[GNPS] major update of In Silico Tools content

[alexeigurevich]

Hi Ming @mwang87 ! I, @lfnothias, and @hoseinmohimani have several requests & suggestions about updating In Silico Tools webpage. Some requests are related to existing issues, I tried to combine everything together and link the related existing issues.

1. RiPPquest pipeline was significantly improved and redesigned. Now we would like to rename it to "MetaMiner" to be consistent with the recent Cao et al, 2019 publication. Louis and Mauricio made a first draft of the new workflow documentation which will be pushed to the GNPSdocumentation repo. After that, I will add the link to it right to the workflow page (currently it has a link to the documentation of the command-line tool). The related issues are https://github.com/CCMS-UCSD/GNPS_Workflows/issues/228 and https://github.com/CCMS-UCSD/GNPS_Workflows/issues/164

Action item №1 Replace the current RiPPquest description with the following: Title: MetaMiner: a Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products Abstract: MetaMiner is a metabologenomic pipeline that integrates metabolomic (tandem mass spectra) and genomic data to identify novel Ribosomally synthesized and Post-translationally modified Peptides (RiPPs). MetaMiner is compatible with large-scale screening platforms for natural product discovery, supports search with Blind Modifications, and is able to identify RiPPs of various classes including cyanobactins, glycocins, lantibiotics, lassopeptides, linaridins, proteusin etc. It is available [here](https://gnps.ucsd.edu/ProteoSAFe/index.jsp?params=%7B%22workflow%22:%22METAMINER%22%7D). Citations: MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cao et al. Cell Systems. 2019 Oct 16. Automated genome mining of ribosomal peptide natural products. Mohimani et al. ACS Chem Biol. 2014 Jul 18;9(7):1545-51.

Action item №2 Rename RIPPQUEST pipeline into METAMINER on the backend side and increase its memory limit (see the separate email with details).

2. CycloNovo pipeline was improved, well tested and the corresponding paper accepted to Cell Systems (will be out in mid-December). It seems that it is time to add it to the In Silico Tools list. Bahar @bbehsaz and I will work on the documentation, which will be linked from the workflow main page. The related issue is https://github.com/CCMS-UCSD/GNPS_Workflows/issues/229.

Action item №3 Add link and the following description of CycloNovo to the In Silico Tools page: Title: CycloNovo pipeline: Automated De novo cyclopeptide analysis and sequencing of large metabolomics dataset Abstract: Given a tandem mass spectrometry dataset, CycloNovo first finds the spectra that represent cyclopeptides in the sample without any prior knowledge of them. It then tries to find the amino acid sequence of those cyclopeptides (referred to as de novo cyclopeptide sequencing). This workflow is currently in beta development stages so any feedback is welcome to improve analysis and usability. It is available [here](https://gnps.ucsd.edu/ProteoSAFe/index.jsp?params=%7B%22workflow%22:%22CYCLONOVO%22%7D). Citation: De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Behsaz et al. Cell Systems. 2019 Dec 18.

3. Dereplicator pipeline seems to be mature enough to be moved from just In Silico Tools to the list of Advanced Analysis Tools on the main GNPS page. The related issue is https://github.com/CCMS-UCSD/GNPS_Workflows/issues/140.

Action item №4 Create Dereplicator panel in the top left corner of Advanced Analysis Tools and fill it with the following: Title: Dereplicator (just capitalized, not with the only uppercase letters!) Text: In Silico High-Throughput Dereplication and Variable Dereplication (split into two lines between Throughput and Dereplication) Analyze button: https://gnps.ucsd.edu/ProteoSAFe/index.jsp?params=%7B%22workflow%22:%22DEREPLICATOR%22%7D Documentation button: https://ccms-ucsd.github.io/GNPSDocumentation/dereplicator/ (note that there is an inconsistency of this button name (Documentation vs Help) for different tools inside Advanced Analysis Tools)

4. The current text about the In Silico Tools on the main GNPS page is a bit confusing ("Analyze Tools with in silico tools"). We have a suggestion for its improvement:

Action item №5 Modify the description of the In Silico Tools to the following and also move it to the bottom right corner of Advanced Analysis Tools:

Title: In Silico Tools (i.e. keep the current name despite a recent suggestion on renaming to "Advanced In Silico Tools" in #140 -- I feel it is clear that they are advanced since they are a subsection of "Advanced Analysis Tools") Text: Analyze MS/MS Spectra with Bioinformatics Methods (split into two lines between "Spectra" and "with")

Action item №6 Made minor fixes on the actual In Silico Tools page: Rename the title to: GNPS Theoretical/In Silico Tools (Insilico should be written in two words and there are no Libraries on the page despite it is written in the current title) Update Dereplicator+ citation to: Dereplication of microbial metabolites through database search of mass spectra. Mohimani et al. Nat Commun 9, 4035 (2018)

Let me know if you have any questions/suggestions/issues! Thanks

[alexeigurevich]

Hi Ming @mwang87! The CycloNovo paper was published online today, so it probably makes sense to implement at least item №3 asap. Note: I've just updated the citation accordingly in the action item №3 description above and in the GNPS workflow, too.

Please let me know If I can help with this and other updates in the issue somehow. E.g. if there is a way to create a pull request with the new In Silico Tools webpage content, I can do it and you would need just to accept it :)

[lfnothias]

Reminding here that we still don't have a documentation about using CycloNovo on GNPS. The issue and expected commit from @bbehsaz has been pending for a several months. https://github.com/CCMS-UCSD/GNPS_Workflows/issues/229

I think we need a proper documentation and feedback for CycloNovo before taking the workflow to the GNPS splash page. Beside myself, no one in the lab has been testing it (due to the lack of documentation and link available), so we can expect issues to be revealed, like this one also from several months https://github.com/bbehsaz/cyclonovo/issues/1

[mwang87]

@alexeigurevich We are aiming to have this implemented in the next week. Do you have any updates for CycloNovo Documentation?

Ming

[alexeigurevich]

This is great news! @bbehsaz could you please update us about the status of CycloNovo documentation?

[mwang87]

@alexeigurevich Apologies for delay on the main GNPS page. We're held up on some bugs from the MassIVE teams' side before we can deploy proteosafe. Do you know if there are any updates with regards to documentation for CycloNovo?