Scientific Toolbox

BioArt Source offers curated illustrations from the National Institute of Allergy and Infectious Disease (NIH) and independent medical illustrators. Each illustration can be freely downloaded (no account required) as the following file type: .ai, .svg and .png. BioArt Source also featured 3D illustrations of equipment and protein structures via their secondary webpage NIH 3D.

Usage and license: Illustrations are free to use and can be shared, modified and used in any medium, format or purpose. 96% of the featured illustrations are in the public domain and do not require attribution. The remaining 4% fall under the Creative Commons BY 4.0 license, meaning that, while still being free, proper credit is due. Appropriate licensing is indicated for each entry of BioArt source.

Theme: anatomy, viruses, cells and organelles, lab equipment, proteins, animals, people, bacteria, arthropods, cellular and molecular biology, molecules, plant, data plots, general

BioIcons is an open source graphics repository developed by Dr. Simon L. Dürr. It hosts high-resolution scientific illustrations made by the scientific community. These resources can be downloaded without any login and are free to use.

Usage and license: Illustrations are free to use and can be shared, modified and used in any medium, format or purpose. Most of the featured pictures are in the public domain (Creative Commons 0 license) and therefore do not require attribution. At the discretion of their respective creators, some illustrations fall under the Creative Commons BY 4.0 license, meaning that, while still being free, proper credit is due. Appropriate licensing is indicated for each entry of BioIcons.

Theme: Nanotechnology, genomics, intracellular components, chemistry, molecules, animals, molecular and cellular biology, viruses, oncology, parasites, procedures, informatics, amino acids, human physiology, lab equipment, data plots, general

Dalhousie’s Digital Asset Library features professional photographs of the people at Dalhousie, as well as some of our infrastructure on the campus.

Usage and license: Dalhousie’s Digital Asset Library allows you to access general-use photography that can be used on internal or external materials including presentations, social media, web, and print media.

Theme: photography, people, building, lab, Dalhousie university

LabIcons features high-quality .png illustrations of lab items such as equipment, instruments, tools, glassware and plasticware. This website hosts a free in-browser editor (no login required) to allow customization without the need for graphic design software.

Usage and license: Free to use for the scientific community, exclusively for educational, academic, scientific (use in publications is authorized) and non-commercial purposes. Attribution is required for all uses of the LabIcons illustration.

Theme: Lab equipment, instrumentation, glassware, plasticware

Pexels offers free (no login) high resolution photographs for your scientific communications. This resource is community-driven with new materials being added on a regular basis.

Usage and license: Free to use under the Pexels license. Images can be shared, modified and used in any medium, format or purpose. No attribution is required (though it is appreciated!).

Theme: photography, people, procedures, computer, lab equipment, general

Protein Data Bank (PDB) is a renowned database gathering peer-reviewed 3D structures of known proteins across several species. On top of gathering key structural information, PDB features a free built-in 3D visualizer (structure tab within each entry), which allows the user to choose a specific orientation and add personalized annotations. Annotated structures can be downloaded for free without any account.

Usage and license: Original 3D structures as well as annotated 3D structures are free to use for the scientific community for educational, academic and publication purposes. Attribution is mandatory for each structure entry by indicating the PDB identifier number, as well as the original published research article linked to this structure.

Theme: peer-reviewed 3D protein structures

SciDraw is a community-driven scientific repository supported by the Sainsbury Wellcom Centre. It offers high-resolution illustrations made by and for scientists around the world. These illustrations are readily available and do not require any account. 

Usage and license: Free to use under the Creative Commons BY 4.0 license. Illustrations can be shared, modified and used in any medium, format or purpose if proper credit is acknowledged.

Theme: animals, anatomy, intracellular components, molecular pathways, lab equipment, glassware, plasticware, procedure, assays, molecules, data plots, general

SMART gathers high-quality scientific illustrations made by professionals at Les Laboratoires Servier. These illustrations are freely available (no account needed) and can be downloaded either as a fixed image or as a PowerPoint illustration to be further customized by the user. 

Usage and license: Free to use under the Creative Commons BY 4.0 license. Illustrations can be shared, modified and used in any medium, format or purpose if proper credit is acknowledged.

