PhenoMeNal: Large scale computing with medical metabolic phenotyping data

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Talk presented at workhop for Establishing a node for FAIRifying metabolomics and phenomics data in the European Open Science Cloud in Leiden

Science

Christoph Steinbeck
and the
PhenoMeNal consortium
European Bioinformatics Institute, Hinxton
Friedrich-Schiller-University, Jena
Large scale computing with medical
metabolic phenotyping data

Reaction times following
external change
• Genetics (decades, centuries…)
• Epigenetics (days, month, years,…)
• Gene Expression (hours)
• Metabolism (seconds)

The Metabolome
is the most accessible and
dynamically changing
Molecular Phenotype

Untargeted Metabolomics
of Cerebrospinal Fluid
AD – red; MCI- blue
Alzheimer’s Disease (AD), Mild Cognitive Impairment (MCI), Cognitive Normal (CN)
AD – red; CN- blue

Metabolomics On The Rise
Source: Google Scholar

Phenome Centres popping
up all over the world
• London
• Birmingham
• Shanghai
• NIH RCMRCs
• …

> 100,000 patient samples / year
> Several PetaBytes/year
=> ExaBytes of human data at
moderate scale-up

Make data FAIR
-
Share them
-
Free and Open

•500 Million people in European Union
•Full Genomes (soon for less than $1000 p. P.)
•Urine/Blood Metabolome < 20 Euros per Patient

Large Scale Computing
with Medical
Metabolomics Data
• EBI lead
• H2020
• 3Years
• 13 Partners
• 8 Mio €
• 830 PM
• Kick-off 9/15
• H2020 e-infra

An e-infrastructure for
Large Scale Computing
with Medical
Metabolomics Data

PhenoMeNal Objectives
1. Integrate existing open source tools, resources
into a secure and sustainable e-Infrastructure

PhenoMeNal Objectives
2. Operate and consolidate the PhenoMeNal e-
infrastructure based on existing internal and external
HPC (High-performance computing) resources

PhenoMeNal Objectives
3. To improve and scale-up tools used within the
infrastructure to cope with very large datasets
4.To establish technology for a water-tight audit trail

PhenoMeNal Objectives
5. To establish privacy-protection methods
6.To foster the worldwide adoption of PhenoMeNal
7. To develop a model to ensure sustainability of the
PhenoMeNal network

Large Scale Computing
with Medical
Metabolomics Data

Networking Activities -EOSC
As part of EOSC and
GO FAIR,
PhenoMeNal helps
building a hub for
verifying
FAIR metabolomics
data

Funding and Collaborators
UK Research Councils (BBSRC, MRC)
European Commission

Slides on
http://www.slideshare.net/csteinbeck

PhenoMeNal: Large scale computing with medical metabolic phenotyping data

This document discusses large scale computing with medical metabolic phenotyping data. It notes that genes are not the full story and that the metabolome is the most accessible and dynamically changing molecular phenotype. It describes how investigating metabolomes at large scale can help disentangle the exposome conundrum. Phenome centers are emerging around the world to study over 100,000 patient samples per year, generating several petabytes of data annually. The MetaboLights database serves as an experimental repository for this type of data.

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学校原件一模一样【微信：741003700 】《(salfor毕业证书)索尔福德大学毕业证》【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。本公司拥有海外各大学样板无数，能完美还原。 1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700 【主营项目】一.毕业证【q微741003700】成绩单、使馆认证、教育部认证、雅思托福成绩单、学生卡等！二.真实使馆公证(即留学回国人员证明,不成功不收费) 三.真实教育部学历学位认证（教育部存档！教育部留服网站永久可查）四.办理各国各大学文凭(一对一专业服务,可全程监控跟踪进度) 如果您处于以下几种情况： ◇在校期间，因各种原因未能顺利毕业……拿不到官方毕业证【q/微741003700】 ◇面对父母的压力，希望尽快拿到； ◇不清楚认证流程以及材料该如何准备； ◇回国时间很长，忘记办理； ◇回国马上就要找工作，办给用人单位看； ◇企事业单位必须要求办理的 ◇需要报考公务员、购买免税车、落转户口 ◇申请留学生创业基金留信网认证的作用: 1:该专业认证可证明留学生真实身份 2:同时对留学生所学专业登记给予评定 3:国家专业人才认证中心颁发入库证书 4:这个认证书并且可以归档倒地方 5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息 6:个人职称评审加20分 7:个人信誉贷款加10分 8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才

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Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...

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Equivariant neural networks and representation theory

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Or: Beyond linear. Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory. Disclaimer: No one is perfect, so please mind that there might be mistakes and typos. dtubbenhauer@gmail.com Corrected slides: dtubbenhauer.com/talks.html

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mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt

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Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.

The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx

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Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024). Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).

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Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.

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As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus, high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology, and analysis methods, numerous infrastructure platforms have been developed for phenotyping.

