[
  {
    "start": 1.82,
    "end": 7.58,
    "text": "How does molecular substructure annotation help prioritize and interpret metabolomic data?"
  },
  {
    "start": 8.92,
    "end": 13.5,
    "text": "how do communities shape both individual careers, the direction of field."
  },
  {
    "start": 14.62,
    "end": 21.58,
    "text": "And what is place for open science and interoperable tools in the future of Metabolomics ?"
  },
  {
    "start": 22.38,
    "end": 24.02,
    "text": "These are just a few questions."
  },
  {
    "start": 24.1,
    "end": 28.34,
    "text": "we address this episode with my guest, Justin van der Hoeft."
  },
  {
    "start": 35.22,
    "end": 42.94,
    "text": "Welcome to season five of the Metabolomist podcast where we dive into the communities that are transformed by metabolomics."
  },
  {
    "start": 43.96,
    "end": 51.24,
    "text": "I am your host, Alice Limonciel and this year i will engage with scientists who not only use metabolomics"
  },
  {
    "start": 51.66,
    "end": 51.76,
    "text": "but"
  },
  {
    "start": 51.84,
    "end": 53.82,
    "text": "who leverage it for greater good."
  },
  {
    "start": 55.08,
    "end": 60.78,
    "text": "people know that metabolomics is a tool which holds promise in transforming our society."
  },
  {
    "start": 65.3,
    "end": 68.02,
    "text": "Metabolomics needs to be part of something greater."
  },
  {
    "start": 69.02,
    "end": 77.18,
    "text": "Projects, networks infrastructures they all form around a common goal and make use of the best tools at their disposal."
  },
  {
    "start": 78.1,
    "end": 87.46,
    "text": "so this year in the podcast I talk to passionate people who build communities through any strategy from grassroot movements to decades of networking."
  },
  {
    "start": 88.4,
    "end": 95.3,
    "text": "Join me to discover the creations of these community builders and how Metabolomics is helping them advance their mission."
  },
  {
    "start": 98.8,
    "end": 129.039,
    "text": "I really love the work that you do using computational methods to make most of the measures made with different instruments people use for metabolomics."
  },
  {
    "start": 129.66,
    "end": 135.0,
    "text": "And so every year, i like someone who talks a bit more about the computational aspects."
  },
  {
    "start": 135.399,
    "end": 143.76,
    "text": "So we understand where field is going but also learn from your work and how have been growing in last years"
  },
  {
    "start": 145.119,
    "end": 145.339,
    "text": "Sure!"
  },
  {
    "start": 145.859,
    "end": 151.14,
    "text": "Well first thanks for having me on now a very famous metabolomics podcast."
  },
  {
    "start": 151.22,
    "end": 154.22,
    "text": "so it's also first for me to do uh a podcast."
  },
  {
    "start": 154.28,
    "end": 165.76,
    "text": "So in that sense I also look forward with this interview, well i started my metabolomics career one could say during my PhD here in Wageningen, where I now also work."
  },
  {
    "start": 166.04,
    "end": 180.42,
    "text": "And a particular because of the manuscript of the thesis that was reviewed by somebody in the metabolomics field and i got a lot of feedback on how could improve especially reporting my results?"
  },
  {
    "start": 181.16,
    "end": 184.239,
    "text": "That really led me into the Metabolomics Field."
  },
  {
    "start": 184.559,
    "end": 212.92,
    "text": "then I joined the Metabilomics Conference in Edmonton Canada in quite a few people that I still now meet nowadays when i go to the metabolomics meeting and so it is very nice because it kind of gives you an idea of whole research family rather than... Of course there are colleagues as well, some have become almost like friends but the sense of this family is there as well."
  },
  {
    "start": 213.0,
    "end": 223.339,
    "text": "Because every four or five years new generation starts grows into the scientific majority, just like myself."
  },
  {
    "start": 223.959,
    "end": 232.579,
    "text": "And then after my PhD I left for Glasgow in Scotland where i did my postdoctoral time or most of it anyway."
  },
  {
    "start": 233.299,
    "end": 244.42,
    "text": "so there I kind of grew slowly more towards the computational side by doing more and more analysis and also collaborating with computing sciences."
  },
  {
    "start": 244.519,
    "end": 250.799,
    "text": "so Simon Rodgers and we will get to talk about that in a bit more detail later."
  },
  {
    "start": 251.16,
    "end": 258.2,
    "text": "And then after that, I returned to Wageningen first on the shared contract with Peter Dorstein from San Diego at"
  },
  {
    "start": 258.3,
    "end": 258.52,
    "text": "U.S.,"
  },
  {
    "start": 258.8,
    "end": 277.36,
    "text": "and Manis Medema here in Wageninge... ...and as soon thereafter got my own grant or actually wrote for majority myself which was with the Netherlands e-sign centre where you can already hear it's more and more drifting towards the more computational side."
  },
  {
    "start": 277.98,
    "end": 285.96,
    "text": "And then in January, I was able to start my own team here as an assistant professor."
  },
  {
    "start": 286.64,
    "end": 294.64,
    "text": "so that is now Six years ago, it was a bit of challenging time as I think many of you will remember that soon after the January twenty-twenty."
  },
  {
    "start": 295.12,
    "end": 308.48,
    "text": "The virus also came to Europe and all education had to be online like we do now by the way And gave its own kind challenges and struggles."
  },
  {
    "start": 309.08,
    "end": 315.48,
    "text": "So I'm really happy that nowadays we can do the teaching again in a classroom and have more personal contact with students."
  },
  {
    "start": 315.86,
    "end": 320.82,
    "text": "And same is true for supervision of PhD students, postdocs and master thesis student."
  },
  {
    "start": 321.7,
    "end": 337.24,
    "text": "so by now my team consists of more than ten different people that I supervise and co-supervise PhD students postdoc working on different aspects of metabolomics."
  },
  {
    "start": 337.92,
    "end": 343.78,
    "text": "It must have been a really interesting time to start your group at the same when people basically can't meet each other."
  },
  {
    "start": 344.6,
    "end": 345.72,
    "text": "Must've been very difficult!"
  },
  {
    "start": 346.38,
    "end": 356.34,
    "text": "Um, it was challenging... At the same time The look that I had or have is in many aspects Computation work Can be done behind a laptop."
  },
  {
    "start": 356.68,
    "end": 373.52,
    "text": "But having said this i think we underestimate the importance of personal contact And I think it's really important to not only talk with each other through screens, but also be physically in the same room or at least close."
  },
  {
    "start": 374.98,
    "end": 379.86,
    "text": "Because you will hardly ever have a chance encounter like this right?"
  },
  {
    "start": 379.92,
    "end": 384.64,
    "text": "You always have to agree and meet these encounters."
  },
  {
    "start": 384.7,
    "end": 389.24,
    "text": "they often bring unexpected developments new ideas."
  },
  {
    "start": 390.44,
    "end": 393.26,
    "text": "Yeah, and I think especially when you build a new community."
  },
  {
    "start": 393.38,
    "end": 396.52,
    "text": "so communities is the topic of this year for the podcast."
  },
  {
    "start": 396.58,
    "end": 400.8,
    "text": "But even at that scale of maybe four or five people to build community."
  },
  {
    "start": 400.92,
    "end": 405.78,
    "text": "You really need to have these Unprompted connections or interactions?"
  },
  {
    "start": 405.9,
    "end": 406.14,
    "text": "Yes"
  },
  {
    "start": 409.52,
    "end": 412.26,
    "text": "The difference between now and back then it's."
  },
  {
    "start": 413.08,
    "end": 422.04,
    "text": "I also see competition with those related things on my boards where people have been brainstorming about new approaches or projects."
  },
  {
    "start": 422.2,
    "end": 431.86,
    "text": "And that's very nice to me because when i started here as a postdoc in September, the topic was there but not so big right?"
  },
  {
    "start": 431.92,
    "end": 435.84,
    "text": "I mean how anybody directly worked on development of tools."
