https://thevirtuallaboratory.com/blog daily 0.75 2025-05-30 https://thevirtuallaboratory.com/blog/biology-first monthly 0.5 2025-05-30 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/aced3c21-3fd3-45d7-8fae-03c903eb1a7c/Screenshot+2025-05-30+at+11.37.45.png Blog - Biology-first modelling: why? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/4374bea9-9128-4ac0-97d5-f613b34a7b2d/Screenshot+2025-05-30+at+10.59.05.png Blog - Biology-first modelling: why? - Make it stand out Artist impression of TIktaalik, the intermediate form between fish and amphibians. https://thevirtuallaboratory.com/blog/the-virtual-laboratory monthly 0.5 2022-07-11 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1657482144006-H0LAV86YXK85L571CYY1/complex+models+shine+light.png Blog - The Virtual Laboratory - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1657480347891-Y9RC1RDDZ3589HF1H2IP/virtual_lab_2.png Blog - The Virtual Laboratory - Make it stand out By building multi-level biological systems from the bottom up, you have your own “Virtual Laboratory” with which you can experiment! https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1657484740030-NNGZ4WXEKEUQMX1IGZQF/plusplus.png Blog - The Virtual Laboratory - Make it stand out The result++ in the image above refers to the “self-mixing” effect of cross-feeding behaviour observed in Virtual Microbes. https://thevirtuallaboratory.com/blog/the-secret-lives-of-mobile-genetic-elements monthly 0.5 2021-12-01 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1637933348232-ZXK0726D69RSBY62FNER/Capture.PNG Blog - The secret lives of mobile genetic elements: a multi-level perspective - Make it stand out On a scale smaller than microbes, a rich zoo of mobile genetic elements (MGEs) is replicating, mutating, and differentially surviving (image by Ellie Harrison) https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1637828605586-SXRN6JGM9S5Q83QWIQTB/Capture.PNG Blog - The secret lives of mobile genetic elements: a multi-level perspective - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1637759591524-ST1BIQ0Q6UW8XAK60KS0/logo.png Blog - The secret lives of mobile genetic elements: a multi-level perspective - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1637322538994-4DG19I7SUN5FYXR4BEQR/5urlcv.jpg Blog - The secret lives of mobile genetic elements: a multi-level perspective - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1637759501916-QFPG3IRX01U11DYJYK4G/kisspng-max-planck-institute-for-developmental-biology-max-research-5ac7d8ef3d5926.4665492215230466392513.png Blog - The secret lives of mobile genetic elements: a multi-level perspective - Mke it stand out https://thevirtuallaboratory.com/blog/splitting-a-multi-fasta monthly 0.5 2021-07-28 https://thevirtuallaboratory.com/blog/2020/11/20/javascript-programming-part-iii-game-of-life monthly 0.5 2021-07-27 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038663253-TKTMBPI994PC5KNKE3CR/5.gif Blog - Javascript programming - Part III (Game of Life) https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038666655-IQTL5NN6DZSGO3DPNH0Z/image-5.png Blog - Javascript programming - Part III (Game of Life) https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038666031-KRIS8F6A1OY42V8KFZLW/image-6.png Blog - Javascript programming - Part III (Game of Life) https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038663285-RO3XUBM81BQOIDGPZ4NT/4.gif Blog - Javascript programming - Part III (Game of Life) https://thevirtuallaboratory.com/blog/2020/11/20/javascript-programming-part-ii-my-setup monthly 0.5 2021-07-06 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038665840-3QECAUBX48HTUJ2D5JWU/browser.gif.gif Blog - Javascript programming - Part II (My setup) https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038666827-ZDRA5IBF318FIV0YQP63/image.png Blog - Javascript programming - Part II (My setup) https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038665827-2EJ58268W008ERHOF429/image-1.png Blog - Javascript programming - Part II (My setup) https://thevirtuallaboratory.com/blog/2020/11/20/javascript-programming-part-i-introduction monthly 0.5 2021-07-06 https://thevirtuallaboratory.com/blog/2020/09/07/tips-for-visualising-grid-data-in-ggplot2 monthly 0.5 2021-07-06 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038662920-MZZOMJXY9PPZF4IW4ZZ9/image-13.png Blog - Tips for visualising grid-data in ggplot2 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038662247-T1PLOV57KRLU984K2TW9/image-22.png Blog - Tips