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Functional Metabolomics Lab
Приєднався 23 чер 2021
VMOL Seminar #25 - GNPS2 en Español: Feature-based Molecular Networking (Daniela Herrera Rosero)
Seminar Shared Folder: drive.google.com/drive/folders/1J8Open78G0aUGaXpzcUadRFq9mDelC10
Seminar Program: docs.google.com/document/d/1ZIsOKB6BivM9GOQuQvfWoiuVJWYefuAz0y0iTi_u_uk/edit?usp=sharing
Signup link: docs.google.com/forms/d/e/1FAIpQLSfmmtDk5KH6C0L0dPT3IzNDqMUwgDnuUbJ4b0nIRdmOOKneTw/viewform?usp=sf_link
Seminar Program: docs.google.com/document/d/1ZIsOKB6BivM9GOQuQvfWoiuVJWYefuAz0y0iTi_u_uk/edit?usp=sharing
Signup link: docs.google.com/forms/d/e/1FAIpQLSfmmtDk5KH6C0L0dPT3IzNDqMUwgDnuUbJ4b0nIRdmOOKneTw/viewform?usp=sf_link
Переглядів: 93
Відео
VMOL Seminar #24 - GNPS2 en Español: Classical Molecular Networking (Mauricio Caraballo)
Переглядів 16519 годин тому
Seminar Shared Folder: drive.google.com/drive/folders/1J8Open78G0aUGaXpzcUadRFq9mDelC10 Seminar Program: docs.google.com/document/d/1ZIsOKB6BivM9GOQuQvfWoiuVJWYefuAz0y0iTi_u_uk/edit?usp=sharing Signup link: docs.google.com/forms/d/e/1FAIpQLSfmmtDk5KH6C0L0dPT3IzNDqMUwgDnuUbJ4b0nIRdmOOKneTw/viewform?usp=sf_link
VMOL Seminar #23 - GNPS2 em Português: MASST (Paulo Wender Gomez)
Переглядів 17114 днів тому
Links: drive.google.com/drive/folders/1FcGXRcgVRnye0qCVlJWZXZ00X3oswqLh fasst.gnps2.org/fastsearch/ gnps2.org/status?task=1d11e5e9487c42b582634ce6901e99bc USI: mzspec:GNPS2:TASK-1d11e5e9487c42b582634ce6901e99bc-nf_output/clustering/spectra_reformatted.mgf:scan:3377 masst.gnps2.org/foodmasst2/ masst.gnps2.org/microbemasst/ Plantmasst: masst.gnps2.org/plantmasst/ mzspec:GNPS2:TASK-1d11e5e9487c42b...
VMOL Seminar #22 - GNPS2 em Português: FBMN-STATS (Fernanda Anselmo Moreira)
Переглядів 20621 день тому
Links: drive.google.com/drive/folders/1qCp4C_4fIQn0rVXzISZPi7XTwNo_bihr?usp=sharing Massive ID: MSV000082312 www.functional-metabolomics.com/resources fbmn-statsguide.gnps2.org/ gnps2.org/status?task=1d11e5e9487c42b582634ce6901e99bc Task ID: 1d11e5e9487c42b582634ce6901e99bc Seminar Program: docs.google.com/document/d/1ZIsOKB6BivM9GOQuQvfWoiuVJWYefuAz0y0iTi_u_uk/edit?usp=sharing Signup link: doc...