  },
  {
    "start": 436.8,
    "end": 444.62,
    "text": "it was mostly left at kind of application or sometimes as a side project, over larger projects."
  },
  {
    "start": 444.96,
    "end": 450.36,
    "text": "And now it is one of the main kinds of directions that we do here at the Biometrics Group"
  },
  {
    "start": 451.68,
    "end": 454.68,
    "text": "and maybe there's a side note just from my own career."
  },
  {
    "start": 454.78,
    "end": 467.36,
    "text": "so when you were starting with Metabolomics I was also in the year a large consortium and then we got our first metabolomic dataset."
  },
  {
    "start": 467.7,
    "end": 473.22,
    "text": "We were really excited but there was absolutely no annotations of the... the metabolome."
  },
  {
    "start": 473.3,
    "end": 483.06,
    "text": "So it was a lot of features and we could see just mathematically that's, there changes in those features... We had kinetic experiments so you can see like The profile is changing over time."
  },
  {
    "start": 483.1,
    "end": 488.52,
    "text": "It was matching really well what were looking at an experiment But we didn't know any of those metabolites where."
  },
  {
    "start": 489.18,
    "end": 496.3,
    "text": "And then our collaborators would love to do this but they will take whole PhDs To annotate their data set."
  },
  {
    "start": 497.18,
    "end": 498.42,
    "text": "Then come make investment."
  },
  {
    "start": 498.5,
    "end": 501.54,
    "text": "right now I think thanks for you and other scientists."
  },
  {
    "start": 501.64,
    "end": 507.2,
    "text": "there are now tools that make it much, much easier for scientists to annotate metabolic data sets."
  },
  {
    "start": 507.24,
    "end": 510.34,
    "text": "So just give an idea of like how far we've come."
  },
  {
    "start": 510.38,
    "end": 518.799,
    "text": "in the last fifteen-twenty years That went from... We need think about getting a whole PhD student To do that work and annotated dataset too."
  },
  {
    "start": 519.459,
    "end": 521.62,
    "text": "Now, you can do it with a few pieces of software."
  },
  {
    "start": 521.74,
    "end": 523.099,
    "text": "And I think he will tell us about that."
  },
  {
    "start": 523.159,
    "end": 532.099,
    "text": "but... You have to be diligent in the assumptions you make and parameters so we can guarantee quality for your work."
  },
  {
    "start": 532.599,
    "end": 538.459,
    "text": "But still now you can annotate hundreds or thousands of features in one dataset."
  },
  {
    "start": 538.78,
    "end": 540.979,
    "text": "So there's really been a lot progress."
  },
  {
    "start": 541.819,
    "end": 551.599,
    "text": "Yes, I think one of the driving factors for myself was that during my own PhD it took me also a lot of time to kind of dig into one file."
  },
  {
    "start": 551.76,
    "end": 559.62,
    "text": "One profile, one hyphenated LC liquid chromatography, MOSFETROMETRY and then tandem MOSFetrometry."
  },
  {
    "start": 559.78,
    "end": 573.14,
    "text": "so LC MSMS profile... I think i spent like two months to kind of really almost factor by spectrum deciphering what is in this tomato extract."
  },
  {
    "start": 573.68,
    "end": 584.76,
    "text": "and nowadays you wouldn't imagine that anymore because you run the available tools, get an overview then start to prioritize."
  },
  {
    "start": 586.439,
    "end": 590.439,
    "text": "Back then, I mean what it did learn me is a lot about spectral quality."
  },
  {
    "start": 590.699,
    "end": 594.86,
    "text": "About our real fragments how they look like."
  },
  {
    "start": 594.92,
    "end": 603.3,
    "text": "so It really allowed to interact very closely with the data and i still benefit from that nowadays in my supervision as well."
  },
  {
    "start": 604.9,
    "end": 604.9,
    "text": "I"
  },
  {
    "start": 605.38,
    "end": 606.8,
    "text": "mean, as you say this."
  },
  {
    "start": 607.079,
    "end": 613.38,
    "text": "And i'm going to sound like a very grumpy old lady but do you get the feeling that's painful work?"
  },
  {
    "start": 613.719,
    "end": 623.66,
    "text": "Like really being so close to the data... You just said was something really beneficial for you Do feel like next generations are less and less close to their data."
  },
  {
    "start": 623.979,
    "end": 630.439,
    "text": "maybe they don't have quality connection with your data at all because it didn't have any other"
  },
  {
    "start": 630.959,
    "end": 631.26,
    "text": "tools."
  },
  {
    "start": 632.079,
    "end": 632.74,
    "text": "Well, yes and no."
  },
  {
    "start": 633.0,
    "end": 636.959,
    "text": "I mean there are directions that are kind of shooting."
  },
  {
    "start": 638.599,
    "end": 655.74,
    "text": "If you use tools to really take away a lot of this pain on the one hand it's nice because you can more quickly gain insight in the trends or patterns whether data is going to need somewhere interesting or not."
  },
  {
    "start": 657.24,
    "end": 666.28,
    "text": "but as also tools allow you different aspects of the process in more detail."
  },
  {
    "start": 666.68,
    "end": 681.099,
    "text": "The visualization, I mean with our team we had last year review on metabolomics and visualization And then also highlight how different tools allow you to visualize different aspect of the metabolomics workflow."
  },
  {
    "start": 684.04,
    "end": 699.219,
    "text": "What i think what took away from that is Yes, at some point if there are really important molecules in your data that you see annotations for then you need to be able to trace back the original spectra or actual data."
  },
  {
    "start": 699.86,
    "end": 702.28,
    "text": "That led those annotations too."
  },
  {
    "start": 702.339,
    "end": 704.979,
    "text": "make sure that You're on the right track"
  },
  {
    "start": 705.74,
    "end": 712.12,
    "text": "and as I said As you say this i'm thinking perhaps it is The developers of the tools that we use than that kind Of."
  },
  {
    "start": 712.24,
    "end": 725.599,
    "text": "take this responsibility For us decide where the cutoffs are made or like which parameters can be decided by the user and make it possible, sometimes not possible."
  },
  {
    "start": 725.64,
    "end": 734.62,
    "text": "I'm sure you'd choose to make it impossible for people do something because they want to prevent mistakes that maybe someone who's less of an expert could make."
  },
  {
    "start": 734.68,
    "end": 739.04,
    "text": "so... I assume there must be a kind of responsibility when we develop those tools."
  },
  {
    "start": 739.26,
    "end": 739.86,
    "text": "is this case?"
  },
  {
    "start": 741.219,
    "end": 741.76,
    "text": "Well yes!"
  },
  {
    "start": 741.86,
    "end": 744.52,
    "text": "Of course but its shared responsibility."
  },
  {
    "start": 745.4,
    "end": 750.24,
    "text": "As with anything, you can use tools for the better or worse."
  },
  {
    "start": 750.88,
    "end": 757.719,
    "text": "So yes there is a responsibility of developers like my team to ensure that there's"
  },
  {
    "start": 758.42,
    "end": 758.64,
    "text": "true"
  },
  {
    "start": 759.219,
    "end": 782.479,
    "text": "transparency on what different parameters mean and how they affect end result but also a responsibility from user to spend some time in trying understand what these different parameters do and go beyond the defaults, especially if also finding out what the default are meant for or intended."
  },
  {
    "start": 782.9,
    "end": 794.36,
    "text": "Because we have so many different metabolomics settings and disciplines and directions that it would be very coincidental If those defaults aren't need ideally for your case."
  },
  {
    "start": 794.4,
    "end": 795.12,
    "text": "So share"
  },
  {
    "start": 797.74,
    "end": 805.219,
    "text": "responsibility Absolutely, and you could even think that for the users of a sticker like we have for alcohol drink sensibly."
  },
  {
    "start": 805.3,
    "end": 807.02,
    "text": "You can have something like analyze sensibly."