for visualising grid-data in ggplot2 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038663030-HY3494WWZ4J6NA28IRQK/image-8.png Blog - Tips for visualising grid-data in ggplot2 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038662816-26YSUP0YGPVMPN9T9BFH/image-18.png Blog - Tips for visualising grid-data in ggplot2 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038661540-SV0GA7R2F5POWSJZ1GYC/digest_striking-edited.png Blog - Tips for visualising grid-data in ggplot2 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038662179-BJQP64D0ATN46EYASDL0/image-16.png Blog - Tips for visualising grid-data in ggplot2 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038662058-UECP1WW96I6BZDJ9ZI9Z/image-17.png Blog - Tips for visualising grid-data in ggplot2 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625038661865-S5HYPTYPJVDC3YAP5RK6/image-9.png Blog - Tips for visualising grid-data in ggplot2 https://thevirtuallaboratory.com/blog/2019/11/23/video-abstract-trusting-the-hand-that-feeds monthly 0.5 2021-07-06 https://thevirtuallaboratory.com/blog/2019/09/21/can-phenotypic-plasticity-accelerate-evolution monthly 0.5 2021-07-06 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625492895413-EHXDCWFDTNNLKCWC1F7J/Screenshot-2019-09-21-at-16.29.05-1024x340.png Blog - Can phenotypic plasticity accelerate evolution? - Make it stand out Figure from Espinosa-Soto et al. 2011 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625492972048-4IBSNKZ0ZHLZMFES2N5R/Screenshot-2019-09-21-at-16.31.00.png Blog - Can phenotypic plasticity accelerate evolution? - Make it stand out The organization of gene circuit genotype space favors plasticity-mediated adaptive evolution Shapes and colors have the same meanings in the diagram as in Figure 1. Starting from the blue genotype network, it is easier to find a genotype that produces a red alternative phenotype than finding the red genotype network. Many genotypes that produce the red alternative phenotype have direct mutational access to the red genotype network. Such genotypes are neighbors of other genotypes that produce the same alternative phenotype. Among genotypes that produce the red alternative phenotype, a high penetrance is associated to easier access to the red genotype network. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625492873570-2U0V1KRVD6QGOHTS1T7Y/exploring.jpg Blog - Can phenotypic plasticity accelerate evolution? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://thevirtuallaboratory.com/blog/2019/04/14/glycolysis-and-tca-cycle-in-virtual-microbes monthly 0.5 2021-07-06 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625562093618-RZ72J79R6JB87SYMGG3S/Artboard-1-1.png Blog - Glucose metabolism in Virtual Microbes - Make it stand out Virtual Glycolysis implementation – Different metabolites are represented as blocks, with the number of squares representing the number of carbon atoms in the molecule. The energy carrier ATP is depicted as a red pentagon. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625562201363-EG6BQPT5XS96K40ZCJ4E/Artboard-3-3.png Blog - Glucose metabolism in Virtual Microbes - Make it stand out Virtual Glycolysis and TCA Cycle – Different metabolites are represented as blocks, with the number of squares representing the number of carbon atoms in the molecule. The energy carrier ATP is depicted as a red pentagon (as only a little pyruvate needs to be coverted to oxaloacetate, I assume in this figure that merely 1 less atp is now produced per glucose) https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625562218833-YYKQS13PCFFC6DWXG794/Artboard-5-3.png Blog - Glucose metabolism in Virtual Microbes - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625562960929-5E79RZ7087MRIOGM2PTT/Artboard-4-1.png Blog - Glucose metabolism in Virtual Microbes - Make it stand out Esstential metabolites for making building blocks – Building blocks in Virtual Microbes are necessary to express proteins and grow the cells. All building blocks that are not used to synthesize proteins are available for growth. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625562237277-O6RG5HKA8UCZQCP72700/Artboard-6-1-768x735.png Blog - Glucose metabolism in Virtual Microbes - Make it stand out When the system is simulated with mutations, high growth rate mutants invade, and eventually take over the population. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625563103813-L309GHEGK22DD68KLFNE/waves.gif Blog - Glucose metabolism in Virtual Microbes - Make it stand out Virtual Microbes growing in waves – Only a single clone (cyan, displayed in top grid) is used to start this simulation. This cyan “metabolic type” has all the reactions described above, and does not evolve. Black grid points are empty, and contain no cell. In the bottom grid the productivity of the same cells is displayed, with the black-red-yellow gradient showing building block production rates. Here, grey positions are empty. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625562169435-FPKPYI0YM3FBF4TC0543/Artboard-3-2.png Blog - Glucose metabolism in Virtual Microbes - Make it stand out (initial) Virtual TCA Cycle – Different metabolites are represented as blocks, with the number of squares representing the number of carbon atoms in the molecule. 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A subpopulation of simulated competent bacteria (green/yellow colours) is overgrowing non-competent bacteria (blue/purple) by “rescuing” a rescuable gene. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/d6622d08-cf59-4def-aba6-56ee0b50b473/cartoon.png Projects - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625659013830-NODK3ZC8UZABOEDWA756/openeco.PNG Projects - Analysing pathway completion in compost communities (w.i.p.) A cartoon of “open”, “closed”, and “leaky” ecosystems. https://thevirtuallaboratory.com/publications daily 0.75 2023-09-07 https://thevirtuallaboratory.com/software daily 0.75 2022-10-31 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1636624994014-SU9SFBO1HWD1SLMS76GT/68747470733a2f2f6272616d76616e64696a6b38382e6769746875622e696f2f63616361746f6f2f696d616765732f656c657068616e745f63616361746f6f2e706e67.png https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1667244537009-IS6MMPEEURUY5Z2ZX3LJ/xenoseq2.png https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625221512404-01UNCZOUV84UOBDDSYD7/virtualmicrobes_overview.png Software - Microbial evolution with artificial chemistry Virtual Microbes is a computer simulation model to study the eco-evolutionary dynamics of microbes (Thomas Cuypers, 2018). Virtual Microbes is unsupervised, meaning that it targets to combine relevant biological structures (genes, genomes, metabolism, mutations, ecology, etc.) without a preconceived notion of “fitness”, which is instead an emergent phenomenon. By not explicitly defining what the model should do, it allows for a serendipitous approach to study microbial evolution: How do complex cross-feeding communities form? What happens when a complex microbe “wild type” is transferred to lab-like conditions? What is the influence of horizontal gene transfer (HGT) on the productivity and diversity of a microbial community? https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625221734189-ZY9YWMMZ4HPZ3J4GTKI8/cheater.gif Software What is Cash2.1? Cash2.1 is an easy-to-use library to make a program simulating Cellular Automata (CAs). It is based on Cash1.0 (RJ de Boer & AD Staritsk) and was further developed by Nobuto Takeuchi (2s) and Bram van Dijk (2.1), and used in the course Computational Biology given by Paulien Hogeweg at Utrecht University. Downloading and installation The software is freely* available for download here. A complete user manual is available for usage and installation. https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1625222224584-KSQJMV3OPZ4FZBNEQUD9/200.gif Software https://thevirtuallaboratory.com/cacatoo daily 0.75 2021-07-02 https://thevirtuallaboratory.com/cacatoo-1 daily 0.75 2021-07-02 https://thevirtuallaboratory.com/contact daily 0.75 2023-08-28 https://thevirtuallaboratory.com/swarming-cells daily 0.75 2021-07-05 https://thevirtuallaboratory.com/cooperation daily 0.75 2021-09-15 https://images.squarespace-cdn.com/content/v1/60dacdce4150d42a4b762c56/1631690121909-4ES9G2XKHA0J9X1OOO32/coop.png Cooperation - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://thevirtuallaboratory.com/microfluidic-simulator daily 0.75 2022-11-12 https://thevirtuallaboratory.com/microbial-warfare daily 0.75 2022-11-17 https://thevirtuallaboratory.com/allele-surfing daily 0.75 2022-11-17 https://thevirtuallaboratory.com/transposon-evolution daily 0.75 2022-11-12 https://thevirtuallaboratory.com/videos daily 0.75 2024-03-23 https://thevirtuallaboratory.com/microbial-warfare-1 daily 0.75 2023-03-06 https://thevirtuallaboratory.com/squiggly-friends daily 0.75 2023-04-26 https://thevirtuallaboratory.com/arrythmia daily 0.75 2024-03-06 https://thevirtuallaboratory.com/foraging-monkeys daily 0.75 2024-09-09