My idea in a paragraphI want a virtual body to facilitate research, teaching and general understanding of how we all work. The more we understand how we work the better prepared we are to maintain our bodies given the daily challenges we all face. I want to see a human body exercising, zoom in to see the heart pumping, zoom further to see the blood platelets rushing through, zoom further to see a blood cell. Then zoom inside to see the cell contents, then further, to the oxygen and carbon dioxide. So I could zoom in and out of cells, organs and even people to see what’s happening at every layer.
Here’s a bit more detail about the where, why, and howGames already simulate human activities over time and I'd show how simple cellular mechanics have the big impact they do. You'd be able to zoom into the cell and see what happens, then zoom out again to see the wider implications. You can fast forward in time, go backwards, pause. And highlight cells or organs and change values. Because it's digital you can save state and share it.
Now we're getting to the creative aspect. A virtual laboratory. Your lecturer asks you to figure out why diabetes is occurring in a given population. You work on this tool that has the population and tweak their lifestyles looking for the answer. Reading the research you hear about glut4 a glucose transporter on the cell walls. They are activated by insulin and fit people have more of these than unfit. The transporters regulate carbohydrate flow from the blood to the cell. Hence you've found a reason why fitness could be directly related to diabetes risk. You experiment with the settings now you know what to look for. You set up your virtual experiment and get the results. You've now got your answer. You export your settings, send to a friend who confirms it. Then send to your professor and receive an A.
It surprises me that the means to build this exists yet it hasn’t yet been built. it's the definition of good science. Repeatable, sharable, uses standards etc. Year on year it could improve with more knowledge etc. so you could test more.
I'm probably not the first to think of it, but I don't see one on the market and I don't see any reason, why it can't be done. It's incredibly difficult but it's definitely possible. I might take the rest of my life and then some but it would be an amazing journey.
The best example I can find of an existing project is the Virtual Physiological Human program headed by Professor Denis Noble of Oxford. It is a very well funded programme that seems to be delivering at a fantastic rate.
The only problem with this is that it is a closed project delivering software and tools for health and medicine but not for everyday people. So I'm very happy to see the progress of the VPH project but I don't feel it will help me or the average person any time soon.
I have a lot of research in this area which I will add to this post in time. For now I just want to start the topic and provide a place to relevant details as I go. This is one of the most core articles to this blog. I've been investigating this topic for almost a decade now and is why I will often cover wider topics like technology, programming, marketing, economics and other areas in detail. They become important when you consider such a lofty aim.
Virtual CellOf course the first goal is to build a virtual cell. My plans have always been to build something incredibly simple. Share it and go from there. I've already built a very simple cell in using Unity as my 3d software. I've searched around and tried many solutions including html 5 but found unity to be the best for what I need.
ConversationsUntil now I've very much been wondering where the best conversation are happening. Current topics include
- Computational Biology
- Synthetic Biology
- Systems biology: looking at biology as a holistic process. on linkedin systems biology
Useful ReadingI have found so much research I will post it here and then start to organise it as I go.
- The don't stop the beat talks about the preDiCt project which models the electrical activity of the heart.
- A very nice article on the potential of whole-cell modeling.
- A Whole-Cell Computational Model Predicts Phenotype from Genotype
- The Dawn of Virtual Cell Biology
- Living Human Project: is developing a worldwide, distributed repository of anatomo-functional data and of simulation algorithms relative to the human musculoskeletal apparatus, fully integrated into a seamless simulation environment and directly accessible by any researcher in the world. This infrastructure will be used to create the physiome of the human musculoskeletal system.
- Living Human Digitial Library : aims to create the technical infrastructure for the Living Human Project (LHP). LHP will create a silico model of the human musculo-skeletal apparatus which can predict how mechanical forces are exchanged internally and externally, from the whole body down to the protein level. This model will be designed as an infrastructure that can be updated and extended whenever new data and algorithms become available. LHDL aims to develop this infrastructure
- Virtual Physiological Human: a methodological and technological framework that, once established, will enable collaborative investigation of the human body as a single complex system. VPH: wikipedia on pubmed
- VPH-Share: An organisational and coordination framework for the virtual physiological human project. Run by the Open university
- Toward continuous Medical Education By Roni Zeiger, head of google health. Outlining ways in which lifelong learning via the web could vastly improve the quality of care we all receive by simplifying the continual development of medical practitioners.
- Lifelong learning, Self development and expression
- Jane McGonigal believes Gaming can make a better world and has an avant game blog where she’s launching gameful to help people make games to improve the world
- myelin repair foundation. Also using games to educate and promote their cause
- Genetics in 3d by utah university Amazing collection of animations and tools about anything related to genetics. A lot of money was put into this and they might be worth trying to work with.
- a long 3D animation of the fight or flight response.
- project health design: is forging a new vision of personal health records (PHRs) by exploring practical ways to capture and integrate patient-recorded observations of daily living (ODLs) into clinical care
- Wolfson research institute: UK organisation that conducts research on human health and well-being.
- You make me sick. Excellent game about designing a pathogen (virus or bacteria) to infect a human host. Really fun and friendly game.
Useful Projects and Tools
- centre of the cell
- systems-biology.org cell designer.exe
- biomodels database curated set of models viewable online: BioModels Database is a repository of peer-reviewed, published, computational models. These mathematical models are primarily from the field of systems biology, but more generally are those of biological interest
- biopax (biological pathway exchange) a standard language for exchanging . BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups
- Human protein atlas search for proteins or genes and find protein expression profuiles, subcellular localisation, transcript expression
- xvivo.net: david bolinsky presented the inner life of a cell on TED. They have a vision, along with harvard, to explore biology through immersive applications.
- The gadget show : a recent programme simulator challenge part 1 part 2 showed simulations helped the team pass real life challenges like learning to fly and achieve a high grade in martial arts entirely through simulations. The first time ortis flew a real plane was during his test which he passed. The first time jason met a real opponent was in his grading which he passed.
- wikipathways: In the new tradition of Wikipedia, WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community
- bigcat: turning heaps of data into biology. department of bio-informatics at Maastricht University
- Simulation-based textbook for Cancer Biology The textbook utilizes a dynamic simulation approach and software, Cell Collective (www.thecellcollective.org Mammalian Cell Cycle), that enables students to learn about biological systems from a systems and dynamical perspective rather than by memorizing static pictures of pathways in textbooks.
- Andrew Hessel: Programming Living Things - The Next Generation Of Computing a fascinating talk explaining how synthetic biology allows us to build DNA scripts and update bacteria like you write computer code or put lego together. I think that tied to Unity a lot of fun could be had.
Personal informaticsHow to track your life and get data to analyse
- http://quantifiedself.com/self-tracking-links-to-get-you-started/ list of sites and apps to track personal stuff.
- http://personalinformatics.org/ site dedicated to tracking yourself.
Apis for each scientific discipline. What lots of us need are basic physical, chemical and biological processes coded as basic function calls of an api. Thigns like the krebs cycle and photosynthesis, foir biology the maillards reaction for chemistry, not sure what for physics. It really depends on what you want to achieve but long term wouldn't it be nice if the equations had already be converted to code and you could just implement the appropriate api.
Could be modelled on jQuery. We need libraries and apis that do standard calculations for each science. No sure if the jQuery approach fits Just create some basic examples first.