HACC: "Hacking Ecology"
35c3 meetup @Day 3 @17:00
original note-taking: pau + ~10 people
20200822 touch <dcht00
Table of Contents
This is the collaborative pad to write down notes from the meeting:
Read Version of this Document:
This group can become a subgroup of Hackers Against Climate Change (HACC).
IF YOU WANT TO JOIN SEE COMING MEETUP INFO:
<--------------------------------------------------------------- please add yourself and your field here:
- Manuel (Bioinformatician, OMICS pipelines and data analysis), m.koes17 at google mail
- Stephan (Physicist, Data Scientist), reach me via the mailing list, https://twitter.com/@data_raccoon
- Andreas/beneroth: database programmer, contact via mailing list
- Niels, (creating datasets from digital sources) , contact via mailing list
- Rainer (Physics, Neuroscience), knowledge on Dynamical Systems, mathematical modelling of biological systems , contact via mailing list
- Andi, available on mailing list, knowledge on electricity generation & transmission, focus on wind energy & grid integration
- Micha (Physicist, Data Engineer), experience with data pipelines, some machine learning, infrastructure and clusters (e.g. spark cluster)
- Sandro (computer science)
- Thorsten (thho) Geographer, spatial data, satellite remote sensing, datascience
- Rene, web/frontend developer, permaculture enthusiast
- Steffen (Physicist, Data Scientist) https://twitter.com/sroecker
- Pau (hackbase & CHT collaborator) firstname.lastname@example.org
- Emilien (research and HCI, art, collaborative and trandisciplinary work) email@example.com
- Merlin (ecology & modelling) merlin@wandertiere.
- David (physics, ecology & behavioral science), can do machine learning stuff well, work on stability of ecological networks and agent modeling (behaviors of bees) firstname.lastname@example.org
- Anna, some little knowledge in maths/computer science
- Felix (enos), Geographics (airborne & sat. remote sensing soil and forest), Soziology, see ya on the maillist
- Lukas (Physics, Population Genetics), email@example.com
- Veck (DevOps basically everything to do with computer automation) https://twitter.com/futuroerahoy
- Theo (Bioinformatics: Microbial Lake Ecology using machine learning), https://twitter.com/TSperlea
- Constantin (water science b.sc., biochemistry student), on mailinglist, contact: constantin.soffner -at- posteo dot de
- Henning (ridoo) Geoinformatics, via ML, contact: h.bredel at gmx dot de
- Fnark (computer science, ride sharing) firstname.lastname@example.org
- Nana (dynamic modeling, PhD on resilience/climate adaptation/economic transformation/landuse conflicts/food security, am in hacker and environmental realm since 90s)
- Fump (@email@example.com, software engineer)
- Markus Strauss (via physics to computational and data science) https://twitter.com/@MarkusJStrauss
* this group
- mailing list: https://lists.posteo.de/listinfo/hackingecology
- event wiki page: https://events.ccc.de/congress/2018/wiki/index.php/Session:Saving_Ecology_with_Data_-_First_Steps
- main event in schedule: https://fahrplan.events.ccc.de/congress/2018/Fahrplan/events/9456.html
- main event video: https://media.ccc.de/v/35c3-9456-hacking_ecology
- HACC pad: 🔗hacc
- HACC wiki page: https://events.ccc.de/congress/2018/wiki/index.php/Session:Hackers_Against_Climate_Change
- Bits und Bäume conference: https://bits-und-baeume.org
- CCC Camp: https://events.ccc.de/category/camp/
- Open Knowledge Fundation: https://okfn.org/
- Air quality links HERE <-------------------------------------------------------------------------------
- Real time air quality info: https://waqi.info/ [data and API: https://aqicn.org/api/]
Mass extinction of animal species
There are a lot of data used by scientists, but there are still a lot of insights in the data that have not been explored
As a researcher, working in a hurry and on your own doesn't work:
too little time, not all ideas
There are batch effects on datasets when you do analyses (not possible to work with all datasets at the same time)
Conceptual background/reference needed for thresholds/interpretation/complexity of relations, e.g.:
someone has already done that task in some extent: https://ecologicaldata.org/find-data
- ENTSO-E, European Network of Transmission System Operators for Electricity, https://www.entsoe.eu/
- weather services
- NCBI, National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/
- NCBI is mostly for biomedical and biotechnological data; however, some of the datasets in the SRA (Sequence Read Archive - https://www.ncbi.nlm.nih.gov/sra) are ecological in nature, meaning that they contain DNA/RNA data gathered from habitats. However, it is some work to find out which datasets are helpful for us
- Spatial data
- Global database for tracking data of animals by MPI, www.movebank.org
- Curated global database for plant traits by MPI, www.try-db.org
- Repository for research data underlying scientific publications, incl. plenty of ecological data: www.datadryad.
