Doctoral thesis summary, covering neuroscientific FOSS technology development, an imaging profile of dopaminergic function, and serotonergic imaging of a longitudinal drug intervention.

Slides, including list of external references: http://chymera.eu/phd/slides.pdf
On YouTube: https://youtu.be/WrliLYF0SBY

Educational lecture on monoaminergic systems, focusing on their relevance for preclinical research and small animal imaging, and including primary research examples from mouse and rat functional magnetic resonance imaging (fMRI). This lecture is part of the seminar events of the Animal Imaging Center at the Institute of Biomedical Engineering of the ETH and University of Zurich.

On YouTube: https://youtu.be/QnT-2CCXArY
Version tracked slides available at: https://bitbucket.org/TheChymera/education-neuroanatomy

Introductory fMRI analysis lecture with a focus on preprocessing and data structures, and using examples from small animal magnetic resonance imaging. Originally presented as part of the Winter 2018 Experimental Neuroimaging Course at the ETH and University of Zurich.

On YouTube: https://youtu.be/ePamp9v5Z0U

Newest version of Live and reproducible slide sources available at:
https://bitbucket.org/TheChymera/education-fmri_analysis/src/master/

Slide record (as seen in the video) available at:
https://bitbucket.org/TheChymera/education-fmri_analysis/raw/ac3c50eb4d26a6eccba35170432b6f04a0a99c83/slides.pdf

ETH/UZH Linux Days introductory lecture, providing a brief overview of the history, key concepts, benefits, and user base of Free and Open Source Software.

Version tracked slides available at: https://bitbucket.org/TheChymera/ld_foss/src/master/

On YouTube: https://youtu.be/wD_TpW0M8Iw

The COSplayer is a pyboard-based device with specific input and output capabilities, designed to provide microsecond-range stimulus delivery in biomedical or psychological experiments.

Based on a single trigger event (e.g. as obtained from most temporally precise measuerement devices), the COSplayer can deliver a fully configurable stimulus train of arbitrary length, which is specified by the user via a BIDS-formatted tab separated values file. Sequence delivery can be monitored via LEDs on the device, and output capabilities include 2x transistor (i.e. short-circuit interrupt) channels, 2x TTL output (~4.2V) channels, and 2x variable amplitude TTL output channels.

Optionally, via the free and open source COSplay software, the device can interface with a user terminal and reposit tab separated values files containing delivered stimulation reports into the Bruker Paravision directory structure.

DOI: 10.6084/m9.figshare.7227626.v1
On Figshare: https://figshare.com/articles/A_Guide_to_Assembling_the_COSplayer_an_Open_Source_Device_for_Microsecond-Range_Stimulus_Delivery_with_broad_Application_in_Biomedical_Engineering_and_fMRI/7227626
On YouTube: https://youtu.be/YakrW-PoAgM
Corresponding Software: https://cosplay.readthedocs.io/
Corresponding Peer-Reviewed Article: https://cosplay.readthedocs.io/en/latest/
Corresponding Peer-Reviewed Article DOI: https://doi.org/10.21105/joss.01171

RepSeP: Reproducible Self-Publishing for Python-Based Research

Presentation and example of how to use the integrated power of LaTeX and Python to generate high-quality live documents summarizing your scientific work.

DOI: 10.6084/m9.figshare.7247339.v1
On YouTube: https://youtu.be/WbjQYBuyKdk
On Figshare: https://figshare.com/articles/Reproducible_Self-Publishing_for_Python-Based_Research/7247339
On Vimeo: https://vimeo.com/296237720

Reference Implementation (and newest version) of the technology: https://github.com/TheChymera/RepSeP

LabbookDB is a relational database application framework for life sciences—providing an extendable schema and functions to conveniently add and retrieve information, and generate summaries. The core concept of LabbookDB is that wet work metadata commonly tracked in lab books or spreadsheets is more efficiently and more reliably stored in a relational database, and more flexibly queried. We overcome the flexibility limitations of designed-for-analysis spreadsheets and databases by building our schema around atomized physical object interactions in the laboratory (and providing plotting- and/or analysis-ready dataframes as a compatibility layer). We keep our database schema more easily extendable and adaptable by using joined table inheritance to manage polymorphic objects and their relationships. LabbookDB thus provides a wet work metadata storage model excellently suited for exploratory ex-post reporting and analysis, as well as a potential infrastructure for automated wet work tracking.

09:45 - should be “if the answer is _yes_”
13:16 - should be “_input_ formats”

DOI: 10.5281/zenodo.833542
On Vimeo: https://vimeo.com/228636389
On YouTube: https://youtu.be/FKWznqP6rcE

Neuroscience, one of the most computation-reliant fields in the natural sciences, is dependent upon dozens of highly complex software suites, which scientists are often forced to manage manually. Upstream developers often ship bundled dependencies to better support this flawed workflow, and in the resulting mess documenting and reproducing analysis pipelines is neigh-impossible. We seek to correct these shortcoming of both modern software distribution as well as modern data science, by integrating high-quality ebuilds for neuroscientific software into the Gentoo Science Overlay. We also seek to publish a simple NuroGentoo world file (along with appropriate usage instructions) to allow scientists with access to OpenStack, Amazon Elastic Computing, or Docker to launch up and build a system fit for reproducing data analysis run on other NeuroGentoo systems with minimum effort.

Alternative Locations:
DOI: 10.5281/zenodo.833534
On YouTube: https://youtu.be/l4gF3y9btw4

Related Documents:
Research Paper: https://riojournal.com/article/12095
Podcast Episode: https://flossforscience.com/podcast/season-1-episode-6
Main Project Resource: https://github.com/gentoo/sci

Theory and Practical course demonstrating the intricacies of managing scientific software, and how they can be handled in a free and open source environment.

For this lecture we choose the excellent Gentoo Linux distribution. See the subsequent talk ( https://www.youtube.com/watch?v=l4gF3y9btw4 ) and publication ( https://riojournal.com/article/12095/ ) for more details on Gentoo for scientific software management.

On YouTube: https://youtu.be/qE-N__XjJg8

The city lights of Dubai from Marina to Deira as seen in a time lapse from the city's driverless metro.