Dendron workspace sync

## Synced vaults:
- commons-dws-public

Dendron version: 0.124.0
Hostname: wifi-unifr-159-135.unifr.ch

vault/open-notebook.commons.pmallard.2024.02.20.md

@@ -2,7 +2,7 @@
 id: gyjosjmyok544holtu4m195
 title: '2024-02-20'
 desc: ''
-updated: 1708422450301
+updated: 1708426368507
 created: 1708421807416
 traitIds:
   - open-notebook-commons-pmallard
@@ -27,8 +27,79 @@ See [[viewpoint]]
 
 ## Doing
 
+### Training Pascal
 Dendron training with [[people.pascal-amrein]]
 
+Shared https://doi.org/10.5281/zenodo.8137605
+
+
+### MIBIG workshop
+
+MiBIG workshop 
+MIBIG started in 2015 
+https://mibig.secondarymetabolites.org/
+
+Apparently had some notes over there [[projects.commons-public.wikidata.mibig]]
+
+Interoperable with
+
+- npatlas
+- GNPS
+- Rhea
+
+Launching MiBIG 4.0 
+3 annotathon rounds
+
+Substantial contribution : actively participating in at least 2-hour annotathon sessions or equivalent (reviewing entries, writing)
+
+
+MiBIG organization team
+Coordinators
+Interest groups
+
+MIBIG 4.0 Data Standard
+
+- separate between biosynthesis vs. compound classification
+- use controlled vocabulary where possible
+- keep citations close to claims
+- keep related data points together
+- make parts of the schema reusable elsewhere 
+
+- More DB cross links (e.g. MITE db) https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2376-y
+
+[operon](https://en.wikipedia.org/wiki/Operon "In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splicing to create monocistronic mRNAs that are translated separately, i.e. several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are either expressed together or not at all. Several genes must be co-transcribed to define an operon.Originally, operons were thought to exist solely in prokaryotes \(which includes organelles like plastids that are derived from bacteria\), but their discovery in eukaryotes was shown in the early 1990s, and are considered to be rare. In general, expression of prokaryotic operons leads to the generation of polycistronic mRNAs, while eukaryotic operons lead to monocistronic mRNAs.
+Operons are also found in viruses such as bacteriophages. For example, T7 phages have two operons. The first operon codes for various products, including a special T7 RNA polymerase which can bind to and transcribe the second operon. The second operon includes a lysis gene meant to cause the host cell to burst.")
+
+
+MITE minimum information about a tailoring enzyme/maturase
+
+
+During this meeting, we will inform you about the scope and focus of the annotathons, some organizational improvements, and our upcoming MIBiG Online Submission system. We will also discuss the new roles of Coordinators and Reviewers in detail. Make sure to tune in!
+
+We also want to announce the dates of the annotathons. Please bear in mind that for co-authorship on the next MIBiG publication, participation in at least two 3-hour annotathon sessions (or an equivalent contribution) is necessary. The MIBiG annotathon dates are:
+
+    • March 19th 7 am – 10 pm and 4 pm – 7 pm (GMT)
+    • April 23rd 7 am – 10 pm and 4 pm – 7 pm (GMT)
+    • May 14th 7 am – 10 pm and 4 pm – 7 pm (GMT)
+
+Further, we want to make a call for contributions to our MIBiG Literature table (http://tinyurl.com/mibig-literature). In this table, we are collecting recent publications on biosynthetic gene cluster that are currently missing in the MIBiG database, but also publications that report additional information on already existing MIBiG entries. This collection of publications will be used as a starting point during the annotathons. If you have publications that you want to see covered during the annotathons, please feel free to add them to the table. We have prepared an explanatory document in case of any uncertainties (http://tinyurl.com/mibig-literature-explanation). 
+
+Colleagues who have indicated to be interested in acting as Coordinators or Reviewers will receive an additional email about these roles in the next few days.
+
+We are looking forward to welcome you at the Kickoff meetings!
+
+Kind regards, 
+
+Marnix Medema, Mitja Zdouc, and the MIBiG team
+
+
+They mention the https://www.contributor-covenant.org/
+
+
+
+
+
+
 ## Paused
 
 ## Done