Theme: anatomy, animals, plants, cellular and molecular biology, genetics, lipids, proteins, intracellular components, lab equipment, cardiology, dermatology, embryology, endocrinology, immunology, infectiology, neurology, ophthalmology, drugs and treatments, food, people, world maps, general

Unsplash harbours free (no login) high resolution photographs to illustrate your various projects. This resource is community-driven with new materials being added on a regular basis.

Usage and license: Free to use under the Unsplash license. Images can be shared, modified and used in any medium, format or purpose. No attribution is required (though it is appreciated!).

Theme: photography, people, procedures, computers, lab equipment, general

This table from the University of Washington's Proteomics Resource gathers the monoisotopic and average mass for amino acids, peptide modifications and common chemical elements.

Many protocols involving LC columns use the column's volume as a measure unit. As this unit is dependent on the column dimension, particle size and porosity, the LC Column and Tubing Calculator available on Agilent's website provides an easy way to determine the column volume of your own setup. Other key numbers, like optimum volume flow, injection volume or maximum tubing length, can also be calculated.

Among the many online tools for mass spectrometry offered by the University of Washington, its in-browser element mass calculator lets users determine the theoretical monoisotopic neutral mass of their compounds and predict the expected m/z ratio based on the number of charges.

This toolbox from Millipore Sigma offers a wide range of calculators and unit convertors for everyday use in wet labs. It covers many aspects of wet labs including interactive tools for chemistry, chromatography, life science and unit conversion.

The HPLC Column database gathers over 750 reversed-phase HPLC columns from more than 30 manufacturers. Its online tool allows users to simultaneously compare parameters from several columns using the Hydrophobic Subtraction Model (HSM).

In High-Performance Liquid Chromatography (HPLC), working pressure is a critical parameter that affects both system efficiency and instrument safety. Whether you are using commercial or in-house columns and tubing, it is important to know the maximum pressure your setup can withstand. This online calculator allows users to determine this key value based on the component’s material, as well as its inner and outer diameters.

This fragmentation tool from the University of Washington allows users to predict expected m/z ratios for a custom peptide sequence. To obtain accurate predictions, several parameters, such as the mass type, the product charge and the type of fragment ion, are available.

ProteinProspector from the University of California in San Francisco harbours numerous tools (online tutorials available)  for mass spectrometry, including in-browser applications for in-silico peptide digestion, peptide-tag or modifier identification, isotope distribution and more. The MS-Digest app is particularly useful to choose the best enzyme to digest your proteins by comparing different sequence coverages, digested peptide lengths as well as cutting sites for your proteins of interest.

This table by the Paulovich Lab provides estimated protein yields for many FFPE specimens, fresh frozen specimens, blood-derived cells and cultured cells. Protein yields are classified based upon the collection method (biopsy, cell culture, tissue core, etc.) as well as their origin (cell line, type of tissue, organ, etc.). These numbers provide a good starting point to scale up or down your experiment before submitting samples to the BMS Core.

For samples derived from cell culture, this resource can be used alongside the Useful Cell Culture Numbers table from ThermoFischer Scientific to determine your requiered Petri dish or flask size.

This table by ThermoFischer Scientific shows surface area, seeding density and the number of cells at confluency for many sizes of dishes and flasks. These numbers provide a good starting point to scale up or down your experiment before submitting samples to the BMS Core.

This resource can be used alongside the Typical Protein Yields table from the Paulovich Lab to determine your protein protein yield after cell lysis.

Alphapept is an open-source environment which provides tools for many steps of proteomic analysis and proteomics research, ranging from raw data analysis to data visualization. Each tool is available as a specialized package containing downloadable scripts, a graphic user interface, example datasets and relevant additional documents.

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work. Attribution depends on the tool used in your work: the appropriate peer-reviewed article is indicated in each package.

ClustVis is an online tool designed to help users create Principal component analysis (PCA) plots and clustered heatmaps. Data can be processed directly in ClustVis and the resulting plots are customizable. Final figures can be downloaded under several file formats (.pdf, .eps, .svg and .csv).

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work.

Colour selection for impactful and accessible data visualization plays a big part in scientific communication. Nowadays, most editors require scientific figures to feature a good colour contrast and be readable by people with colour vision deficiency. Below are some free online tools to help you choose accessible colour palettes as well as check the colorblind friendliness of pre-existing figures.

