1st Advanced Open Labware workshop Trend in Africa


#1

Dear Gosher’s,

it is with immense pleasure that I share with you that applications are open for the 1st Advanced Open Labware Workshop from Trend in Africa in collaboration with the University of Tuebingen the University of Cape Town and funded by the Volkswagen Foundation.

The idea for it came up at the last workshop in Nigeria, mainly from the heads of @neuro3en and Samyra. It has been under development for a while and has certainly benefited from the discussion over the Gosh Nodes thread!

In very short lines, the idea is to give people who are already building open source hardware the time and space to focus on one project for two weeks, with a strong focus on documentation of the work in a academic publication / pre-print format, as well as deposit of all information on repositories, such as github/gitlab.

The application deadline is February 14th, and should be done in groups of 3 people. Due to constraints in the grant, people appplying should be working/affiliated in African countries or Germany.

It conveniently takes place in between April 16th and 27th, in Cape Town, right after the http://www.africaosh.com/.

The application form can be found here.

We are still looking for people to complete the documentation team, so if you like to join our effort into documenting: A) the workshop itself, so that more people can benefit from it, or B) the projects individually in an academic format, please get in touch!

We would appreciated extremely, if you could share this in your networks and forward it to potential participants!

@thomasmboa, @jorgeappiah, @LawrenceN.
@vektor, @lu_cyP, @jcm80
@unixjazz, Please also tag others in Germany or Africa that I might have forgotten!

@Tobey, @kaspar: Think we could discuss implementing the tools you guys are involved with for documentation/BOM/build instructions?


#2

@gbathree, completely forgot to tag you here! I think this is/would be interesting for you too?


#3

@amchagas this is a very good call, i will organize my team. On the documentation issue i think i can during this period have time to join in,


#4

This is super cool, I’d love to be more involved but it’s probably too great a time commitment.

This is a little self-serving, but I feel it could be really useful here. We’ve been building a new, simplier, cheaper, more flexible platform for collecting sensor, survey, and API data and sharing the results. Thankfully, we’ve been able to get it funded through specific use cases, and we’ll have a very nice product in the next 2 - 3 months.

I mention it because many hardware projects nail the hardware part, but fall short on the data/storage/sharing/visualization part. Everyone reinvents the wheel and their reinventions then don’t get maintained.

We have a rudimentary tutorial here - https://gitlab.com/our-sci/measurement-scripts/tree/master/hello-world. But our work is changing so fast that’s already a little out of date, so here’s a more recent version of the kind of visualizations we can do. It’s super flexible and script based - as long as your talking Serial or USB or Bluetooth this will probably work well.

This is complex data from a sensor displayed on an android app in real time. We pull, parse, analyze, display the results, and push it to a server where it is viewable. It also pulls + displays data from SoilGrid (https://soilgrids.org/) using their REST API.

Anyway, I’d love to see if any projects could use this to save time and get their concept / product to a more professional level.


#5

@gbathree, this is pretty cool!
Would you (or people who are developing this with you) be willing/have time to have remote sessions with the participating groups to support them to set this up in their projects, in case there is a need for it? (we still don’t know which groups will be selected and what they will build).

I think if there is already a working system, there is no need to reinvent the wheel. One question that I have though, and forgive my ignorance, would it be possible to use this system without an android app? I guess my question is, needing an android app implies that I need a smartphone or some system running android in some point of the transmission? would it be possible to setup this system in a laptop running windows for instance?


#6

Mmm… well, the development environment is designed for a computer yes. So when you’re creating a new protocol (measurements, surveys, etc.) you build and test it all on a computer. But the development environment isn’t really built for submitting data points - it’s built for creating those complex surveys. Data submission is pretty much only from the Android app. If we had a clear use case and someone willing to fund it, I’m sure we could build something for a laptop but absent that it wouldn’t fit within our next set of development goals.

I just use an android tablet / keyboard combination when I have lots of data entry that requires typing if that’s the issue.

Yes, I’d definitely be available, and would be happy to help folks get set up - just let me know when and where. I don’t think it’s the best fit for every project, but for certain types of projects it will likely save devs a ton of time.


#7

If I understand this correctly, what you are building is a system that allows people to program (using a computer) the pull pretty much any kind of data and display it using android device. Is this correct? I think it would interesting to be able to pull, work and display data with a computer (extra points if it works with a raspberry pi :slight_smile: ).

How much time and fund are we talking about? I can see use (if I understood the tool correctly) for one of the projects @neuro3en wants to implement - Ben, does this make sense for the beehives?

I’ll let you know when I know more! thanks for being available!


#8

Yes, your assessment is correct.

I would say the ideal use case is when you have a person collecting data in the field, and they are collecting data from a sensor, as well as metadata from the person (survey), and perhaps they also want to call an API based on local information like GPS or time/date (weather, soil data for example). While there are more applications, that’s the ideal ideal case.

Greg


#9

Hey!
We want to do exactly that. We have a around 35 monitoring systems across Germany with GPS and several sensors. The monitoring system is a bee hive and we want the data of the sensors to be plotted over time in a browser or program. The sensors are sampling in the order of seconds and minutes. The survey aspect is also very interesting we tried to motivate the corresponding apiarist to tell us about the state of the hive and the surrounding conditions (pesticides).
Right now we are redesigning everything. When the system runs in a month or so I would come back with example data, maybe we can make this work together.


#10

Timing is good, actually. We are going to be finishing up some features for another client which would be useful here (dashboard-type data display and anonomyzation).

Do you have a link to the project with the hardware? If not, just tell me the hardware your using, how the hardware is communicating (cell, bluetooth, wifi, etc.), the basic structure of the communication (JSON, comma separate values, etc.), and the information you want to collect from the apiarists (just roughly, like 50 questions, 10 question, once a month, once a week, etc.).