- Global Light Pollution Data http://ngdc.noaa.gov/eog/viirs.html (is currently down because of the US government shutdown)
- Different Large-Scale Microbial Ecology Projects (with very spotty data, and usually no timeseries):
- Tara Oceans: Microbial Ecology data from Oceans https://oceans.taraexpeditions.org/en/m/about-tara/les-expeditions/tara-oceans/ and https://www.ebi.ac.uk/services/tara-oceans-data
- Earth Microbiome Project http://www.earthmicrobiome.org/data-and-code/
- The WWF hosts a set of maps that delineate different ecoregions - which are regularly used in conservation science (as well as other tools) https://www.worldwildlife.org/pages/conservation-science-data-and-tools -- the map of the ecoregions is also available here: https://ecoregions2017.appspot.com/
- GBIF (Global Biodiversity Information Faciliy, https://www.gbif.org/) hosts a lot of species occurence data and is searchable for regions, species and datasets
- The United States Forest Service Forest Inventory and Analysis (USFS FIA) hosts some data regarding the well-being and size of forests in the USA https://www.fia.fs.fed.us/
*** MEET UP Day3
Figure out what infrastructure we need
for now we have a mailing list (see link above)
the pad here for discussion and documentation (it's a proposal)
workflow and tools are discussed @HACC 19:00 @komona !!!
join if you're interested in this !!!
Formulate a goal (realistic or not)
Short discussion on the name
(Theo) During my talk, I received a mail with the suggestion CODEco (COmmunity for Digital Ecology), which I really like, because you can hear both "code" and "ecology" and it also sounds a little bit like "code red"
(Sandro) Sounds reasonable. I read this suggestion earlier and wanted to see what happens. If thats the common stance then I hope my reply will encourage others to show signs of life. :)
(Theo) In the mailing list, beneroth suggested to just use "Hacking Ecology" as name - and already registered http://hackingecology.org . Actually, I like this more than CODEco, because it is so simple.
(Manuel) Im fine with both, however I think that some people still have a negative connotation with the word "hacking", especially people outside the IT field.
Short summary of the talk on day 1 "Hacking Ecology"
- Talk description: https://fahrplan.events.ccc.de/congress/2018/Fahrplan/events/9456.html
- Video: https://media.ccc.de/v/35c3-9456-hacking_ecology
Open Knowledge Foundation can be interested in joining this. They already organize citizen science : https://okfn.org/
We should list data sources
Biological data can be accessible, but ecological data can be more expensive (as you need a lot of different data)
We can mix with other approaches: Komona, Hackers against climate change
For this first meeting, we'll try not to get lost in the details
We should formulate a goal
In ecology, many people do think that technology could not help and that it can mess up everything
Some of us do not have precise idea of what we can find by working on these topics in this manner:
what are variables than we want to tune?
how can it help make ecosystems more robust?
POINTS OF VIEW FROM ECOLOGY
habitats have been disrupted, mainly by agriculture
- We can analyze data to make it easier to see, understand, have a better understanding of it
- Use remote sensing data (satellite). Start with image analysis, web crawling, statistics
- In these fields, people use top notch algorithms, but do not longer use simple algorithms
- We can use them, optimize them, automatize them, make them available on a web interface
- start, e.g., by classifying land usage types, how this changes over time
- It is possible to start with Romania, where forest is detroyed illegally at a tremendous rate
- We still need data "from the ground", which are harder to find (please someone define what exactly is needed!!!)
- -> I think a nice idea is something like a raspberry pi kit with some sensors, which people can set up for a small price and register the location at a website or similiar.
- I've seen a documentary where people used raspberrys for recognizing and locating chainsaw sound in the rainforest, however I'm not sure about energy supply
- Maybe some farmers would be interested in that, if we create some sort of win-win situation (Please move if this is not the right section)
Various ideas before wrapping up the meeting
- There are projects working on Air quality, they will be added to the pad or wiki later
- Visualize where areas are already protected, also see https://www.half-earthproject.org/
- We might need to work based on some assumptions that we know are broken (to some degree)
- are we ok with that? what do our scientists say to that?
- Keep climate change and ecology separate
- Climate change is a problem affecting ecology
- Even if climate change is solved, ecology still needs solving
for Ecologists and conservationists to formulate problems and needs and then ask us for tasks to do
We need a job system as the one for the Angels (organization of the CCC) or as from Katia from Komona
We need infrastructure. What we have now: a mailing list
* Define an identity
* Prioritize and start with something simple !!!
- We can start to work with easily accessible data
- inital goal should be small and representative.
- Then talk about new research ideas, new data analysis project
- Then search for additional necessary data
- list publicly available data sources, their content&quality and put it into an overview
- have some examples to show why&how all this is important
- list tiny projects to start with
- make a list of skills
- participate together to other events : bits und bäume (https://bits-und-baeume.org/de) - CCC Camp (https://events.ccc.de/category/camp/)
- find an existing job assigment system, or collaborate with people working on it
- get in touch with ecologists that are not convinced by the interest of using technology for ecology
- start a first project, e.g., analyse some data and create first insighs
- define a project in some weeks
IDEAS FOR A FIRST PROJECT
are discussed here:
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