VMOL Seminar #21 - GNPS2 em Português: FBMN (Paolo Stincone)
Переглядів 43428 днів тому
Links: drive.google.com/drive/folders/123xh_wMwjN22HpLmVcucG34ldQA4no8c?usp=sharing Massive ID: MSV000082312 gnps2.org/status?task=1d11e5e9487c42b582634ce6901e99bc Seminar Program: docs.google.com/document/d/1ZIsOKB6BivM9GOQuQvfWoiuVJWYefuAz0y0iTi_u_uk/edit?usp=sharing Signup link: docs.google.com/forms/d/e/1FAIpQLSfmmtDk5KH6C0L0dPT3IzNDqMUwgDnuUbJ4b0nIRdmOOKneTw/viewform?usp=sf_link
VMOL Seminar #20 - GNPS2 em Português: Molecular Networks Clássico (Helena Mannochio Russo)
Переглядів 680Місяць тому
Links: drive.google.com/drive/folders/1Gwe7GlXr6i67cWR7X_rWmLfP1vG1fQs7?usp=sharing Massive ID: MSV000082312 gnps2.org/status?task=37c833ba726643909c221bacc8e850e5 Seminar Program: docs.google.com/document/d/1ZIsOKB6BivM9GOQuQvfWoiuVJWYefuAz0y0iTi_u_uk/edit?usp=sharing Signup link: docs.google.com/forms/d/e/1FAIpQLSfmmtDk5KH6C0L0dPT3IzNDqMUwgDnuUbJ4b0nIRdmOOKneTw/viewform?usp=sf_link
VMOL Seminar #19 - GNPS2: High-Throughput ModiFinder (Reza Shahneh)
Переглядів 130Місяць тому
Seminar Program: docs.google.com/document/d/1ZIsOKB6BivM9GOQuQvfWoiuVJWYefuAz0y0iTi_u_uk/edit?usp=sharing Signup link: docs.google.com/forms/d/e/1FAIpQLSfmmtDk5KH6C0L0dPT3IzNDqMUwgDnuUbJ4b0nIRdmOOKneTw/viewform?usp=sf_link
VMOL Seminar #18 - GNPS2: ChemWalker (Ricardo Da Silva)
Переглядів 3102 місяці тому
Seminar Program: docs.google.com/document/d/1ZIsOKB6BivM9GOQuQvfWoiuVJWYefuAz0y0iTi_u_uk/edit?usp=sharing Signup link: docs.google.com/forms/d/e/1FAIpQLSfmmtDk5KH6C0L0dPT3IzNDqMUwgDnuUbJ4b0nIRdmOOKneTw/viewform?usp=sf_link
Microspot Reader Tutorial (Simon Knoblauch)
Переглядів 722 місяці тому
Microspot Reader Tutorial (Simon Knoblauch)
VMOL Seminar #17 - GNPS2: LLMs in GNPS2 (Mingxun Wang)
Переглядів 2552 місяці тому
Links for hands-on example: massql-analysis.gnps2.org/ documentationai.gnps2.org/GNPS2_Chatbot Seminar Program: docs.google.com/document/d/1ZIsOKB6BivM9GOQuQvfWoiuVJWYefuAz0y0iTi_u_uk/edit?usp=sharing Signup link: docs.google.com/forms/d/e/1FAIpQLSfmmtDk5KH6C0L0dPT3IzNDqMUwgDnuUbJ4b0nIRdmOOKneTw/viewform?usp=sf_link
UCR MS Symposium: Microbiome clears Ameliorates Hepatic Steatosis (Sunhee Jung)
Переглядів 593 місяці тому
www.cs.ucr.edu/~mingxunw/symposium/
UCR MS Symposium: Probing Lipid Binding to Membrane Proteins (Michael Marty)
Переглядів 473 місяці тому
www.cs.ucr.edu/~mingxunw/symposium/
UCR MS Symposium 2024: Ocean Metaproteomics (Noelle Held)
Переглядів 453 місяці тому
www.cs.ucr.edu/~mingxunw/symposium/
UCR MS Symposium: Finding Metal-Binding Molecules (Allegra Aron)
Переглядів 583 місяці тому
www.cs.ucr.edu/~mingxunw/symposium/
UCR MS Symposium: Discovery of Polybrominated Enamides (Vikram Shende)
Переглядів 1223 місяці тому
UCR MS Symposium: Discovery of Polybrominated Enamides (Vikram Shende)
UCR MS Symposium: Learning from Repository-Scale Metabolomics Data (Wout Bittremieux)
Переглядів 513 місяці тому
UCR MS Symposium: Learning from Repository-Scale Metabolomics Data (Wout Bittremieux)
UCR MS Symposium: Evolutionary Origin of Stereodivergent Glycoalkaloids (Adam Jozwiak)
Переглядів 633 місяці тому
UCR MS Symposium: Evolutionary Origin of Stereodivergent Glycoalkaloids (Adam Jozwiak)
VMOL Seminar #16 - GNPS2: CMMC Knowledge-base and Enrichment Analysis (Helena Mannochio Russo)
Переглядів 2283 місяці тому
VMOL Seminar #16 - GNPS2: CMMC Knowledge-base and Enrichment Analysis (Helena Mannochio Russo)
VMOL Seminar #15 - GNPS2: Transitive Alignments (Xianghu Wang)
Переглядів 1604 місяці тому
VMOL Seminar #15 - GNPS2: Transitive Alignments (Xianghu Wang)
VMOL Seminar #14 - GNPS2: Modifinder (Reza Shahneh)
Переглядів 3104 місяці тому
VMOL Seminar #14 - GNPS2: Modifinder (Reza Shahneh)
VMOL Seminar #13 - GNPS2: Feature-Based Molecular Networking (Giovanni Vitale)
Переглядів 6795 місяців тому
VMOL Seminar #13 - GNPS2: Feature-Based Molecular Networking (Giovanni Vitale)