  },
  {
    "start": 808.24,
    "end": 810.939,
    "text": "don't just put all their responsibility on the developers."
  },
  {
    "start": 811.06,
    "end": 815.54,
    "text": "but now if they do it in your hands... ...you need to understand it as well."
  },
  {
    "start": 815.839,
    "end": 816.16,
    "text": "Exactly!"
  },
  {
    "start": 816.219,
    "end": 818.56,
    "text": "I think this is very good message."
  },
  {
    "start": 818.8,
    "end": 833.66,
    "text": "But there are also for the developer's responsibilities who not Pretend that it's not important to investigate some time in understanding what the pyramids are doing and also encourage users."
  },
  {
    "start": 834.4,
    "end": 839.099,
    "text": "But do you think future generations, how will those go?"
  },
  {
    "start": 839.339,
    "end": 848.16,
    "text": "Well I see on one hand development, good developments because QA quality assessment becomes easier with some tools."
  },
  {
    "start": 848.219,
    "end": 855.86,
    "text": "Because the visualizations become more easy and the experimental designs that people are choosing now becoming more and more robust."
  },
  {
    "start": 856.24,
    "end": 859.68,
    "text": "there's also more literature on that has more teaching on that."
  },
  {
    "start": 859.78,
    "end": 877.079,
    "text": "Now this workshops There is I mean does a lot of resources That can help you to set up The right experimental design with the proper controls both for, let's say comparatively the belongs but also more MS based than MMS-based strategies."
  },
  {
    "start": 878.199,
    "end": 878.9,
    "text": "So that is good!"
  },
  {
    "start": 879.579,
    "end": 886.64,
    "text": "But what we should be wary about is representation of all the results in a small table with some numbers."
  },
  {
    "start": 887.5,
    "end": 890.76,
    "text": "it's great summary and may look fantastic."
  },
  {
    "start": 892.199,
    "end": 894.24,
    "text": "those numbers come from somewhere."
  },
  {
    "start": 894.74,
    "end": 902.52,
    "text": "so there are whole trace back of decisions, parameter settings that led to this small table of numbers."
  },
  {
    "start": 902.68,
    "end": 929.54,
    "text": "And somehow we need to make sure that we shouldn't focus too much on just single numbers in a table especially when you also consider all the developments with AI which I think we should mention at this podcast as well and uses in metabolomics of AI and our team, we mostly I would say working with machine learning."
  },
  {
    "start": 929.78,
    "end": 934.06,
    "text": "And then we will come to talk about that i think shortly."
  },
  {
    "start": 934.959,
    "end": 939.479,
    "text": "but also Of course We keep an eye out on developments In the AI."
  },
  {
    "start": 939.699,
    "end": 946.319,
    "text": "it's similar To what happened in protein structure prediction where alpha fold really make a big impact?"
  },
  {
    "start": 946.719,
    "end": 950.14,
    "text": "And I Think at some point in future something similar."
  },
  {
    "start": 950.54,
    "end": 957.64,
    "text": "Well, it's likely to happen in the middle below this where data will become so rich and well annotated."
  },
  {
    "start": 957.74,
    "end": 966.459,
    "text": "And curated and harmonizable that we are able to learn and transfer information across datasets more easily."
  },
  {
    "start": 967.42,
    "end": 974.8,
    "text": "but until then I think is a hard work of everybody who has listened into these podcasts and beyond to report their."
  },
  {
    "start": 977.28,
    "end": 986.479,
    "text": "It will make it possible to compare results, to compare annotations and really transfer knowledge and information from one experiment to the other."
  },
  {
    "start": 987.26,
    "end": 998.02,
    "text": "Before we dive deeper into those methods that you've developed... We wanted also take a moment to talk about any lessons learned by working with genomics and metabolomics."
  },
  {
    "start": 998.479,
    "end": 1000.86,
    "text": "I know you wrote paper on this a few years ago."
  },
  {
    "start": 1001.36,
    "end": 1002.74,
    "text": "there are lots of people, let's say."
  },
  {
    "start": 1003.26,
    "end": 1007.36,
    "text": "There're a lot more people who were familiar with genomics than with metabolomics."
  },
  {
    "start": 1007.939,
    "end": 1013.92,
    "text": "so maybe we can learn from that and also help the community to communicate better in the genomics community?"
  },
  {
    "start": 1016.36,
    "end": 1019.819,
    "text": "The paper you referred is on the Paratomics data platform."
  },
  {
    "start": 1020.28,
    "end": 1036.7,
    "text": "it really... It was used when the idea came out by registering or recording sequence genomes of bacteria, fungi and plants to publicly available metabolomics data."
  },
  {
    "start": 1037.18,
    "end": 1040.02,
    "text": "that can help us to also develop the methods."
  },
  {
    "start": 1040.12,
    "end": 1044.72,
    "text": "That kind of exploit this paired datasets with a pair dataset."
  },
  {
    "start": 1044.96,
    "end": 1062.68,
    "text": "here I mean we mean in the paper The sequence genome is of the same bacteria as the metabolomics data has been acquired from."
  },
  {
    "start": 1062.96,
    "end": 1083.5,
    "text": "From the extracts, sorry I should specify that more clearly and all kind of incentive was that we noticed how information was scattered not always easily retrievable form publications or simply not there."
  },
  {
    "start": 1083.82,
    "end": 1102.66,
    "text": "And the thing is about developing methods that use this different heterogeneous data types and sources, it takes a lot of time for people not involved in experiments to make sure these connections are correct."
  },
  {
    "start": 1102.8,
    "end": 1118.24,
    "text": "so if we can help each other We're involved in either the sequencing of the genomes or measuring of the metabolomics data."
  },
  {
    "start": 1118.74,
    "end": 1132.82,
    "text": "That can help us to make sure that all public data there is, connections are there and they can easily be retrieved... ...and this platform has one way for doing it right?"
  },
  {
    "start": 1133.68,
    "end": 1139.9,
    "text": "Yeah, now that's a great way to enable so the use of multiple omics together rather than just looking at your little corner."
  },
  {
    "start": 1140.5,
    "end": 1151.86,
    "text": "And I think if you ask me Metabolomics and Geonomics... I mean, Geonomic started earlier but you see that Metabolomics underwent similar kind of process in the file formats."
  },
  {
    "start": 1152.4,
    "end": 1160.54,
    "text": "So there are still different file formats also in Geonomix or Metabolomex But they get more and more interchangeable."
  },
  {
    "start": 1161.14,
    "end": 1164.04,
    "text": "You can making the data available."
  },
  {
    "start": 1164.48,
    "end": 1171.54,
    "text": "in beginning, there was not a thing in Metabolomics and now you see that are different resources repositories."
  },
  {
    "start": 1172.06,
    "end": 1182.22,
    "text": "Available like GMS Massive, like Metabolox Workbench, like metabolites That each have their own kind of pros and cons but they all Have shared common goal."
  },
  {
    "start": 1182.44,
    "end": 1188.68,
    "text": "And let's say make The Data available for reuse For verification validational findings."
  },
  {
    "start": 1189.1,
    "end": 1197.84,
    "text": "I think this harmonization is really a way forward and it must be difficult when you work on developing methods to decide at what stage."
  },
  {
    "start": 1197.9,
    "end": 1206.92,
    "text": "You want that more harmonized or if you have to commit in certain format, then leave the rest alone because i assume your tools are usable by whole community."
  },
  {
    "start": 1207.08,
    "end": 1209.78,
    "text": "so that probably complicates for you?"
  },
  {
    "start": 1210.08,
    "end": 1226.48,
    "text": "Well there are different communities right This pairedomics platform is really targeting, let's say the network product community where people are working with either genomics or metabolomics."
  },
  {
    "start": 1226.8,
    "end": 1231.78,
    "text": "Or both because many also work in both and they're interested in network product discovery."