• ColorBrewer 2 offers a selection of pre-established sequential, diverging and qualitative colour palettes. Initially designed for maps, it supports up to 9 data groups and provides the user with HEX colour codes compatible for colour transfer between different analytical and design software. Credits: C. Brewer, M. Harrower and The Pennsylvania State University.
• Colorblind Image Tester is a scientific figure-oriented online tool that allows users to test their pre-existing figures for deuteranopia (the most prevalent colour blindness). It will show a version of your image that approximates how it would look to people with a color vision deficiency. Credits: Stevens HP, Winegar CV, Oakley AF, Piccolo SR. Estimating the prevalence of images in the biology literature that are problematic for people with a color-vision deficiency. [In Preparation].
• Cooler Contrast Checker rates your colour choices for contrast for both small- and large-sized items (text, data points). This tool is also useful for researchers preparing scientific posters or presentations. Additional online tools for colour palettes are available on the Cooler website. Credits: F. Bianchi.
• Viz Palette is an online tool that lets users test for their figures' colours by entering the desired HEX colour codes. It features an extensive list of test options, such as color palettes, contrast against backgrounds of a specific colour, effects of strokes around your letters of data points, and color vision deficiency (all types of color blindness are available). Credits: S. Lu and E. Meeks.

DIA-NN is an open-source software (local installation requiered) used for Data-Independent Acquisition (DIA) proteomics data analysis. Starting with version 2.3, it also implements a beta-stage support of DDA data. DIA-NN can be used to generate custom spectral libraries, identify peptides, detect post-translational modifications, and perform several kinds of peptide quantification.

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work.

FragPipe is a software (local installation requiered) from the Nesvizhskii for the analysis of mass spectrometry-based proteomics data, available for Windows and Linux. It can be used to identify peptides, detect post-translational modifications, and perform SILAC, TMT, iTRAQ, and label-free quantification. FragPipe is compatible with both DDA and DIA mass spectrometry data.

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work.

MaxQuant is a software (local installation requiered) for proteomic dataset analysis using the Andromeda peptide search engine. Initially designed for Data-Dependent Acquisition (DDA) data, it now also support Data-Independent Acquisition (DIA). MaxQuant can be used for peptide identification, various kinds of peptide quantification and post-translational modifications detection. MaxQuant results can be directly analyzed into Perseus (see section below), as the two softwares shared the same work environment.

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work.

Perseus is a free software (local installation requiered. supported operation system 64-bit Windows 10, 64-bit Windows 11, and 64-bit Windows server 2016, 2019 or 2022) for mass spectrometry analysis. Perseus is an extensive tool that supports data integration, advanced statistical analysis and many data visualization options. Available analysis and figures include (but are not limited to) Principal Component Analysis (PCA), volcano plots, scatter plots, heatmaps (clustered or not), histograms, correlation plots, density plots and functional enrichment analysis.

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work.

ProHits-Viz is a free suite of in-browser tools for analyzing and visualizing protein-protein interaction data. This resource notably features a file format convertor to  easily switch between common analysis pipelines used in mass spectrometry or different databases, a built-in analysis tool, as well as several data visualization options like heatmaps, scatter plots, dot plots and functional enrichment figures. All data vizualization options are interactive and allow each user to create a figure tailored for their own needs (the final figure is downloadable under several formats).

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work.

ShinyGO is a gene-set enrichment tool for animals and plants, providing a fast way to generate and edit enrichment bubble plots, hierarchical clustering trees, and gene networks. An additional tab also allows users to explore known pathways through the KEGG pathway database. Final figures are downloadable under several file formats.

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work. If the KEGG pathway tool is used during the analysis, additional attributions are necessary.

Significance Analysis of INTeractome (SAINT) consists of a series of software tools (local installation requiered) for assigning confidence scores (i.e., a probability between 0 and 1) to protein-protein interactions based on quantitative proteomics data in Affinity Purification-Mass Spectrometry (AP-MS) experiments. 3 versions of SAINT are currently available depending on your analysis requirements: SAINT v2, SAINTexpress and SAINTq. To determine which versions better suit your needs, directly refers to the link provided above. After analysis, SAINT scores can be used in any data visualization tools to create additional figures such as dot plots or heatmaps.

