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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 7h

Formula, has similar number of precursors but missing products. This work can improve new formula's of the future.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 7h

Some theories for the difference between formula and mothers milk. Further work to be done on this.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 7h

Problem might be the complete lack of dcSAM in the formula.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Next step was to compare commercial formulas for preterm infants. 17/20 of analytes is more present in real mothers milk (can be 22 to 49x for some metabolites). 3 are more present in formula.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Principal component analysis shows that mothers are very unique (QC samples is instead very well clustered). Mothers milk changes in response to the state of the infants. Validates theory on polyamide concentration differences.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Difference between mothers is significant as well, and have an unique signature of nutrients.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Violin plot shows that the measurements differ a 100,000 fold difference between n!,n12-DiAcSpm to Lysine.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Accuracy is good, moved to 20 human milk samples of mothers with pre-term children.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Solution: 20 measures and 20 standards covering the whole Polyamide synthesis pathway.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Q? how much Polyamine in breast-milk? Challenge: small, highly-polar, multiple charged.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Polyamines, are key for cell growth and proliferation and protein synthesis. For newborns and pre-term babies this must be supplemented in the diet.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

#SwissMetabolomics Decoding the Polyamine Signature of Human Breast Milk: A High-Coverage, Derivatization-Free LC–MS/MS Assay (by www.researchgate.net/profile/Tony-T…) is the second talk.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Another approach is correlative workflows, MRI work (7 tesla !) supporting and being supported by mass spec (Medical of University of Vienna). Number of patients is low due to specific disease requirements for this to work.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

With good standards, then mass-spec can evaluate both targeted and non-targeted.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

In tissue samples, injection of isotopic reference standards allow determining where signal is lost due to homogenisation or other experimental factors.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Then a few slides I don't have enough background knowledge on to describe ;( Key take home is for mass-spec reference libraries of chemicals with known properties is critical for the field. If missing they need to be imputed and that can give problems. This is a problem for tissue samples.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

#ESI (Electrospray Ionization) qualification work, depended on building on references and community standards work.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

New work on QC-Suites will improve the state of the art. 80 to 1000 -> chemical reference standard values. (NIST work)

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Presents a tool pubs.acs.org/doi/10.1021/acs.analch…. And talks about the importance of standard reference materials. Problem is that some reference materials are getting rare.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

13C labelled yeast as a source for quantitative library is new, improving on the use case of bench-marking..

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

Prof. Koellensperger's team worked on isotopically large volume enriched biomass (yeast). This plus external and internal standards allows quantification.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 8h

In lipidomics, there are a great set of standard sets of isotopically labeled lipids. This is not true (yet) for the wider metabolimics mass-spec work.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 9h

swiss-metabolomics.ch annual meeting started today. First keynote is by Prof. Koellensperger. Mentions that there is a decrease in target work. More non-targeted work, improving chemical scope less quantification.

swiss-metabolomics.ch

swiss-metabolomics.ch |

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Reposted by Jerven Bolleman

Geoff Hutchison @geoffhutchison.net · 16/10/2026

I'm going to follow up.. #chemsky How do we make chemical structures (either 2D or 3D), reactions accessible to alt-text and screen readers, etc. Do I turn it into a name "this diagram indicates caffeine or 1,3,7-trimethylxanthine" I'd really welcome thoughts and discussion...

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Reposted by Jerven Bolleman

#!/usr/bin/env rm -f @lofty.fieldprogrammable.gay.ap.brid.gy · 25/12/2025

The two hardest problems in Computer Science are: 1. Getting up in the morning 2. Going to bed at a reasonable time

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 02/10/2026

This is also a reminder to support your local fedi instance, don't be a total leach.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 02/10/2026

So the content is from previous talks, tutorials and even some e-mails. The bling is claude and llm derived.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 02/10/2026

Do you want to know how to get more (or anything) out of the #uniprot #kg? I had claude gather my training materials and present it on the web in a way that is easier to engage with. Would you like to have a look? sib-swiss.github.io/sparql-training

sib-swiss.github.io

SPARQL training · SIB SPARQL training

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 02/10/2026

I have migrated from @akademienl , which was a wonderful instance but unfortunately and understandably shutting down. I hope to share here on genomics.social some of the work I do with #uniprot #rhea and #swisslipids. Specifically around keeping that data #FAIR and useable. I am most vocal […]

genomic.social

Original post on genomic.social

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Reposted by Jerven Bolleman

BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 18/09/2026

"Building InterMine databases from RDF Portal" doi.org/10.37044/osf.io/dqm3j_v1 #biohackathon #rdf #intermine #BH26JP "The public HumanMine has not had a data release since February 2022. RDF Portal, operated by the Database Division for Life […] [Original post on fediscience.org]

Figure 1:How a mine gets its data. (a) Today each HumanMine source has its own loader, written and maintained as code by the mine’s developers. (b) With RDF Portal and rdfc2im, the work for each dataset moves upstream: RDF Portal holds each dataset’s RDF and an rdf-config model written in rdf-config’s common form, made once and reused by every consumer. rdfc2im is one tool for all sources, and what remains for each source is a curated mapping, kept as data with the evidence for every row. Tags show scope (per source, per dataset, shared, reused), effort (manual, automatic) and form (code, template, data).