  },
  {
    "start": 1232.12,
    "end": 1235.52,
    "text": "And then there isn't a community interesting."
  },
  {
    "start": 1235.66,
    "end": 1242.22,
    "text": "this we had at conference in Leuven not long ago February from the EU consortium, Dr."
  },
  {
    "start": 1242.3,
    "end": 1255.86,
    "text": "Training Network Magic Morphin and there were like hundred twenty people that also came together to discuss genome, genomics, metabolomics... ...and also the computational tools to analyze this omics data."
  },
  {
    "start": 1256.34,
    "end": 1262.26,
    "text": "And we also spent some time where they had talks on integration between these Genomics and Metabolomics."
  },
  {
    "start": 1262.48,
    "end": 1269.26,
    "text": "So There is certainly a community interested in further developing those tools and using them."
  },
  {
    "start": 1269.82,
    "end": 1283.46,
    "text": "And there's also, by the way, interest from companies that are now part of this toolkit to mine omics data for discovery in drugs and antibiotics."
  },
  {
    "start": 1286.1,
    "end": 1286.38,
    "text": "Thank you!"
  },
  {
    "start": 1287.12,
    "end": 1290.7,
    "text": "So I think we're ready to shift into our paper discussion."
  },
  {
    "start": 1290.84,
    "end": 1293.38,
    "text": "so we wanted to discuss two papers today."
  },
  {
    "start": 1294.3,
    "end": 1297.34,
    "text": "one is your earlier paper papers."
  },
  {
    "start": 1297.68,
    "end": 1309.26,
    "text": "And another one is a preprint that came out last year, so the first one is entitled Topic Modeling for Untargeted Substructure Exploration in Metabolomics and I'm going to let you explain what"
  },
  {
    "start": 1323.96,
    "end": 1328.96,
    "text": "it annotate, elucidate all the structures in data."
  },
  {
    "start": 1329.16,
    "end": 1331.88,
    "text": "Especially if you look at plant and microbial data."
  },
  {
    "start": 1332.5,
    "end": 1335.74,
    "text": "I mean even more so than human data."
  },
  {
    "start": 1335.9,
    "end": 1343.34,
    "text": "there's so much different structure it is very hard to really characterize them or their complete structures of all of them."
  },
  {
    "start": 1343.92,
    "end": 1348.68,
    "text": "but then also realize yeah what i'm doing this time is analyzing substructures."
  },
  {
    "start": 1350.56,
    "end": 1358.28,
    "text": "for example if we consider flavonoids glycosides achlecon, let's say cursitin or chamferol."
  },
  {
    "start": 1358.64,
    "end": 1367.9,
    "text": "Those are recognizable scaffolds of backbones structures and then they are decorated with sugars, sugar moieties right?"
  },
  {
    "start": 1368.04,
    "end": 1371.32,
    "text": "So what I basically did in my head was okay."
  },
  {
    "start": 1371.4,
    "end": 1375.64,
    "text": "i see this peak so that must be cursitine or this...I see this peaks to eight five."
  },
  {
    "start": 1376.02,
    "end": 1387.48,
    "text": "there must be a chamferole uh or an isomer And I see these losses or this peaks and oh that must be in hexos, or deoxyhexose etc."
  },
  {
    "start": 1388.1,
    "end": 1396.4,
    "text": "So In my head i was kind of using the mass spec information to annotate The molecules at a sub-structural level?"
  },
  {
    "start": 1397.02,
    "end": 1411.08,
    "text": "Then you can make new decisions are interested in This particular group of flavonoids right before You move on to full structural elicitation because To do That for all the molecules it's just too much work."
  },
  {
    "start": 1411.72,
    "end": 1443.04,
    "text": "So you'll also see that in my current work, we say that we do develop the methods to organize, prioritize and annotate spectra in metabolic data to get through their final insights And so this substructure annotation is part both of organization but also of annotation and prioritization because if we can more quickly kind of annotates substructures We could make more quick decisions on whether or not we're interested in this particular metabolite feature."
  },
  {
    "start": 1444.36,
    "end": 1459.18,
    "text": "So, and then I had a nice discussion at brainstorm with Simon Rodgers and Joe Wondey from Computing Sciences in Glasgow And there you realize that not long before the other's discussion This topic modeling was introduced for texts."
  },
  {
    "start": 1460.24,
    "end": 1477.02,
    "text": "Basically it uses text documents It looks more often co-occurring words More often than on average And it assumes that if this which are more often called occurring in documents, That they belong together as a topic."
  },
  {
    "start": 1477.14,
    "end": 1502.62,
    "text": "Let's say related to European politics related to economy related to sustainable energy and we also realized one document can contain multiple topics the same topic occur in multiple documents one or more substitutes and also the substitute."
  },
  {
    "start": 1502.66,
    "end": 1508.34,
    "text": "this can occur in multiple molecules because nature I think is quite efficient."
  },
  {
    "start": 1508.52,
    "end": 1515.74,
    "text": "If something works it will be reused, and they'll be reinvented then built upon right?"
  },
  {
    "start": 1516.22,
    "end": 1519.36,
    "text": "So with that information we decided let's give you a try!"
  },
  {
    "start": 1519.78,
    "end": 1538.54,
    "text": "Let's apply these topic modelling on the MSMS of the tandem mass spectra And lets see what happens...and i still remember at some point not long into this trial phase, I opened the file and i could see that two peaks that under nineteen and hundred thirty six."
  },
  {
    "start": 1538.98,
    "end": 1545.42,
    "text": "That kind of belong to add in the base right like the purine or pyridine."
  },
  {
    "start": 1545.8,
    "end": 1546.38,
    "text": "you can correct me."
  },
  {
    "start": 1547.36,
    "end": 1549.46,
    "text": "um never remember always have to check it as well."
  },
  {
    "start": 1549.76,
    "end": 1549.9,
    "text": "yeah"
  },
  {
    "start": 1550.62,
    "end": 1556.74,
    "text": "so but i still remember that i saw that combination and i realized okay this could really work right?"
  },
  {
    "start": 1556.84,
    "end": 1562.48,
    "text": "And now Ten years later, quite a few groups around the globe have been using it."
  },
  {
    "start": 1562.68,
    "end": 1575.28,
    "text": "And and uh... It's still used in discovery of groups of fragments losses or a combination thereof that belong to A specific sub-sector or scaffold To help us do more quickly."
  },
  {
    "start": 1575.4,
    "end": 1579.32,
    "text": "annotate prioritize The data in metabolomics profiles."
  },
  {
    "start": 1580.5,
    "end": 1581.66,
    "text": "That's really great method."
  },
  {
    "start": 1581.86,
    "end": 1592.16,
    "text": "I love this about computer science because you often see these methods just shifting from one field to a completely different field, as you explained now with the document reading."
  },
  {
    "start": 1592.28,
    "end": 1599.12,
    "text": "And it makes sense because we also... As humans, we project structures and patterns that we understand."
  },
  {
    "start": 1599.18,
    "end": 1603.56,
    "text": "We project on many different questions and things that we look at."
  },
  {
    "start": 1603.64,
    "end": 1604.56,
    "text": "so It make sense."
  },
  {
    "start": 1604.62,
    "end": 1607.44,
    "text": "that same logic applies too To different thing."
  },
  {
    "start": 1608.98,
    "end": 1613.46,
    "text": "The way that we build our text is somehow similar to the way that our biology's built."
  },
  {
    "start": 1613.9,
    "end": 1617.8,
    "text": "I love this kind of parallel, but when you come to the computational techniques."
  },
  {
    "start": 1617.86,
    "end": 1624.62,
    "text": "then you can really put it in action and see how much you can leverage from these parallels that you can build with the same logic."
  },
  {
    "start": 1625.14,
    "end": 1628.56,
    "text": "Thank you for explaining this, by the way In a way which i could understand."
  },
  {
    "start": 1628.6,
    "end": 1629.7,
    "text": "so thank-you very much."
