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Johnson: Opening Remarks

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Johnson: Opening Remarks
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2015
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platform informatics silicon plant chemical man cell Oceans tool active site board biotechnology packing biochemistry molecular organizations synthetic biology galena genome complexes slides systems synthetic biological systems coupling standards pharmaceutical
platform informatics Digital elevation model Bohr protein engineering Primärer Sektor case man specific tool processes biochemistry organizations regulation genetic engineering formal synthetic biology Katalase complexes chemical slides firm Chemische Industrie systems biological systems model metabolic pathway standards
platform informatics Digital elevation model mechanism Primärer Sektor plant solutions blocks chemical man variety synthetic tool active site Einschlüssen biochemistry standards organizations DNA synthetic biology Ethylen-Vinylacetat-Copolymere biological systems coupling Gamma standards
board over 20 so I propose we get started so let me introduce myself I will be I have the owner to be there the sessions of today or chairman so my name is Patrick Johnson actually I don't come from academia I come from the industry so that would be a let's say a different angle of approach for synthetic biology and molecular and cell bio tech I work in a software company and we have been of course investing a lot in computational biology and now we are moving forward to synthetic biology and so I will host the two sessions this morning and this afternoon this morning is more dedicated to a plant biotech and synthetic biology in the plant arena site and this afternoon although we had to change a short minute the agenda with Francois I would say it more oriented towards technology platforms and maybe a little bit of computational approaches for synthetic arena so what I propose because plant is not at all my arena to kick the day I propose just a couple of slides to provide you with a perspective from the industry from the software industry for synthetic biology just to give you a context and of course since we are in a i HS also the math that actually the industry companies are working on towards a synthetic biology so just a couple of slides I won't be long I was told by Francois 15 minutes so by 40 minutes and 59 you can throw tomatoes and and and week and we can kick to the next session with them yeah yeah plenty exactly so actually a of course when we talk about synthetic biology we talk about engineering living systems and complex biosystems and of course in my company and in another field in software software arena people are coming from I would say the more classical engineering field where it's a of course a bottom-up approach where people are designing parts then assembling them then design then testing them simulating them and ultimately producing them and this is what we have been doing for the past 30 years in my company so pure engineering work pure systems engineering field enduring Sciences which at first glance doesn't seem to have one dime in coming with what we want to do in in synthetic biology at first glance I said of course at second glance of course there are a lot of questions that could be a reason in terms of modernity standardization emergency merchants of phenomenon and of course in terms of industrial pipelines and production pipelines a lot of industries not only pharmaceutical actually but a lot of industries cpg agro chemical the green the white biotechs are right now actually leading the way and asking companies like mine to provide tools industrial tools to assist them in synthetic biology in systems biology and synthetic biology and so this is what we have been we have
been doing I would of course not not not show you things that actually you guys know more than we do but right now the let's say the in silico approach is ramping up in the industry pharmaceutical is actually behind lagging behind when we you look at energy field for example or even agrochemical and from the industrial pool the demon is that all coming from pharmaceutical if you look at the organizations within industries like the center fees of the world Pfizer's of the world's oceans of the world of course there are some departments for in silico approaches and they have been for quite some time now but if you look to excellence or to energy or players for example or even of course agrochemical those guys are more advanced and actually launching programs in the field public-private partnership to to to generate tools that would be scalable and in the and so starting with genomics of course and of course linking them with a more
classical computational biology that that what we are that the sector was using so the slides that I'm showing you is what we have been developing in my company and it's more I would say from the design and engineering space but the production space has not been tackled so far in the industry at least if if you look to again the center fees of the world or even the energy sector those guys are using right now in silico tools to do modeling protein engineering let's say at least but when it comes to product from pipeline bio processes manufacturing chemical manufacturing and of course genetic engineering and production it's very shy to say to say the least and my company for example who has been investing already 1 billion on the systems biology side is now looking for mature mathematical tool and technological platform to link that with production platforms for bio production so we have been working in systems biology and of course when I come back to the Boeing example that you saw in the first light already design principles are starting to be modified or changed when we zoom into living systems or modified modified systems I have to say that systems biology today at least in the life science sector is is almost non-existent from an individual standpoint and so for the synthetic biology and bioproducts in' approaches it's even worse so all the all the marvelous presentation that we are discussing today I would be of course and my company and all the other players in the software arena are watching that we with a lot of focus because there is the pool but there is none no practices no standardized standardization methodologies and and and of course when when it comes to ramping up in the industrial Field it's inevitable that we have to come up with something that is more standardized of course when it
