Open Source seminars

NeuroFedora is an initiative to provide a ready to use Fedora Linux based Free/Open source software platform for neuroscience.

Modern biological methods often require a large number of experiments to be conducted. For example, dissecting molecular pathways involved in a variety of biological processes in neurons and non-excitable cells requires high-throughput compound library or RNAi screens. Another example requiring large datasets - modern data analysis methods such as deep learning. These have been successfully applied to a number of biological and medical questions. In this talk we will describe an open-source platform allowing such experiments to be automated. The platform consists of an XY stage, perfusion system and an epifluorescent microscope with autofocusing. It is extremely easy to build and can be used for different experimental paradigms, ranging from immunolabeling and routine characterisation of large numbers of cell lines to high-throughput imaging of fluorescent reporters.

Research tools are paramount for scientific development, they enable researchers to observe and manipulate natural phenomena, learn their principles, make predictions and develop new technologies, treatments and improve living standards. Due to their costs and the geographical distribution of manufacturing companies access to them is not widely available, hindering the pace of research, the ability of many communities to contribute to science and education and reap its benefits. One possible solution for this issue is to create research tools under the open source ethos, where all documentation about them (including their designs, building and operating instructions) are made freely available. Dubbed Open Science Hardware (OSH), this production method follows the established and successful principles of open source software and brings many advantages over traditional creation methods such as: economic savings (see Pearce 2020 for potential economic savings in developing open source research tools), distributed manufacturing, repairability, and higher customizability. This development method has been greatly facilitated by recent technological developments in fast prototyping tools, Internet infrastructure, documentation platforms and lower costs of electronic off-the-shelf components. Taken together these benefits have the potential to make research more inclusive, equitable, distributed and most importantly, more reliable and reproducible, as - 1) researchers can know their tools inner workings in minute detail - 2) they can calibrate their tools before every experiment and having them running in optimal condition everytime - 3) given their lower price point, a)students can be trained/taught with hands on classes, b) several copies of the same instrument can be built leading to a parallelization of data collection and the creation of more robust datasets. - 4) Labs across the world can share the exact same type of instruments and create collaborative projects with standardized data collection and sharing.

Open science hardware (OSH) as a concept usually refers to artifacts, but also to a practice, a discipline and a collective of people pushing for open access to the design of science tools. Since 2016, the Global Open Science Hardware (GOSH) movement gathers actors from academia, education, the private sector and civic organisations to advocate for OSH to be ubiquitous by 2025. In Latin America, GOSH advocates have fundraised and gathered around the development of annual "residencies" for building hardware for science and education. The community is currently defining its regional strategy and identifying other regional actors working on science and technology democratization. In this presentation I will give an overview of the open hardware movement for science, with a focus on the activities and strategy of the Latin American chapter and concrete ways to engage.

The public has a fascination with the brain, but little attention is given to neuroscience education prior to graduate studies in brain-related fields. One reason may be the lack of low cost and engaging teaching materials. To address this, we have developed a suite of open-source tools which are appropriate for amateurs and for use in high school, undergraduate, and graduate level educational and research programs. This lecture will provide an overview of our mission to re-engineer research-grade lab equipment using first principles and will highlight basic principles of neuroscience in a "DIY" fashion: neurophysiology, functional electrical stimulation, micro-stimulation effect on animal behavior, neuropharmacology, even neuroprosthesis and optogenetics! Finally, with faculty academic positions becoming a scarce resource, I will discuss an alternative academic career path: entrepreneurship. It is possible to be an academic, do research, publish papers, present at conferences and train students all outside the traditional university setting. I will close by discussing my career path from graduate student to PI/CEO of a startup neuroscience company.

The Open Science movement advocates for more transparent, equitable and reliable science. It focusses on improving existing infrastructures and spans all aspects of the scientific process, from implementing systems that reward pre-registering studies and guarantee their publication, all the way to making research data citable and freely available. In this context, open source tools (and the development ethos supporting them) are becoming more and more present in academic labs, as researchers are realizing that they can improve the quality of their work, while cutting costs. In this talk an overview of OS tools for neuroscience will be given, with a focus on software and hardware, and how their use can bring scientific independence and make research evolve faster.