  },
  {
    "start": 1631.58,
    "end": 1635.2,
    "text": "And so I understand that really this method, now you still use it."
  },
  {
    "start": 1636.08,
    "end": 1639.7,
    "text": "Is the basis of what do or is just one way?"
  },
  {
    "start": 1640.22,
    "end": 1642.5,
    "text": "I would say"
  },
  {
    "start": 1643.28,
    "end": 1660.68,
    "text": "in current work we are also further building on the model networking principle introduced by Peter Dorstein's lab for first time and working continue to work with that."
  },
  {
    "start": 1660.84,
    "end": 1664.36,
    "text": "We are also exploring vast spectral embeddings, right?"
  },
  {
    "start": 1664.4,
    "end": 1671.98,
    "text": "So the more without these direct edges or connections between features."
  },
  {
    "start": 1672.3,
    "end": 1691.66,
    "text": "we put all of our features in a chemical space and try to learn...we tried to model the spaces such as way that areas for example connected to chemical compound classes chemical information, so that when we look at this chemical space."
  },
  {
    "start": 1692.18,
    "end": 1697.36,
    "text": "We get a sense of what our metabolomics profile may contain right?"
  },
  {
    "start": 1697.52,
    "end": 1715.06,
    "text": "So those are other directions but for sure because the substructure information also can help us to link from the metabolomics back key driver to also continue this work."
  },
  {
    "start": 1715.46,
    "end": 1729.9,
    "text": "And the other one and there is a recent preprint on that as well, it's use it as the substructure patterns as spectral alerts for non-target screening... ...and I'm just back from a conference in Switzerland on Non-Target Screening."
  },
  {
    "start": 1731.7,
    "end": 1741.98,
    "text": "Actually if you think about that we are looking for permanent residues like drugs or pesticides in samples where they do not belong, right?"
  },
  {
    "start": 1742.1,
    "end": 1743.86,
    "text": "Or we don't want to see them actually."
  },
  {
    "start": 1744.2,
    "end": 1745.48,
    "text": "But also those molecules."
  },
  {
    "start": 1745.54,
    "end": 1757.14,
    "text": "they are often the scaffold and of course there are transformation products because of the microbes in the environment or because of photochemical reactions."
  },
  {
    "start": 1757.44,
    "end": 1764.14,
    "text": "but then you also get a group of molecules that are connected through common scaffold or at least circular similarity."
  },
  {
    "start": 1764.9,
    "end": 1766.18,
    "text": "And so what?"
  },
  {
    "start": 1769.1,
    "end": 1777.16,
    "text": "the new version of MSTILDA to help us create a curated set of fifties vector alerts for pesticides screening."
  },
  {
    "start": 1777.2,
    "end": 1781.7,
    "text": "Yeah, that's great because as you were explaining this I was also thinking about exposomics."
  },
  {
    "start": 1782.64,
    "end": 1790.88,
    "text": "we call it maybe more exposure for human exposures but i mean its same idea to find pesticides whether in plants or animals and humans."
  },
  {
    "start": 1791.28,
    "end": 1793.12,
    "text": "It is really clever approach."
  },
  {
    "start": 1793.38,
    "end": 1798.96,
    "text": "A lot of those chemicals have very peculiar structures, sometimes things that you wouldn't even find in nature."
  },
  {
    "start": 1799.02,
    "end": 1801.66,
    "text": "So it must make them relatively easy to find"
  },
  {
    "start": 1802.9,
    "end": 1822.54,
    "text": "some of the... Yes and no because as long we don't really fully understand how mass metrometry works In a sense so they can fully predict what happens to structures inside the mass pack And also How much information will get out from this spectra?"
  },
  {
    "start": 1823.62,
    "end": 1834.0,
    "text": "then it may still be a challenge to recognize specific molecules in very complex background matrix."
  },
  {
    "start": 1834.58,
    "end": 1840.68,
    "text": "Now, I noticed that's lot of your work is focused on agricultural topics."
  },
  {
    "start": 1840.76,
    "end": 1845.68,
    "text": "so plants bacteria fungus and thats the field where you develop your tools."
  },
  {
    "start": 1845.8,
    "end": 1850.1,
    "text": "but i'm sure there are lots people who use this tool."
  },
  {
    "start": 1851.44,
    "end": 1857.22,
    "text": "But I'm wondering, do you ever need to develop adaptation-specific?"
  },
  {
    "start": 1857.4,
    "end": 1864.48,
    "text": "Are there specific requests for these mammalian models that you would have to add sometimes or demand specific attention."
  },
  {
    "start": 1865.5,
    "end": 1870.16,
    "text": "Well...I always say the mass spec doesn't really care what you inject into it."
  },
  {
    "start": 1870.24,
    "end": 1875.38,
    "text": "well of course if she starts to clock in whatever then they'll complain."
  },
  {
    "start": 1875.58,
    "end": 1879.22,
    "text": "but So it's a context of methods, right?"
  },
  {
    "start": 1879.34,
    "end": 1889.88,
    "text": "If you're interested in mammalian metabolites then use the spectral libraries that contain mostly mammalian reference data and used structure databases."
  },
  {
    "start": 1889.98,
    "end": 1897.3,
    "text": "That contains relevant molecules, so when your annotation pipeline they will show up."
  },
  {
    "start": 1898.36,
    "end": 1914.48,
    "text": "And if we get more and more reference available than You can also start to train models specifically on On the many a part of the metabolome or on the microbiome by the metabolism, all in the plant part off the metabolism."
  },
  {
    "start": 1915.04,
    "end": 1915.9,
    "text": "that is possible."
  },
  {
    "start": 1916.36,
    "end": 1925.0,
    "text": "But I think you can also start to create more creative motive sets that are dedicated to specific parts of the Potembaloma."
  },
  {
    "start": 1925.26,
    "end": 1941.52,
    "text": "We already started that, one of the follow-up papers on the first paper in two thousand sixteen which is by the way ten years ago now was also MotiveDB where we started too share several sets of curated motifs back then mostly curated by myself."
  },
  {
    "start": 1941.64,
    "end": 1959.42,
    "text": "but we hope also that new version introduced last year will yield renewed interest in jointly, as a scientific community building up curated motive sets for other species."
  },
  {
    "start": 1959.56,
    "end": 1961.52,
    "text": "Other sample types etc."
  },
  {
    "start": 1964.0,
    "end": 1966.28,
    "text": "And maybe it's good place to go."
  },
  {
    "start": 1966.56,
    "end": 1973.12,
    "text": "the other paper we wanted to discuss which is much more recent from last year I think to this day, it's still a preprint."
  },
  {
    "start": 1973.34,
    "end": 1979.7,
    "text": "So the title is large scale discovery and annotation of hidden substructure patterns in mass spectrometry profiles?"
  },
  {
    "start": 1980.5,
    "end": 1981.68,
    "text": "What would you discuss on this paper?"
  },
  {
    "start": 1982.6,
    "end": 1986.46,
    "text": "It's like completely renewed version off-the-tool."
  },
  {
    "start": 1987.12,
    "end": 2001.18,
    "text": "one of the challenges of academic software development is that we normally don't have full time software engineer working on projects active and stable."
  },
  {
    "start": 2001.42,
    "end": 2013.26,
    "text": "And also MSTLDA, the first version is a typical prototypical example of tool-based or code based that grew organically right?"
  },
  {
    "start": 2013.46,
    "end": 2014.2,
    "text": "Very natural."
  },
  {
    "start": 2014.64,
    "end": 2028.46,
    "text": "so on one hand you could argue it's very good because there needs to be room for exploration but at the same time It becomes harder and harder to add new things Because when you add something here."
  },
  {
    "start": 2029.12,
    "end": 2039.82,
    "text": "something may break in the completely different part of, let's say code base or three and that also means it becomes harder to work with."
