Brain imaging
MRI, fMRI and diffusion: from scanner files to statistics.
Research tools
A directory of free software and online resources for neuroscience and in silico research, arranged by research task. Each entry links to the official website of the tool and to the paper to cite.
GloNeuro tools
- Experiment Design Studio
Planning of a study in nine stages, from the research question to sample size, bias control, analysis and data sharing.
- Research design
Study types, bias and validity, and the differences between association, correlation and causation, with interactive figures.
- Literature search
A search of PubMed, the biomedical literature database of the US National Library of Medicine.
- Sequence tools
Analysis of pasted DNA and protein sequences in the browser: translation, alignment and phylogenetic trees.
Tools by research question
Brain signals
EEG, MEG, sleep and electrophysiology, from recording to analysis.
Cells, tissue and behaviour
Calcium imaging, microscopy, atlas registration, behaviour and experiments.
Models and networks
Simulating neurons and circuits, analysing brain networks and machine learning.
Molecules and in silico
Docking, drug-likeness, molecular dynamics, structures, genes and omics.
Data, methods and learning
Open data, atlases, statistics, study design, literature and community help.
Common workflows
GloNeuro tools
Brain anatomy
The structure of the human and mouse brain in three dimensions and in section, and of the human and mouse spinal cord.
3D brain atlas
A three-dimensional model of the human brain with 34 labelled regions. It describes the function of each region and ten brain systems, and the changes in Parkinson’s disease, Alzheimer’s disease, stroke, epilepsy and multiple sclerosis.
Atlas library
Sections of the brain and spinal cord of six species in one viewer, with every region named: the human brain (MRI template and BigBrain histology) and spinal cord; the adult and developing mouse brain and the mouse spinal cord, from the Allen Institute; and the rat, marmoset, larval zebrafish and fruit fly brains.
The atlases are openly published; each viewer gives its source, licence and the paper to cite.
Experiment planning
Planning a study with appropriate controls, an adequate sample size and a sound analysis.
Experiment Design Studio
A nine-step planner that leads from the research question to a complete plan. It calculates sample size with power curves for two groups, paired measures, one-way ANOVA, repeated measures, correlation, two proportions and survival, with rank-based options for ordinal or skewed outcomes (Mann–Whitney, Wilcoxon, Kruskal–Wallis). It covers randomisation, blinding, controls and the experimental unit for in silico, in vitro, ex vivo, animal and human studies, audits the plan as a reviewer would, and exports it to Markdown or to a file that can be reopened.
Power for t-tests and ANOVA uses the noncentral distributions that G*Power uses, and the results match G*Power for standard reference cases. Methods and references are given on the page. For a funded study or an ethics application, have the plan checked by a statistician.
Literature
Searching the published literature, including the publications of GloNeuro researchers.
PubMed search
A search of the biomedical literature indexed by PubMed, with abstracts shown on the page. Searches cover all fields, title and abstract, title, author or journal, and can be filtered by article type, publication year and free full text. Each result links to the PubMed record, the publisher and any free full text in PubMed Central.
Results are retrieved live from the US National Library of Medicine through its public E-utilities service.
GloNeuro publications
A search of all papers by GloNeuro researchers, including their abstracts, by theme, type and year. Matching words are highlighted, papers newly listed on PubMed with a GloNeuro affiliation are added automatically, and each paper links to PubMed and to the publisher.
The publication list is checked against PubMed.
Sequences
Analysis of DNA, RNA and protein sequences.
Sequence tools
Analysis of DNA, RNA and protein sequences pasted from NCBI, Ensembl or UniProt. For DNA and RNA: translation in six frames, open reading frames, CpG islands, restriction maps with a virtual gel, primer melting temperatures and in silico PCR. For proteins: molecular weight, extinction coefficient, isoelectric point, hydropathy, protease digests and PROSITE motifs. Also alignments, neighbour-joining and UPGMA trees, dN/dS, and mutations with their effect on the protein in HGVS-style notation.
All calculations run in the browser; nothing is stored or sent. Methods and references are given with each tool.
Notes on the directory
How tools are chosen
The directory lists software and online resources that are free to use for academic research, widely used, and published or documented by their developers.
Licences and features
Licence terms and features change and should be confirmed on the website of each tool, particularly for commercial or clinical use. “Good place to start” marks a common, well-documented choice for a task; it is GloNeuro’s editorial suggestion, not a ranking. GloNeuro is not affiliated with these projects.
Suggest a tool
Missing tools and changed links or licences can be reported through the contact page; each report is checked before the directory is updated.
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