如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样

yqqaatn0

原版纸张【微信：741003700 】【(uvic毕业证书)维多利亚大学毕业证】【微信：741003700 】学位证，留信认证（真实可查，永久存档）offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma 1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700 留信网认证的作用: 1:该专业认证可证明留学生真实身份 2:同时对留学生所学专业登记给予评定 3:国家专业人才认证中心颁发入库证书 4:这个认证书并且可以归档倒地方 5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息 6:个人职称评审加20分 7:个人信誉贷款加10分 8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才

原版制作(carleton毕业证书)卡尔顿大学毕业证硕士文凭原版一模一样

yqqaatn0

原版纸张【微信：741003700 】【(carleton毕业证书)卡尔顿大学毕业证】【微信：741003700 】学位证，留信认证（真实可查，永久存档）offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma 1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700 留信网认证的作用: 1:该专业认证可证明留学生真实身份 2:同时对留学生所学专业登记给予评定 3:国家专业人才认证中心颁发入库证书 4:这个认证书并且可以归档倒地方 5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息 6:个人职称评审加20分 7:个人信誉贷款加10分 8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才

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在线办理(salfor毕业证书)索尔福德大学毕业证毕业完成信一模一样

Eukaryotic Transcription Presentation.pptx

Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...

Equivariant neural networks and representation theory

Randomised Optimisation Algorithms in DAPHNE

mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt

Describing and Interpreting an Immersive Learning Case with the Immersion Cub...

The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx

Cytokines and their role in immune regulation.pptx

Compexometric titration/Chelatorphy titration/chelating titration

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Authoring a personal GPT for your research and practice: How we created the Q...

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如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样

原版制作(carleton毕业证书)卡尔顿大学毕业证硕士文凭原版一模一样

PhenoMeNal: Large scale computing with medical metabolic phenotyping data

1. Christoph Steinbeck and the PhenoMeNal consortium European Bioinformatics Institute, Hinxton Friedrich-Schiller-University, Jena Large scale computing with medical metabolic phenotyping data

2. Understanding Phenotypes

3. Reaction times following external change • Genetics (decades, centuries…) • Epigenetics (days, month, years,…) • Gene Expression (hours) • Metabolism (seconds)

4. The Metabolome is the most accessible and dynamically changing Molecular Phenotype

5. Untargeted Metabolomics of Cerebrospinal Fluid AD – red; MCI- blue Alzheimer’s Disease (AD), Mild Cognitive Impairment (MCI), Cognitive Normal (CN) AD – red; CN- blue

6. Untargeted Metabolomics of Cerebrospinal Fluid AD – red; MCI- blue Alzheimer’s Disease (AD), Mild Cognitive Impairment (MCI), Cognitive Normal (CN) AD – red; CN- blue Basis for a diagnostic tool

7. Metabolomics On The Rise Source: Google Scholar

8. Phenome Centres popping up all over the world • London • Birmingham • Shanghai • NIH RCMRCs • …

10. > 100,000 patient samples / year > Several PetaBytes/year => ExaBytes of human data at moderate scale-up

11. Metabolomics On The Rise

12. How do you make sense of all that data?

13. Make data FAIR - Share them - Free and Open

14. •500 Million people in European Union •Full Genomes (soon for less than $1000 p. P.) •Urine/Blood Metabolome < 20 Euros per Patient

15. Large Scale Computing with Medical Metabolomics Data • EBI lead • H2020 • 3Years • 13 Partners • 8 Mio € • 830 PM • Kick-off 9/15 • H2020 e-infra

16. An e-infrastructure for Large Scale Computing with Medical Metabolomics Data

17. Why Research Infrastructures?

18. PhenoMeNal Objectives 1. Integrate existing open source tools, resources into a secure and sustainable e-Infrastructure

19. PhenoMeNal Objectives 2. Operate and consolidate the PhenoMeNal e- infrastructure based on existing internal and external HPC (High-performance computing) resources

20. PhenoMeNal Objectives 3. To improve and scale-up tools used within the infrastructure to cope with very large datasets 4.To establish technology for a water-tight audit trail

21. PhenoMeNal Objectives 5. To establish privacy-protection methods 6.To foster the worldwide adoption of PhenoMeNal 7. To develop a model to ensure sustainability of the PhenoMeNal network

22. Generic Cloudiﬁcation

23. Large Scale Computing with Medical Metabolomics Data

24.

25. Large Scale Computing with Medical Metabolomics Data

26. Networking Activities -EOSC As part of EOSC and GO FAIR, PhenoMeNal helps building a hub for verifying FAIR metabolomics data

27. Funding and Collaborators UK Research Councils (BBSRC, MRC) European Commission

28.

29. Slides on http://www.slideshare.net/csteinbeck

30. Metabolights-help@ebi.ac.uk Thank you!

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