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LARA and SiLA2.0/AnIML
– an integrated open source laboratory automation suite, also for sample management ?

dr. mark doerr

institute for biochemistry, university greifswald
2019.03.11

uni-logo
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greifswald-map
* lara intro

the greifswald protein screening platform LARA

lara
* lara intro

scientific data - structure

scientific-data
* In the very early days of personal computing, I was wondering, why the computer was not used

scientific work and data

how do we organise / structure scientific experiments that they are reproducible, even in 100 years ?

how do we store the scientific data, even to be read in 100 years ?

how do we organise the scientific data, that new knowledge can re-interpret / re-evaluate the old data ? (coping with evolution in science)

* In the very early days of personal computing, I was wondering, why the computer was not used in every scientist should have a laptop to document his experiments share data , faster evaluation, search, combining results, re-interpret when more knowledge First devices every single devices has its very own software HPLC, NMR own data formats only propieatary sotware to open the formats later robotics very limited view only control so I decided to create my onw software with the massive help and back of the open source community everything is out there....

holistic approach of the LARA suite

LARA-workflow
* In the very early days of personal computing, I was wondering, why the computer was not used

LARA suite - architecture

LARA-structure
* In the very early days of personal computing, I was wondering, why the computer was not used

LARA suite - main components

  • robot project planning
  • robot process design / code generation
  • process control / scheduling (planned)
  • data collection
  • data evalution and visualisation
  • people / experimentalists
  • compound and device database
* feature

LARA suite - componens for sample/compound management

  • compound and device database
    • Logarithm of partition coefficient (LogP)
    • Molecular weight (MW)
    • Hydrogen bond donors / acceptors (HBD / HBA)
    • Topological polar surface area (TPSA), Rotatable bonds (Rot), etc.
  • compound and device inventory / ordering system
    • supplier, price,
  • container database
  • people / experimentalists
* feature

LARA suite - techniques

LARA - open source code repositories

gitlab.com/LARAsuite

github.com/LARAsuite

we need you as a open source developer / tester !

what is sila_logo ?

sila_logo

sila-standard.org

* feature

who is sila_logo ?

* feature

sila_logo 2 lab automation communication standard

sila2 structure
* SiLA 2

sila_logo 2 - applications

sila2_integration
*

sila_logo 2 - server / client architecture

sila2_server_client communication
*

sila_logo 2 - main concepts

* feature

sila_logo 2 - technical background

* gRPC “wire format” - and - for simplicity - the gRPC libraries as a base * restricted use of HTTP Methods and Status Codes * Based on HTTP2

sila_python: a fast entry to sila_logo 2

setup

  1. download repository
    2. git clone
  2. run installer
    3. python3 sila2installer
  3. go to examples directory
    4. cd sila_python/examples/HelloWorld
  4. run Hello SiLA 2 Server
    5. python3 python HelloSiLA2_server.py
  5. run Hello_sila2 client
    6. python3 python HelloSiLA2_testclient.py
*

sila_python: the code generator workflow

  1. create Features (currently in SiLA XML Feature Definintion language)
  2. put them all in one directory with a server description file
  3. run the sila2codegenerator
    4. sila2codegenerator -d my_new_labdevice_project
  4. this will result in
    1. all protobuf files, describing the interface
    2. a ready-running server and testclient
    3. server / client stub classes for subclassing
    4. a simulation implementation
    5. a real hardware implementation template
  5. run my_new_labdevice_server / client
* gRPC “wire format” - and - for simplicity - the gRPC libraries as a base * restricted use of HTTP Methods and Status Codes * Based on HTTP2

sila_logo 2 - repositories

gitlab.com/SiLA2

sila-standard.org

raspi Raspberry Pi repository: sila_python/raspberry_pi

image source: https://www.raspberrypi.org

what is AnIML ?

www.animl.org

source: www.animl.org

* feature

labPy - a python GUI library
for interacting with lab devices

labPy features

  • simple to use graphical user interface elements (QT5 based)
  • hardware interfaces (serial, USB)
  • reusable code
  • flexible use cases
  • much cheaper and more modern than NI LabView (R)
Software that makes the usage of everything less complex

labPy - open source code repositories

simple installation via pip:

pip install labpy

gitlab.com/LARAsuite/labpy

summary

  • the power of open source ('matters') - construction of very powerful tools with standard solutions
  • fast, script based / automatized data processing with LARA, using one single language paradigm to access all data
  • SiLA2 based communication - customers, please ask vendors for SiLA 2 compliance !
  • if you need a GUI, use labPy
Software that makes the usage of everything less complex

acknowledgements

robot hard- and software

  • Peter Neubauer with his group (TU Berlin)
    • Sebastian Hans (TU Berlin)
    • Shaon Debnath (TU Berlin)
  • Stefan Born (TU Berlin)
  • Johannes Kabisch with his group and associates (TU Darmstadt)

SiLA team

  • Daniel Juchli (wega-it.com)
  • Maximilian Schulz (unitelabs.ch)
  • Stefan Koch (equicon.de)
  • Oliver Peter (idorsia.com)

general

  • uwe Uwe Bornscheuer (University Greifswald)

THANX !