbiomes data platform.
MG-RAST — Metagenomics analysis server for microbial communities.
GISAID — Global database for influenza and SARS-CoV-2 genomic data.

Structural Biology & Molecular Modeling Databases

CATH — Classification of protein domain structures.
SCOP — Structural Classification of Proteins based on hierarchies.
ModBase — Comparative protein structure models.
EMDB — Electron Microscopy Data Bank for 3D structures.
SwissSidechain — Database for molecular modeling in drug design.

Clinical & Epidemiology Databases

ClinicalTrials.gov — Registry of clinical trials worldwide.
WHO Clinical Trials Registry — International clinical trial registration platform.
SEER — Cancer incidence and survival data in the U.S.
GHDx — Global health metrics and epidemiological datasets.
BioLINCC — Access to clinical and epidemiologic study resources.

Biological Illustration Tools

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.
Reactome: Reactome is a free, open-source, curated, and peer-reviewed pathway database that provides insights into molecular processes and pathways in human biology.
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.