VMOL Seminar #12 - GNPS2: Intro and Classic Molecular Networking (Mingxun Wang)
Переглядів 6735 місяців тому
VMOL Seminar #12 - GNPS2: Intro and Classic Molecular Networking (Mingxun Wang)
Eco-Metabolomics Workshop 2024 - Day 4 Session 19 - STATS and Network Integration (Daniel Petras)
Переглядів 2035 місяців тому
Eco-Metabolomics Workshop 2024 - Day 4 Session 19 - STATS and Network Integration (Daniel Petras)
Eco-Metabolomics Workshop 2024 - Day 4 Session 18 - FBMN STATS II (Abzer Shah)
Переглядів 1895 місяців тому
Eco-Metabolomics Workshop 2024 - Day 4 Session 18 - FBMN STATS II (Abzer Shah)
Eco-Metabolomics Workshop 2024 - Day 4 Session 17 - FBMN STATS (Abzer Shah)
Переглядів 2465 місяців тому
Eco-Metabolomics Workshop 2024 - Day 4 Session 17 - FBMN STATS (Abzer Shah)
Eco-Metabolomics Workshop 2024 - Day 4 Session 16 - STATS II (Jos Hageman)
Переглядів 2165 місяців тому
Eco-Metabolomics Workshop 2024 - Day 4 Session 16 - STATS II (Jos Hageman)
Eco-Metabolomics Workshop 2024 - Day 3 Session 15 - Community-Scale Metabolomics Tools (Ming Wang)
Переглядів 2585 місяців тому
Eco-Metabolomics Workshop 2024 - Day 3 Session 15 - Community-Scale Metabolomics Tools (Ming Wang)
Eco-Metabolomics Workshop 2024 - Day 3 Session 13 - Cytoscape Hands-On (Daniel Petras)
Переглядів 3815 місяців тому
Eco-Metabolomics Workshop 2024 - Day 3 Session 13 - Cytoscape Hands-On (Daniel Petras)
Eco-Metabolomics Workshop 2024 - Day 3 Session 12 - SIRIUS Hands-On (Marcus Ludwig)
Переглядів 5655 місяців тому
Eco-Metabolomics Workshop 2024 - Day 3 Session 12 - SIRIUS Hands-On (Marcus Ludwig)
Please, can I have the English version? Thank you for this.
ua-cam.com/video/q_1xfz31fqo/v-deo.html
Great presentation
Hola, ¿es posible que aborden el tema sobre como preparar los archivos de metadata con el ReDU template?. gracias
Hall Jason Lewis Angela Brown Richard
Anderson Angela Thompson Amy Hall Sharon
Gracias por compartir esto en español!!!
Excelente !!! Gratidão.
Excelente !! Muito obrigado por esse video <3
Great talk Reza!👏
can you provide me sample file link
Olá. Por onde entro em contato para pedir o token? Preenchi o formulário mas não recebi
I Analyses my results lcms by mzmine3 after watching your vedios but I have problem at the finaly step all tables of ion identify and fragments and spectral are empty !!! Whyyyy !!!!😢
best if you post an issue in the MZmine Github and provide example mzml. and batch files. With the information you provided its hard to diagnose the issue.
How do I get compound class annotations from Sirius integrated into my GNPS network? I can see the class annotations in the exported TSV summary file but I can't see which column to make the key column, if thats the way you do it?
Hi Captain Wheelbarrow, I assume you mean the CANOPUS class annotations (from "canopus_compound_summary.tsv")? There should be a column with the scan/feature number ("featureId") in the last column this must be selected as the key.
@@functionalmetabolomics Thanks!
Hello, I am a web developer in Korea.I want to use it in the spring framework, but it's hard to find the document, so I'm commenting like this. I have about 5 mzML files locally and I want to analyze the similarity with the mzML files coming in from outside.
hello I use mzmine3 but i have problem he takes a long time to process and don't answer ...any help
SO interesting
Hello, I recently completed metabolomic analyses of a plant species and received an Excel list with the following columns regarding the metabolomic clusters: Size, Charge, Mass, m/z, RT, Base Peak, m/z Width, RT Height, m/z Min, m/z Max, RT Min, RT Max, Shape Distance. Based on this information in Excel, can I identify the metabolites using your software? I really need help with the metabolite identification step. Thank you in advance.
no. for molecular networking and spectrum library search you need MS/MS spectra.
sir, for the raw data files can we upload in .raw format? or we have to covert to MzML?