  },
  {
    "start": 2040.88,
    "end": 2061.56,
    "text": "Luckily I had two PhD students on my team Rosina and Jonas both working on a different project but both very much interested and kind of driven spectral alerts in non-target screening."
  },
  {
    "start": 2062.1,
    "end": 2068.92,
    "text": "So they teamed up, but together with Joe Wandy and he worked on a new version of the visualization app."
  },
  {
    "start": 2069.42,
    "end": 2075.639,
    "text": "we upgraded MSTLDA that actually created a new tool from it."
  },
  {
    "start": 2076.0,
    "end": 2079.38,
    "text": "so full codebase is now based on match-matches."
  },
  {
    "start": 2079.42,
    "end": 2088.4,
    "text": "to find packets their handles must be thrown through data put all well tested functionality to work with it."
  },
  {
    "start": 2088.52,
    "end": 2100.32,
    "text": "So instead of using our own custom functions, we rely on a software tool that is also maintained by the community and then more people are using."
  },
  {
    "start": 2100.68,
    "end": 2105.1,
    "text": "so if things break there's an energy to repair them."
  },
  {
    "start": 2106.34,
    "end": 2113.56,
    "text": "And different LDA algorithm has been implemented to make everything more scalable."
  },
  {
    "start": 2113.64,
    "end": 2116.74,
    "text": "because ten years down the line."
  },
  {
    "start": 2117.3,
    "end": 2125.42,
    "text": "The data sets are growing, people no longer want to do it on a few hundred spectra but often on ten thousand or even one hundred thousand spectra?"
  },
  {
    "start": 2125.58,
    "end": 2127.1,
    "text": "The demand has changed a lot?"
  },
  {
    "start": 2127.18,
    "end": 2127.76,
    "text": "I guess yes"
  },
  {
    "start": 2128.98,
    "end": 2136.3,
    "text": "and what that also means is that the number of motifs or master motives you generate with the surf circuit patterns will also grow."
  },
  {
    "start": 2138.1,
    "end": 2143.54,
    "text": "One thing I didn't really tell you yet about this topic modeling that it sounds fantastic, and it is very nice."
  },
  {
    "start": 2143.62,
    "end": 2146.4,
    "text": "But if doesn't give you an annotation itself right?"
  },
  {
    "start": 2146.48,
    "end": 2150.96,
    "text": "It gives you the groups of words in text or In our world to group of fragments."
  },
  {
    "start": 2151.02,
    "end": 2155.52,
    "text": "are losses or combination thereof that That are often co-occurring."
  },
  {
    "start": 2155.64,
    "end": 2157.32,
    "text": "so still up to you as user."
  },
  {
    "start": 2157.38,
    "end": 2158.12,
    "text": "then too."
  },
  {
    "start": 2158.38,
    "end": 2165.92,
    "text": "annotate Of course, if you have a lot of domain expertise then that you can do it already from the top of your head."
  },
  {
    "start": 2166.1,
    "end": 2172.7,
    "text": "or You can look up in spectral libraries to peaks and kind of try start the process."
  },
  {
    "start": 2172.86,
    "end": 2172.88,
    "text": "Be"
  },
  {
    "start": 2173.02,
    "end": 2173.62,
    "text": "critical."
  },
  {
    "start": 2173.82,
    "end": 2176.26,
    "text": "what you read make decisions based on That yeah"
  },
  {
    "start": 2176.78,
    "end": 2180.72,
    "text": "but we also did is now implemented them."
  },
  {
    "start": 2181.0,
    "end": 2191.94,
    "text": "master motive annotation guidance where uh...you could get some help by leveraging the largest spectral libraries as part of this motive annotation process."
  },
  {
    "start": 2192.6,
    "end": 2198.2,
    "text": "And it's a final thing I think is worth mentioning, because now there is more and more data."
  },
  {
    "start": 2198.7,
    "end": 2205.54,
    "text": "we also made it compatible with these new mass virtuality query language called Masql."
  },
  {
    "start": 2206.06,
    "end": 2218.58,
    "text": "so if you have a pattern it will be all some much easier to then search a large amount particular motif or pattern."
  },
  {
    "start": 2220.2,
    "end": 2221.84,
    "text": "Yeah, yeah that's a very useful thing."
  },
  {
    "start": 2221.94,
    "end": 2229.66,
    "text": "of course we're ready to move to our last big topic because as I mentioned this year we talk about community building."
  },
  {
    "start": 2229.84,
    "end": 2240.52,
    "text": "so you really as i researched your past in preparation and discovered things about your career, but I missed a few things."
  },
  {
    "start": 2241.5,
    "end": 2252.06,
    "text": "Especially you mentioned it at the beginning... You were part of some of the early networks in the Metabolomics Society and i learned that you are part of first team of the EMN."
  },
  {
    "start": 2252.72,
    "end": 2253.7,
    "text": "Can you tell us a bit?"
  },
  {
    "start": 2254.96,
    "end": 2258.76,
    "text": "Because of course The Metabolomic Society is big community in the metabolomics world."
  },
  {
    "start": 2259.18,
    "end": 2268.4,
    "text": "But what made this EMN network come up and what did you feel that it was needed in the bigger community?"
  },
  {
    "start": 2268.66,
    "end": 2271.78,
    "text": "Something for early, early scientists or stage scientist."
  },
  {
    "start": 2273.22,
    "end": 2285.74,
    "text": "Yeah so I think people realized the PIs in let's say two thousand nine to ten and then this is twelve thirteen when they started to come off."
  },
  {
    "start": 2285.84,
    "end": 2294.58,
    "text": "i forgot exact year now but thirteen or fourteen right is that?"
  },
  {
    "start": 2295.94,
    "end": 2304.84,
    "text": "uh like myself, I mean now i'm five six years into this group leader position and slowly you become more."
  },
  {
    "start": 2306.0,
    "end": 2311.9,
    "text": "there's more and more distance between you and the career states that most of your team members are in."
  },
  {
    "start": 2315.38,
    "end": 2324.88,
    "text": "And it's very natural, but also means that the type of questions you get more and more distance."
  },
  {
    "start": 2325.18,
    "end": 2331.78,
    "text": "Of course I will do my best to answer all the question share experiences."
  },
  {
    "start": 2332.1,
    "end": 2335.82,
    "text": "But let us face this The world is changing."
  },
  {
    "start": 2337.54,
    "end": 2342.48,
    "text": "People working now on machines They use different software again Different options."
  },
  {
    "start": 2343.38,
    "end": 2350.86,
    "text": "it makes much more sense to discuss that and kind of find people who are in a similar career stage."
  },
  {
    "start": 2354.04,
    "end": 2366.6,
    "text": "I think this early-career network, like the EMN, we also started Young NMC, which is now the young BMC, Benelux Metabolomics Center."
  },
  {
    "start": 2366.78,
    "end": 2374.9,
    "text": "so another example community in the metabolomics world that has been very active over the last years."
  },
  {
    "start": 2376.22,
    "end": 2391.24,
    "text": "So what I see is, if you start to give early careers trust and also empower them to organize things for themselves... You can see a lot of nice initiatives growing right?"
  },
  {
    "start": 2391.36,
    "end": 2402.24,
    "text": "For example back then it was in I started together with fellow committee members from the E&M, this webinar series."
  },
  {
    "start": 2403.2,
    "end": 2406.08,
    "text": "And it's very nice to see that its still ongoing right?"
  },
  {
    "start": 2406.22,
    "end": 2428.06,
    "text": "After ten years there is often a webinar where people are listening and recorded so they can also go back here from experts around the globe on different aspects of metabolomics has inspired also others."
  },
  {
    "start": 2428.4,
    "end": 2431.96,
    "text": "And I think for these people, it creates community for them."
  },
  {
    "start": 2432.12,
    "end": 2444.44,
    "text": "So It's just so nice to see that you and a few friends basically because i think he becomes friends as we do this started this movement For example with the webinars and now its in the hands of completely different People but who also work together?"