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Reposted by Jerven Bolleman

Marloes de Koning :check: @marloesdekoning.nrc.social.ap.brid.gy · 18/09/2026

Deze video van de Noorse consumentenbond over #enshittification kennen jullie vast al, maar voor mij was hij nieuw en ik moet lachen. vimeo.com/1168468796 Digital products and services keep getting worse. In the new report Breaking Free: Pathways to a fair technological future, the […]

mastodon.nl

Original post on mastodon.nl

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Reposted by Jerven Bolleman

Kingsley Uyi Idehen @kidehen.mastodon.social.ap.brid.gy · 18/09/2026

RE: mastodon.social/@openlink/117288641… Open protocols beat proprietary plumbing. In the age of AI, that advantage compounds: LLMs are trained on those protocols, so the Agents they power become powerful generic clients you drive in natural language.

mastodon.social

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 15/09/2026

@EvoMRI Looking forward to seeing you soon! I am almost there, small delay in the journey to the conference.

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Reposted by Jerven Bolleman

jonny (nonvenomous) @jonny.neuromatch.social.ap.brid.gy · 08/09/2026

OpenAI claims that they used 300 billion output tokens from a swarm of ~10,000 concurrent instances of an internal model that is almost certainly larger and more expensive to run than GPT-6. That's the total token output, including exploring related problems, which, along with spying on other […]

neuromatch.social

Original post on neuromatch.social

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Reposted by Jerven Bolleman

jonny (nonvenomous) @jonny.neuromatch.social.ap.brid.gy · 08/09/2026

> The route to the Clay problem through a smooth force, options c and d in Fefferman’s statement of the problem, is the route Luis and Diego opened and the one Levent and I had quietly chosen to attack. Almost nobody else I know of was working on it. It is not the direction one arrives at in a […]

neuromatch.social

Original post on neuromatch.social

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Reposted by Jerven Bolleman

Charles Tapley Hoyt @cthoyt.scholar.social.ap.brid.gy · 04/09/2026

blogged today about ChEBI, data properties in OWL ontologies, computational chemistry, atomic numbers, and basis sets cthoyt.com/2026/09/04/chebi-atomic-… all part of @NFDI4Chem #obo #owl #chebi #obofoundry #nfdi #nfdi4chem

A diagram showing how ontology inference could be used to connect molecules and applicable basis sets for computational chemistry experiments

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Reposted by Jerven Bolleman

Bert Hubert NL 🇺🇦🇪🇺🇺🇦 @bert-hubert.mastodon.nl.ap.brid.gy · 01/09/2026

RE: social.overheid.nl/@rivm/1171945711… Met dit vaccin zijn we hard op weg baarmoederhalskanker uit te roeien. Het is een wetenschappelijk hoogstandje en wordt aanbevolen voor jongens en meisjes. En het voorkomt ONVOOSTELBAAR VEEL LEED. Ik kan kippenvel krijgen van wat dit […]

mastodon.nl

Original post on mastodon.nl

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Reposted by Jerven Bolleman

Anthony Horton @spacelizard.aus.social.ap.brid.gy · 01/09/2026

Microsoft: Use the web versions of our Office apps! They're great! Me: So how do I create a new document based on my employer's .dotx template? Microsoft: Oh, that's easy, you download it from SharePoint to your computer, use the desktop version of Word to create a new document from the […]

aus.social

Original post on aus.social

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Reposted by Jerven Bolleman

Dr. Serge Zaka @sergezaka.bsky.social · 31/08/2026

Si l’on compare 2026, 2022, 2003 et 1976 en termes d’intensité maximale de la sécheresse (c’est-à-dire le niveau minimal d’eau disponible pour les plantes atteint au cours de l’année) il n’y a pas photo : 2026 se démarque très largement des autres années (première carte). 9/10

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

@SIB Cat-VRS is a way to encode category of variants (think deffining an owl supper class for a set of variants, but in python dataclasses)

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

@SIB Starting from a variant we need to go to a computable identity (VRS). then we need to make it linkable so we go to Cat-VRS, then find patients with the variant(Beacon) and then analyze it in a TRE(trusted research environment) TES

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

@SIB #GA4GH tries to develop standards to link all genomic data. Some standards are VRS->Cat-VRS->Beacon->Tes.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

@SIB "interoperability is a series of hand-offs, not a single standard" -> across transfers the following must be consistent "identity of variant, semantics, query intent, access rights, provenance"

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

@SIB Problem remains: different formats, precision, representation, access environments.

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