add minutes

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.Rproj

README.md

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 # testingGIN
 
-in this repo I will make test and see what one can do.
+In this repo I will make test and see what one can do.
+I will also post my minutes and use it as a main page for organising my work (link to github project page with issues)
 
-# Using with Rstudio
+
+# tests
+## Using with Rstudio
 
 possible via ssh.

minutes/2019-04-09-larkum

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+TODO
+====
+
+- slack (#labreport) integration with other workflow, getting version control + doi in the end ?
+
+- check about server (why what)
+- survey larkum lab/sfb
+- test Rspace?
+
+
+talk with Larkum
+==========================
+
+Long discussion to set up the project aims, good coffee. 
+
+Open data difficult at the end (current problem with elife paper).
+
+
+Timetable: june 2011: next grant sent, we need 1-2 publications by then, with something working at the SFB level. Writing will last about 6 months.
+
+Work with the journal clubs, some figures already on slack. How to work from there? Getting people realise they should put more data, otherwise it is not usable.
+
+Big hopes for the project.
+

minutes/2019-04-09-sourcedata

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+TODO
+====
+
+- learn about texture
+- prepare meeting may
+- work with other tools (gin, hubox,...)?
+
+
+talk with Thomas Lemberger
+==========================
+
+Goals
+-----
+
+Initial (ultimate) goal was to link figures with data, early in the scientific process.
+
+To achieve this goal, the idea was to make some reasonable data curation step, that would be a continous curation, i.e.:
+
+- cost effective, at embo below 10% of costs
+- level of the figure: add some structured metadata to each figure
+- aimed at molecular and cellular biology, expandable ??
+
+How it works?
+------------
+
+- entities are found (text data mining)
+- entity type defined (7-8 possibilities)
+- entity role defined (test or control)
+- link to ontologies
+
+
+Achievement:
+-----------
+
+- 30 000 papers curated
+- test and control conditions tagged differently
+
+Future:
+-------
+
+- collaboration with texture: http://substance.io/texture/
+    - produces jats formats
+    - creation of sourcedata metadata before publication
+- need to restrict ontologies used at the lab level (choose form a small list?)
+- data kept outside sourcedata (link to it)
+- demo should be ready in May
+
+
+Julien's 2 cent
+--------------
+
+- use the material list as source of information to ease the link to ontologies (RRID to gene names for example)
+- need a search engine which makes sense and which starts with more information than a keyword. From what people published, and other info (protocol used, material in stock,...) one could build a context to search data/figures that make more sense. This could be discussed with Peter Kraker: https://www.go-fair.org/implementation-networks/overview/discovery/
+
+Other discussion
+----------------
+
+- convince people by stating what they would need from other researchers
+- Thomas to be in Berlin on May the 8th
+- external dvt, few people
+- ideas for extra funding ?!
+- RDA very abstract, Force11 very idealists
+- develop bioschemas.org
+
+