That’ll give us a sense of how close we already are, and if there are features we lack that you would need.

So cool!!!


#11

Coolio!
There is nothing useful yet, we are changing from a “raspberry pi with 2 arduinos”-fiasco to one STM32 micro controller. The board has an SD card were we will save the data (binary if I understand that correctly). The data consists of the GPS location and the time/date by the GPS. That is daily. every minute we have 2x temperature and 2x humidity and the weight of the hive from 3 load cells. Also 2x 200 samples per second capacitance measures. 6 channels with 5000 samples per second as well. The battery and SD card will be in the field for 2-4 weeks and then send to us by postal service. In the advanced Africa course we will play around with LoRaWAN (ESP32) to connect the system and the data flow to a router that is connected to the internet. We want to get info’s from the apiarist every 2.-4 weeks when they change the SD card and charge the battery. There will be around 10 questions with numerical answers (are the bees happy? 1=yes … 5=no!..)
An other rather important point, but maybe not on your side anyways is that the apiarist has to log in to see their data. they are very paranoid they do not want others to see their data. For now I will let them do that, next round everything will be open, other people will participate that are not so weird.
So that is the general plan. Thanks for the interest.
Ben


#12

Ok - I’ll let Manuel respond re. the constant data flow piece, that’s a little outside our initial application space but certainly possible. In terms of apiarist survey data, that’s a perfect fit. In fact, why not just have a OTG cable with them so they can download the data to their phone on location and get real-time display –

We already do offline data collection so no issues if there’s no wifi/cell in the field - just wait till they are home.

That way, you can directly connect that data with their survey data, reducing the amount of spreadsheet lining up that’s required later and improving traceability.

We have many other folks who also want their data to be anonomyzed. I’ve personally noticed among farmers that they are ok sharing data (and therefore seeing general trends from others who also share data) so long as no one can figure out which data point is from them. We have to solve this problem for other applications so that’s a great fit.

Greg


#13

Ah, okay, I forgot. We sample the data as described but for visualization we will reduce the 6x 5ksps data to 1 channel with the amount of bee dances per minute or something. and the 2 channels with the 200 Hz data capacitance will also be brocken down to once per second data that are behaviorally relevant. So all the data is around once per minute to be honest (after filtering and averaging and what not to preprocess). MAYBE at some point we do preprocessing in the field by the STM32. Then we could think about solar and GSM-module and send a little bit of highly condensed data regularly. The OTG won’t work since we collect around 30-60 GB per cycle of 2-4 weeks. We tried to let them send data to us and we tried fileZilla but they are just not tech savvy enough for that. Our German partner apiarists are 50-80 years old.
Ben


#14

Holy cow that’s a lot of data! Seems like you will be able to recreate bee dances step by step bee by the time your done :slight_smile:

But that’s a bummer you can’t use OTG, it’d really simplify the data process and provide real-time feedback, but I totally see your point… even just trying to analyze that much data on the phone would take forever.

Very Interesting project.


#15

Hi everyone,

we are close to concluding the workshop here in Cape Town and I’m very happy to say that all projects are live and on github, some of the participants are already here in the Forum, and we’re gathering information that I suspect will be useful for other similar events.

Here are the links to the repos:

Bird feeder based on the Nest project, now loaded with weight scale, and camera for bird identification and mapping https://github.com/trendinafrica/SmartNest
by Danielle, Dylan and Adam

Analytical shaker for particle size analysis (powders, granules, etc) https://github.com/trendinafrica/analytical_shaker
Created by @JJato @benneh.ck and Adel

Electroantennogram device for measuring biosignals from Insects’ antennae: https://github.com/trendinafrica/EAG
by @Hez, @kayz44 and Liz

Actifield: a Behavioural box for measuring rodents activity https://github.com/trendinafrica/actifield
by @wumbor, @eli_gh and Mary

DIY Fluorimeter for DNA quantification: https://github.com/trendinafrica/aolw2018-capetown
by Lisa, Robert and Alessandro

Lumino: A stimulation and recording chamber for behavioural studies https://github.com/trendinafrica/lumino
By @dorcas_oluyemi, Shaun, and Dolapo

Spectrocam: a customized spectrometer https://github.com/trendinafrica/spectro_cam
by @ngala @C1970 and Wotchuen

Beehive monitoring system: https://github.com/julianatastro/BEE.EEG and https://github.com/julianatastro/superlogger_non_code
by @neuro3en, Julian and Morgan


Introduce yourself!
#16

Hi
All the participation expressed the need to collabore to improve what they have started or to do more things which will be useful in research.


#17

We are 3D printing a low cost affordable and portable spectrophotometer, Teaching of analytical methods in the fields of biochemistry, chemistry, physics, ecology and earth sciences has been largely theoretical with respect to spectroscopy. The problem is compounded as university enrollments are increasing every year and large numbers of students encamp around one or two spectrophotometers during practical sessions. Most at times, experiments end up being demonstrated at worst still explained or given as assignments.

In our quest to overcome this we set out to build a simple low cost and portable spectrophotometer with the goal of developing a project that will allow students to design and build their own spectrophotometer, giving them hands-on experience of the operational principles of this equipment.


#18

Hi all,

the first report from one of the groups is out! Take a look on what they have done during the workshop here:
https://github.com/trendinafrica/aolw2018-capetown/blob/master/daily_reports/AOLW2018_Final_report.pdf


#19

Happy to see that one of the projects coming out of this workshop is now published as a peer-reviewed paper!

Nice work @wumbor, @eli_gh and Mary!


#20

Thank you for the mentoring and support Andre!
Very grateful.