  },
  {
    "start": 2444.48,
    "end": 2444.62,
    "text": "Yeah!"
  },
  {
    "start": 2444.66,
    "end": 2447.28,
    "text": "I think it is beautiful dynamic and really important"
  },
  {
    "start": 2447.68,
    "end": 2448.84,
    "text": "Across The Globe As well."
  },
  {
    "start": 2448.96,
    "end": 2460.68,
    "text": "In case of early career members network Of the Metabolical Society Which I Think Is Also Nice To See That Despite All The Current terminal that people are still able to work together."
  },
  {
    "start": 2461.6,
    "end": 2464.62,
    "text": "They come from different countries, different backgrounds and expertise."
  },
  {
    "start": 2464.8,
    "end": 2479.06,
    "text": "so I hope we can continue doing this for a long time but also more locally where in the Netherlands Belgium Luxembourg there is quite several groups that work on metabolomics."
  },
  {
    "start": 2479.12,
    "end": 2488.5,
    "text": "Some are bigger, but some people are working on their own as part of a larger team or group and only they're involved in metabolomics."
  },
  {
    "start": 2488.7,
    "end": 2499.54,
    "text": "especially for them having these local communities is also very important I think because you can connect with other students who have similar questions, similar situations."
  },
  {
    "start": 2502.54,
    "end": 2503.38,
    "text": "No, I think it's great."
  },
  {
    "start": 2503.6,
    "end": 2515.26,
    "text": "I know...I benefited from a network like this because i was in European projects and its'a similar vibe with people from different countries and different styles of leadership also on their own labs."
  },
  {
    "start": 2515.38,
    "end": 2519.2,
    "text": "so some people feel less lucky than others."
  },
  {
    "start": 2519.28,
    "end": 2523.22,
    "text": "sometimes they can get support too."
  },
  {
    "start": 2524.8,
    "end": 2539.12,
    "text": "Everywhere where we find community is really something that's good for the soul, but also helps the field rise together and help to benefit from having several brains."
  },
  {
    "start": 2539.26,
    "end": 2543.52,
    "text": "I would say hearts getting together."
  },
  {
    "start": 2544.04,
    "end": 2549.98,
    "text": "There is one community you're a part of that I would call, and i'm not sure if that's how it was called but the open science communities."
  },
  {
    "start": 2550.44,
    "end": 2556.08,
    "text": "And I know It's very common for people in computer science to really push this aspect of Open Science."
  },
  {
    "start": 2556.24,
    "end": 2559.24,
    "text": "so For That Community specifically what?"
  },
  {
    "start": 2560.14,
    "end": 2566.66,
    "text": "What Is important there and why is it such A fight that I see So many Computer Scientists Pushing Forward?"
  },
  {
    "start": 2568.06,
    "end": 2581.22,
    "text": "Well...I mean If we think about The importance Of Open Science for Especially computational groups, I think it's first and foremost that without any data they cannot develop tools."
  },
  {
    "start": 2581.38,
    "end": 2581.68,
    "text": "Right?"
  },
  {
    "start": 2581.8,
    "end": 2583.26,
    "text": "So let's face it right."
  },
  {
    "start": 2583.58,
    "end": 2592.94,
    "text": "so of course there will be advocating for open science because It would mean means that a have access to the two data."
  },
  {
    "start": 2593.08,
    "end": 2599.08,
    "text": "then they can develop at test and validate their own tool models and resources on."
  },
  {
    "start": 2601.1,
    "end": 2602.08,
    "text": "It's not only that."
  },
  {
    "start": 2602.3,
    "end": 2602.86,
    "text": "I think it all."
  },
  {
    "start": 2603.0,
    "end": 2604.62,
    "text": "open size also helps to."
  },
  {
    "start": 2605.42,
    "end": 2614.22,
    "text": "people can reproduce or start to reproduce your results, they can take your data and ask different questions right?"
  },
  {
    "start": 2614.34,
    "end": 2620.18,
    "text": "And you see a lot of tools now that allow you to reuse the data in an asked different question."
  },
  {
    "start": 2620.7,
    "end": 2632.98,
    "text": "yeah for example there has been this discovery Co-production of the Michael Bio and the Mammals in this"
  },
  {
    "start": 2633.14,
    "end": 2633.36,
    "text": "case."
  },
  {
    "start": 2633.42,
    "end": 2633.82,
    "text": "Teamwork!"
  },
  {
    "start": 2633.98,
    "end": 2643.2,
    "text": "Anyway, I'll leave it up to the audience whether they're mainly a microbial or a co-production or everything."
  },
  {
    "start": 2643.74,
    "end": 2645.88,
    "text": "but yeah... This is Coffery right?"
  },
  {
    "start": 2647.62,
    "end": 2649.68,
    "text": "I mean, it brings together a lot of developments."
  },
  {
    "start": 2649.76,
    "end": 2649.96,
    "text": "Right?"
  },
  {
    "start": 2650.2,
    "end": 2671.94,
    "text": "Not only okay we realize that there are these new metabolites right so... Okay and we realized the importance of the microbiome but then using all this infrastructure and the tools they've been developed And in this Moscow language everything else The fact is GPS massive and other resources came out."
  },
  {
    "start": 2672.02,
    "end": 2679.0,
    "text": "So now They could also come back Asked questions like hey But hang on did we actually see this before?"
  },
  {
    "start": 2679.1,
    "end": 2689.16,
    "text": "And then suddenly, thousands of features kind where annotated with okay another potential new bio essence."
  },
  {
    "start": 2689.24,
    "end": 2700.72,
    "text": "So all that data and it wouldn't have been possible without open science because than the data was still somewhere in a drawer or deleted and not accessible."
  },
  {
    "start": 2701.24,
    "end": 2706.64,
    "text": "Now you can start to really see impact on these discoveries as well."
  },
  {
    "start": 2708.06,
    "end": 2708.38,
    "text": "Thank you."
  },
  {
    "start": 2709.1,
    "end": 2711.72,
    "text": "Are there other forms of community that are a part?"
  },
  {
    "start": 2715.38,
    "end": 2729.74,
    "text": "Yes, I think it's one community that i also like to mention because my own work has found inspiration from where this is the the DAX tool community around confrontation with the below mix."
  },
  {
    "start": 2729.86,
    "end": 2741.38,
    "text": "So as of two thousand seventeen, I've been a regular visitor off this particular seminar series and actually The last time in the one that is upcoming next week."
  },
  {
    "start": 2741.62,
    "end": 2756.6,
    "text": "i'm also co-organizing And it's really an opportunity to meet with fortyish people both experience, but also new and upcoming talent in the field of Computation Metabolomics both methods developers."
  },
  {
    "start": 2756.7,
    "end": 2770.86,
    "text": "And also players users and often some people from industry that all together kind of brainstormed for example the concept of modern enhancer which is another tool."
  },
  {
    "start": 2771.56,
    "end": 2785.14,
    "text": "I'm proud because it brings a lot of different tools makes them available together in one network and this whole concept is still used by the community quite heavily."
  },
  {
    "start": 2785.74,
    "end": 2788.44,
    "text": "And that ID, and a concept of paper."
  },
  {
    "start": 2788.5,
    "end": 2810.68,
    "text": "it all started at this German castle in Dachstuhl where we sat down with beer and laptops to discuss how can analysis, different types and browsers more easy for people."
  },
  {
    "start": 2810.8,
    "end": 2824.04,
    "text": "And then we kind of came to this modern enhancer concept where the different annotation layers come together in one network so library matches master motive patterns and everything's."
  },
  {
    "start": 2824.46,
    "end": 2828.74,
    "text": "I can also attest too that the actual meetings are really...I was there a couple years ago."
  },
  {
    "start": 2828.84,
    "end": 2829.42,
    "text": "you invited me?"
  },
  {
    "start": 2830.18,
    "end": 2832.6,
    "text": "It is like a retreat."