I have problem when l select "create batch" this message appears " parent directory not set or does not exist " 😢 any help please
Make sure to great the folder before and then select the file path correctly
@functionalmetabolomics I'm try that ...but I have the same problem 🥺🥺🥺 How I can contact you ?
@@Gladiolus-sl5dq best if you write an issue in the MZmine github then✌
Hi, Will GNPS1 continue to be available, or will GNPS2 be the only option in the future?. Thank you.
Any one can u help me...After I select OK in processing wizard a window appears in which says " parent directory not set or does not exist"
Hi Sinalau, best if you email Robin, and ask him directly.
day 8 of asking if you can share the slide
where can i get sample raw file ?
sir can i have ur email?
Thanks for this informative video. How we can export the data from sirius to the word file, e.g., molecular formula, smiles, sirius score, etc.?
sir, could you share the slide?
Hi sir, can i have the metadata template?
Bonjour, ou peut on trouver le fichier de données que vous utilisez ? Très bonne video et tutorial Merci beaucoup
Thanks! And you can find the data here: massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=8a8139d9248b43e0b0fda17495387756 (FTP link: ftp://massive.ucsd.edu/v01/MSV000082312/)
Sir, i want to create an account for GNPS2 but there no WAY i can get the token? So for people who watch your video from youtube cant register GNPS 2? this is very annoying i must say. Please share the invITE TOKEN.
Sorry Sinalau, it is still a closed beta. To get a token check here: wang-bioinformatics-lab.github.io/GNPS2_Documentation/accounts/
Looks cool! Just wondering when you evaluate the networking to see if similar structures are clustered correctly are you using data from pure chemical standards you ran yourself or are you relying on spectral library matches to tell you what the structure is?
Thanks Daniel for recording and making available these talks. Very neat and useful!
Can I ask how can I get a GNPS2 invite token? Thank you and look forward to your reply.
wang-bioinformatics-lab.github.io/GNPS2_Documentation/accounts/ (shoot Ming or us an email)
Very helpful! Thank you Dr. Steffen!
Cuando se obtiene un análisis con metodo de adquisición DDA, se supone que la fragmentación de los iones queda restringida a una intensidad de los iones precursores fija, por lo anterior, ¿Porqué no se utiliza este valor como intensidad mínima en los parámetros para filtrar el ruido en el software Mzmine?
Muchas gracias. Una idea bien interesante! Quieres decir que el MS1 signal threshold deberia ser el minimum value de los MS2 precursors del survey scan anterior 🤔
@@functionalmetabolomics Sí, ya que ese el el limite con el cual el equipo inicia a fragmentar los iones precursores. Gracias por la respuesta
@@LAGL-1 muy buena idea. Si quieres, mandarnos un email y podemos hablar mas en detalle
After I select "show raw data summary" I am unable to see MS scatter plot (@ 32:00 mins) !!!
Amazing lecture, thanks for sharing us!
Thank you very much for sharing the informative workshop videos.. they are excellent
I could not log ın to the gnps2. I think we need an invite token. Could you provide us an invite token to log in.
Hi Onur. Yes, it is still a closed beta at the moment, but you can get a token from Ming: wang-bioinformatics-lab.github.io/GNPS2_Documentation/accounts/
Awesome Presentation, this was exactly what I needed to see right now.
Do you have an opportunity to tell, will you combine single-cell metabolomics with some of the other omics technologies? And what is the actual future of such technology because, as you mentioned, metabolomic picture constantly changes in the cell? Thank you in advance for the answer.
I have followed your guidance to try molnetenhancer. However, the cluster did not change to different compound classes and they are the same color from both online GNPS and download files. Could you tell me how can I solve the problem? Thank you very much for your help!
hello sir, can i have the slide?
Hey there Daniel! I was wondering whether it would be possible for you to share the very nice slides of this presentation to the public or not really? :) Thanks by advance, and super great lecture as always!
Yes, indeed the audio is of bad quality. Can you do something about it? Thank you!
Hi Stefani, sorry for the bad sound on this one, but we had technical troubles with the recording of the first session. There is little we can do about it, but the rest of the videos from the summer schools and seminars should have better sound quality.
@@functionalmetabolomics Great! Thank you for the reply! :)
Thanks for the quick explanation! But it seems that a crucial step has been forgotten, that is, how to standardize?
Thank you, this package helped me a lot. 06:43 -> Spectrum Similarity 11:25 -> Molecular Networking 16:15 -> Basics of MatchMS python package 25:30 -> Introduction to Jupyter Notebook 48:00 -> Matchms in Jupyter Notebook
sir, in my MS/MS scatter plot, only one single line is coming...what is the reason?
thx, great content !
How can process data to apply machine learning?