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work.

Skyline is an open-source software (local installation required) used for Selected Reaction Monitoring (SRM), Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), Data Independent Acquisition (DIA/SWATH) and Data Dependent Acquisition (DDA) data analysis. Skyline's website features numerous resources, including tutorials, webinars, videos and written documentation.

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work.

STRING features a renowned extensive  protein-protein interactions database, as well as some  free in-browser analytical tools. These tools allow users to create and customize protein-protein interaction networks; perform functional and cellular component enrichments via Gene Ontology. Figures generated via the STRING interface are freely downloadable for scientific presentations and publications.

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work.

Venn diagrams are widely used in mass spectrometry to highlight differences between large datasets. While many Venn diagram generators are available online, InteractiVenn is free, supports up to 6 datasets and provides downloadable Excels files containing every diagram subsection component. Users can also easily customize their Venn digram directly in their browser and download the final figure.

Note: As any other analytical tool, this resource required attribution if used in a poster or a published work.

VolcaNoseR is an online resource which allows the user to quickly generate and edit volcano plots for mass spectrometry data. The final figures can be downloaded under several file formats (.pdf and .png).

Note: As any other analytical tool, this resource requires attribution if used in a poster or a published work.

The Contaminant Repository for Affinity Purification (CRAPome) is a curated database that supports the analysis of interaction proteomics data by providing a collection of negative control affinity purifications. Because affinity purification–mass spectrometry (AP‑MS) often detects background proteins linked to nonspecific interactions, CRAPome gathers and standardizes negative control experiments generated by research groups across the world, allowing users to search specific proteins or view frequently detected contaminants in their samples.

MassBank is an open-source spectral library used to identify small chemical compounds relevant to metabolomics, exposomics, and environmental studies. Its entries include high-resolution mass spectrometry data such as m/z spectrum, precursor type, instrumentation parameters and chemical information. Users can explore the data using either a compound search, a spectral search, a structural search or a MassBank accession ID.

Protein Data Bank (PDB) is a renowned database gathering peer-reviewed 3D structures of large biological molecules (proteins, DNA and RNA) across several species. This database gathers key structural information, experimental annotations, amino acid sequence and genome data. More, PDB also features a free built-in 3D visualizer (structure tab within each entry), which allows the user to choose a specific orientation and add personalized annotations. Annotated structures can be downloaded for free without any account, and serve as a basis to better understand protein-protein interactions.

Reactome is an open-access, open-source, and peer-reviewed database of biological pathways developed by an international team of experts from leading research institutions. It offers intuitive bioinformatics tools that enable researchers to visualize, interpret, and analyze pathway data, supporting research in areas such as basic biology, clinical studies, genome analysis, modelling, systems biology, and education.

The Reactome website provides  an interactive graphical map of known biological processes and pathways, allowing users to explore detailed, verified information about specific components and their interactions. This database cross-references over 100 other public resources, including NCBI Gene, Ensembl, UniProt, the UCSC Genome Browser, the ChEBI chemical database, and PubMed.

The Human Protein Atlas is a Sweden-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues, and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.

The Human Protein Atlas consists of nine separate resources, each focusing on a particular aspect of the genome-wide analysis of the human proteins: tissue distribution, brain distribution, single cell expression, subcellular location, cancer and patient prognostic, blood levels, cell line models, 3D structure and protein-protein interactions.

STRING is a database of both experimentally validated and predicted protein-protein interactions. These interactions include direct (physical) and indirect (functional) associations gathered from several main sources: genomic context predictions, high-throughput experiments, co-expression experiments and text mining from known peer-reviewed publication database.

Protein-protein interactions can be searched by sequences, names, pathways or protein families. STRING also offers a free in-browser analytical tool which allows users to create and customize protein-protein interaction networks; perform functional and cellular component enrichments via Gene Ontology; while exploring associated peer-reviewed publications on Pubmed. Figures generated via the STRING interface are freely downloadable for scientific presentations and publications.

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data, which provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein variant sequence, protein expression, post-translational modification, structure and functional information. UniProt lists the proteins of many organisms, making it a key resource for proteomics studies.