  },
  {
    "start": 2834.52,
    "end": 2840.82,
    "text": "who all want to take that community somewhere, just brainstorm and find ideas of how they can work together."
  },
  {
    "start": 2840.96,
    "end": 2842.24,
    "text": "How can they bring other people together?"
  },
  {
    "start": 2842.44,
    "end": 2843.64,
    "text": "It's really a beautiful initiative."
  },
  {
    "start": 2844.06,
    "end": 2846.38,
    "text": "I'm really happy you continue this."
  },
  {
    "start": 2847.08,
    "end": 2847.76,
    "text": "Yeah exactly!"
  },
  {
    "start": 2847.86,
    "end": 2851.66,
    "text": "And i hope it will be continued also in the future."
  },
  {
    "start": 2852.9,
    "end": 2855.06,
    "text": "So last question about the communities."
  },
  {
    "start": 2855.14,
    "end": 2861.48,
    "text": "so... You're part of a lot of communities maybe I would ask here but the Metabolomics Community But you could choose different one."
  },
  {
    "start": 2862.5,
    "end": 2867.96,
    "text": "Where do like your favorite community, let's say in five or ten years."
  },
  {
    "start": 2868.38,
    "end": 2871.74,
    "text": "Where would you like this common movement to take us?"
  },
  {
    "start": 2873.0,
    "end": 2877.0,
    "text": "Maybe it is true for most larger communities."
  },
  {
    "start": 2877.16,
    "end": 2895.44,
    "text": "I think...I hope we can find the right balance between exploring new things and continuing to develop our own favourite pet tools but also make sure that those tools keep talking to each other, right?"
  },
  {
    "start": 2895.62,
    "end": 2898.14,
    "text": "Much like humans in a community."
  },
  {
    "start": 2899.02,
    "end": 2902.42,
    "text": "Without connections without their interactions there is no Community."
  },
  {
    "start": 2902.96,
    "end": 2908.48,
    "text": "and what you see happening Is that we all have our favorite go-to tools And frameworks."
  },
  {
    "start": 2908.72,
    "end": 2917.8,
    "text": "It's also true for my team myself But at the same time I think it will be crucial For success if we keep communicating."
  },
  {
    "start": 2917.98,
    "end": 2933.58,
    "text": "Make sure That input and output of these tools are somehow talking to each other and compatible so that when a good new idea comes out, then you can also use it or reuse as part of all the pipelines."
  },
  {
    "start": 2933.74,
    "end": 2939.04,
    "text": "And I think the amount work goes into this now is maybe underestimated."
  },
  {
    "start": 2939.52,
    "end": 2943.44,
    "text": "for example we were able to send Nick De Jonga."
  },
  {
    "start": 2943.58,
    "end": 2959.36,
    "text": "he originally graduated in my team And we sent him to Prague, also there together with the MZMine people integrate MZDivscore into an MZmine."
  },
  {
    "start": 2959.7,
    "end": 2962.96,
    "text": "So that is now kind of integrated compatible."
  },
  {
    "start": 2963.08,
    "end": 2968.14,
    "text": "so people who use MZmind can also benefit from MZdivscor."
  },
  {
    "start": 2968.62,
    "end": 2970.08,
    "text": "but if you think"
  },
  {
    "start": 2970.16,
    "end": 2977.4,
    "text": "about the amount of work and time it goes in through then I still try to improve make things even more easy."
  },
  {
    "start": 2979.82,
    "end": 2980.12,
    "text": "Thank you."
  },
  {
    "start": 2980.4,
    "end": 2986.74,
    "text": "Now it's a beautiful goal, I think the community of tools that can work with each other just like we worked with each Other."
  },
  {
    "start": 2987.06,
    "end": 2992.14,
    "text": "this takes us to The last question for this episode what your favorite metabolite and why?"
  },
  {
    "start": 2992.66,
    "end": 2998.16,
    "text": "To be fair i asked You That Question Valencia four years ago And you had A few Already."
  },
  {
    "start": 2998.3,
    "end": 2999.34,
    "text": "so has It Changed?"
  },
  {
    "start": 3000.62,
    "end": 3005.84,
    "text": "Well i thought about it and i will give you a different favorite one because Why not sure right?"
  },
  {
    "start": 3008.36,
    "end": 3015.4,
    "text": "the one I will mention now is called geosmin and i think most of you will have smelled it."
  },
  {
    "start": 3016.38,
    "end": 3030.94,
    "text": "so if you think yourself to like going outside during or just after a heavy rain pour, and you start to smell...and you have smelled this earthy kind of odor in the air then that IS geosmine right?"
  },
  {
    "start": 3031.04,
    "end": 3034.72,
    "text": "So produced by bacteria."
  },
  {
    "start": 3035.04,
    "end": 3036.42,
    "text": "In particular streptomyces."
  },
  {
    "start": 3037.78,
    "end": 3043.66,
    "text": "they produce this when water is released or there are close to water."
  },
  {
    "start": 3043.86,
    "end": 3049.4,
    "text": "And geosmin, it comes from geo the earth and the smell right?"
  },
  {
    "start": 3049.48,
    "end": 3064.9,
    "text": "So the smell of the Earth... ...and I thought that's a very nice molecule to mention because its rather simple twelve carbons twenty-two hydrogen and one oxygen but has just very peculiar smell."
  },
  {
    "start": 3065.58,
    "end": 3067.88,
    "text": "The mammals are very sensitive to it."
  },
  {
    "start": 3068.36,
    "end": 3082.02,
    "text": "We don't know exactly why, but presumably because... ...it may have led us two sources of water and as we all know clean good water is a pivotal kind of condition for us to thrive in life."
  },
  {
    "start": 3082.6,
    "end": 3090.9,
    "text": "And I also felt that It's nice Because first of all its also volatile.. ..and not something i typically work with every day."
  },
  {
    "start": 3091.04,
    "end": 3099.86,
    "text": "So another perspective a molecule that is kind of facilitating inter-kingdom communication."
  },
  {
    "start": 3099.96,
    "end": 3101.5,
    "text": "I mean this bacteria."
  },
  {
    "start": 3101.62,
    "end": 3104.38,
    "text": "they emit something, then mammals."
  },
  {
    "start": 3104.52,
    "end": 3108.6,
    "text": "we can pick up and make decisions on it."
  },
  {
    "start": 3109.62,
    "end": 3125.22,
    "text": "And maybe as final note i think its also nice to stay connected through the earth and kinda make sure that We revalue all life including the bacteria in soil during our work."
  },
  {
    "start": 3125.34,
    "end": 3130.78,
    "text": "so I felt that nicely came together in this small molecule called geosmine."
  },
  {
    "start": 3132.04,
    "end": 3133.52,
    "text": "Thank you, thank you very much for the choice!"
  },
  {
    "start": 3133.76,
    "end": 3141.9,
    "text": "i had no idea there was a molecule responsible for these metal summer storms which is really interesting."
  },
  {
    "start": 3143.78,
    "end": 3146.7,
    "text": "it's one of the main constituents"
  },
  {
    "start": 3150.28,
    "end": 3159.98,
    "text": "But to know that there's one, has this specific relation and I also love your take on it in terms of communication with other species."
  },
  {
    "start": 3161.26,
    "end": 3164.9,
    "text": "We get a lot with volatile compounds so its really interesting."
  },
  {
    "start": 3164.96,
    "end": 3175.82,
    "text": "Thank you very much!"
  },
  {
    "start": 3178.02,
    "end": 3187.82,
    "text": "To make sure that you don't miss out on our next episode, You can follow the podcast on your podcast app or go to TheMetabolomist.com and register for a newsletter."
  },
  {
    "start": 3188.76,
    "end": 3195.14,
    "text": "Until then I wish you get to use Metabolomics with the same passion And dedication as my guest today."
  },
  {
    "start": 3195.84,
    "end": 3201.78,
    "text": "Don't hesitate to reach me on LinkedIn at Alice in Montiel."
  }
]