Joined May 2015
- Tweets 250
- Following 43
- Followers 237
- Likes 235
6 Photos and videos
Omics Discovery retweeted
23 Sep 2020
what do you use for proteomics downstream analysis:
40%
Perseus
35%
Limma ( scripts)
26%
MSstats
167 votes • Final results
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Omics Discovery retweeted
20 Sep 2020
Moving forward with the idea of proteomics pipelines in the cloud, collaboration with @OpenMSTeam. Label-free pipelines in development using @nextflowio @nf_core @BioContainers @OpenMSTeam #MSstats #SDRFproteomics
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Omics Discovery retweeted
17 Aug 2020
Thanks to @JohnRYatesIII and @JProteomeRes for the invitation to publish a perspective on sample metadata in public repositories pubs.acs.org/doi/abs/10.1021… , Thanks to all @EuBIC_ms contributors. Since the publication, we have opened 10 new PRs in the repo github.com/bigbio/proteomics…
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Omics Discovery retweeted
11 Aug 2020
About half of #systemsbiology models fail to directly reproduce #simulation results! Over the past 3 years we investigated >450 models published in 152 journals & identified the root cause for the lack of #reproducibility. Read our #biorxiv_sysbio article doi.org/10.1101/2020.08.07.2…
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Omics Discovery retweeted
14 Jul 2020
Sample metadata in Proteomics repositories youtube.com/watch?v=ybueEagj… github.com/bigbio/proteomics… a project from @EuBIC_ms
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Omics Discovery retweeted
14 Jul 2020
While in genomics transciptomics everyone is in conda containers. In proteomics, we can't distribute the software without clicking a license page. New tool MutCombinator following the same style... I don't know how the field will move to large-scale data analysis.
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Omics Discovery retweeted
7 Jun 2020
The @BioContainers Registry is a light-metadata interface to quickly find the tool and the corresponding container (biocontainers.pro/#/registry). You can get info about NAME, Number of downloads, short description, License. What other information you would like to see?
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Omics Discovery retweeted
4 Jun 2020
For those that would like to know more about SDRF here the link to the @EuBIC_ms Hackathon eventbrite.co.uk/e/eubic-hac…
RT !!!! #ASMS2020 #proteomics @ProteomeXchange
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Omics Discovery retweeted
2 Jun 2020
You can register for the Hackathon next week on Sample metadata annotations hosted by @EuBIC_ms.
31 May 2020
Online Hackathon and Workshop about the sample to data file format (SDRF) in proteomics. @EuBIC_ms #HUPOPSI @pride_ebi @ExpressionAtlas eventbrite.co.uk/e/eubic-hac….
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Omics Discovery retweeted
2 Jun 2020
If you are wondering how to sample annotations will look like in Proteomics. Here an example of the first annotated submission in @pride_ebi with Sample annotations from @GygiLab ebi.ac.uk/pride/archive/proj… . All the annotations have been done based on SDRF (github.com/bigbio/proteomics…)
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Omics Discovery retweeted
31 May 2020
Online Hackathon and Workshop about the sample to data file format (SDRF) in proteomics. @EuBIC_ms #HUPOPSI @pride_ebi @ExpressionAtlas eventbrite.co.uk/e/eubic-hac….
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Omics Discovery retweeted
26 May 2020
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Omics Discovery retweeted
26 May 2020
Thanks to @EuBIC_ms the new SDRF file format for proteomics is really getting adopted. Multiple contributions from @EuBIC_ms members such as @mvaudel @OpenMSTeam @lgatt0 and Lev Levitsky, Johannes Griss github.com/bigbio/proteomics… . We hope more people get involved.
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Omics Discovery retweeted
23 May 2020
Should we make the experimental design based on the SDRF (sample to a data file format - github.com/bigbio/proteomics…) on each PRIDE submission:
53%
Optional
47%
Required
30 votes • Final results
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Omics Discovery retweeted
22 May 2020
Beta version of an Annotator of the SDRF is now deployed annotator.multiomics.info/ semantic auto-complete of ontology terms.
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Omics Discovery retweeted
22 May 2020
The specification is here (github.com/bigbio/proteomics…). If you have submitted a dataset to @pride_ebi help us to re-annotate them.
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Omics Discovery retweeted
22 May 2020
61 projects annotated using the SDRF specification (github.com/bigbio/proteomics…). TMT, SILAC, Label-Free, phospho-proteomics, protein-protein interactions experiments. A validator is now in place, every time a collaborator add a new experiment, the PR will be validate before merge.
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Omics Discovery retweeted
7 May 2020
Finally out: OmicsDI REST interface academic.oup.com/nar/advance…
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Omics Discovery retweeted
1 May 2020
What do you think is the next step for proteomics archives?
45%
Annotations of samples
14%
Automatic QC submissions
20%
support for quant outputs
20%
Creation spec libraries
44 votes • Final results
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Omics Discovery retweeted
23 Mar 2020
Great effort from @OpenMSTeam, @MuenchLab, and myself to annotated the SARS-Cov-2 submission Experimental design in SDRF github.com/bigbio/proteomics…
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