comes to mathematical technologies and and and say tools and frameworks for systems biology of course in my companion in other communities we have been trying to to understand the emerging field so you see on that kind of slide are different approaches not complete of course are when it comes to trying to understand the behavioral and dynamic of complex systems the emergence of complex systems are the multi entities complexity so there's a lot of mathematical say frameworks being proposed today some of which are more coming from the computer science arena some of which I'm are coming from the classical engineering computer science electrical field it's a mess to be honest from an industrial standpoint it's a mess and it's not complete here and and and pretty much what we are observing is that every time you look at one specific case in synthetic biology or systems biology when it comes to fast when it comes to specific organism that we want to tackle you have a different formalism being proposed by the academy or a different mathematical framework there is no overarching underlying layer at least from our understanding and of course this is a demand from my my sector to try to see whether there is a more generic or more or agnostic layer to be able to handle the complexity of all the different for example hosting platforms that could be used within the industry so the reason why I'm showing you this is of course there are the experiments that are being done synthetic biology but the demand from the lease tomorrow customers is also to have some sort of election of a unified framework for modeling simulation analysis and production and today is very fragmented it's very fragmented now if you look at other industries that have been trying to do modeling simulation and production more in the classical product engineering space this was the case 25 years ago it was the same situation 25 years ago if I take an example or in 1980 in the computer aided design industry with so it's more engineering sciences you have 600 company's existing on the field doing modeling design analysis simulation and production the so-called cad/cam CAE market and all of which were were specialized on specific use cases or specific families of products it whole has converged and being unifying today let's say two or three actors that are trying to unify that on end-to-end platform if you look at systems biology and synthetic biology today guess what the market today is around 400 and 500 companies everyone providing a specific language or specific framework or specific technological platform for alwa for for human for Homo sapiens for different kinds of course of hosting organism and we believe in my sector that there will be a convergence path we believe that there will be when of course I am totally unable to to say but at least not only from the modeling perspective and a simulation perspective but also from the production's perspective and the reason why synthetic biology we believe is is actually let's say a catalyst to that convergence pretty much like manufacturing was a catalyst for the engineering sector for the other side of the cat and the CAE classical product design space it is because by by effectively ducing you understand better how it is done and how they I could be modeled so the message here is that the the actual realization is also a catalyst is not also it's it's a key catalyst for modeling and engineering in the first place and this is why we want to invest in that in that sector so right now we are we are at least in my company we are we are trying to gather a number of tools for systems biology synthetic biology of course classical or computational biology in systems biology but not only from the modeling and design perspective but also from the processes bio production and manufacturing perspective and this is why do the synthetic sector is is inevitable today so this is what i
already said we've been monitoring a lot you will see or at least in in some of the presentation this afternoon which are more related to computational that there are some advances also coming from let's say our semantic web approaches so the transdisciplinarity is not only coming from your field from the bio tech sector it is it is also being driven a lot by not only of course mathematics and computer science but also from the semantics and the web technology and just two question marks from my side I showed you a couple of mathematical approaches from the systems biology side there are many from the synthetic biology site people are providing BioBricks framework in terms of grammars in terms of component tool kits in terms of generative frameworks I mean again there is a soul g of mathematical and in computer science framework to do synthetic biology also there is a variety very wide of hosting platforms and technology platforms I don't know if some of you know the for example a company named in fraction which claims to be the number one in us of a synthetic DNA and that company basically is every two or three months buying a new technological platform to have the widest hosting let's say portfolio of organism Synthetica organism to be followed very closely and of course there is the social and a community approach for standardization and I believe that this afternoon will will have a some hint on for example the let's say computational standardization language effort for synthetic biology with a language called call s bowl for example so again my message here is pretty much like for the design side with systems biology there is a in my mind a too wide of a variety of offering synthetic biology is following the same way and as an industry guy of course I'm I'm I'm asking and starving from unification and more standardization approaches so that was just you know let's say not too long I hope an over an overview of the computational sector trying to not only tackle but be part of the discussions in that field so the today's sessions again to two blocks this morning will be will be focusing more on plant organism and synthetic biology and we'll start with an Osborne and this afternoon will be more focusing I guess I try to find a unification because we had some short minute changing the agenda in terms of computational tools and and technological platform and that's all for my site so i propose to welcome Anne Osborne who will talk about mechanism of chemical diversification implants thank you
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