Silver Linings of COVID-19

PLoS headquarters when most of its staff is working remotely (click to enlarge).

A Brady Bunch pun on remote work from our friends at Numenta (click to enlarge).

This potentially tasteless title brings to mind the positive elements of canceling classes, academic conferences, and workplace meetings: the ability to do these activities virtually. Among my current projects, I am involved in a number of working groups that are entirely virtual. These group utilize Zoom and Google Meet to give talks and hold meetings, with Github, Google Docs, and a host of other tools to manage contributions and research products (papers, talks, social media posts). This might be called the "Zoom/Slack" paradigm. Below is a Twitter thread from a Sloan Foundation program officer that asks for thoughts on alternatives to this standard.

Potential support for people collaborating outside the Zoom/Slack paradigm (click to enlarge).

In 2014, I posted on a concept called a theory hackathon, which was held as a hybrid physical and virtual event. The idea is to define and work on problems that are best solved in teams where not all members can meet live. But online meetings are evolving beyond awkward encounters and technical glitches. Often, live physical meetings are meant to cement social ties. Indeed, below is an informal survey that asks this very question.

Why are live events (as opposed to virtual) so important (click to enlarge)? 

In general, live physical conferences seem to be useful for social connection. Revisiting the tweet from Josh Greenberg, perhaps what is needed aside from virtual meeting spaces and file exchange/ chat functionality is a frictionless social platform. This could be conventional social media, or more likely a virtual reality platform integrated with live video/version controlled file exchange/chat capabilities.

Virtual meetings and virtual work are not without their own rhythm and customs. Aside from the potential for social disconnection, it also poses a challenge for personal habituation and ultimately productivity. Below is a link to a Twitter thread that gives tips for meeting virtually for people who are unaccustomed to doing so.

Online meeting tips from Mozilla Open Leaders (click to enlarge).

Carpentries-style tips for synchronous online meetings (click to enlarge).

There are also tips for working from home more generally. As with virtual meetings, capacity to work remotely has been accelerated in the age of social media [1]. The link below gives tips about working from home as an adjustment from working in a large office or public place. Generally, virtual work does require a change in expectations, from dealing with technical glitches to dealing with gaps in social presence [2].

Tips on adjusting to working at home (click to enlarge).

Well-being while working from home (download) (click to enlarge).

Draft workbook on how to host an online conference (click to enlarge).

Online conference are more than simply scaling up virtual meetings. There is a method to conducting and organizing online conferences [3], and there are a number of options regarding the medium. Returning to the issue of greater social connectivity in virtual meeting, one solution is to hold the conference in a virtual world such as Second Life. In this type of meeting, you are able to meet other people as avatars, and even interact with the venue itself. Below are two examples of my experiences with Second Life academic events in the past, one being a continuing lecture series called Embryo Physics, and the other a conference called Simulation and Second Life.

Tour of the Embryo Physics Course @ Silver Bog, Second Life (click to enlarge).

My avatar at the Simulation and Second Life conference, 2007 (click to enlarge).

As a bonus, there is a new agent-based model of COVID-19 transmission created by Paul Smaldino and implemented in NetLogo. This model demonstrates the efficacy of social distancing (hence the resurgent interest in working virtually).

Discussion of COVID-19 transmission model as a Twitter thread (click to enlarge).

Be sure to also check out the Living Computation Foundation's "Pandemic in a Box"! Click to enlarge.

NOTES:
[1] Williams, A. (2017). How the Rise of Social Media Fostered a Culture of Remote Working. Social Media Week, April 14.

[2] Oh, C.S., Bailenson, J.N., and Welch, G.F. (2018). A Systematic Review of Social Presence: Definition, Antecedents, and Implications. Frontiers in Robotics and AI, doi:10.3389/frobt.2018. 00114.

[3] Reshef, O., Aharonovich, I., Armani, A., Gigan, S., Grange, R., Kats, M.A., Sapienza, R. (2020). How to organize an online conference. arXiv, 2003.03219.

Open Data Day 2020

Welcome to Open Data Day 2020! Sponsored by the Orthogonal Research and Education Laboratory.  Our activities start today, and will continue over the course of the next year. For this iteration of Open Data Day, we are looking for software developers, data scientists, statisticians, and quantitative biologists to work on a host of issues related to open data-related activities in the DevoWorm group. Listed below are a series are series of possible goals for the next year.

1) We would like to construct pseudo-data sets for theory-building and modeling. This involves establishing simulated and resampled data sets that can be used as the input to machine learning, statistical, and functional models. Examples of these would include numeric data generated using statistical distributions, a generative approach using selected features (cells) as inputs, or the energy potentials of kinetic processes in an embryo.

2) There is also a need to build towards metadata standards, particularly with respect to the integration of different data types. Metadata helpful to the DevoWorm group includes (but is not limited to) cell division timing, high-level descriptions, positional and geometric information, and other features. The development of metadata repositories according to a schema data structure would be helpful.

3) Also needed is a focus on DevoZoo maintenance, including the addition of datasets, the integration of data sets, and improvements in presentation style/interface design. Since last year's launch, the resources for each species or computational platform have become outdated. We would not only like to provide links to resources such as new data sets and gene expression atlases, but also provide access to “intermediate” resources such as ontologies, metadata, and models from other research groups. There is also a further desire to make DevoZoo sustainable.

Current iteration of DevoZoo (click to enlarge).

4) As an initiative farther off into the future, we would like to add semantic capabilities to our models and data sets. One such example is a “controlled vocabulary” for developmental microscopy images and molecular data. In concert with this, having the capability to attach meanings and other notes to image and simulation features would increase the interpretability of such data.

5) In conjunction with the Data Reuse Initiative, we would like to provide some application of the FAIR principles. FAIR stands for making data findable, accessible, interoperable, and reusable. There are two opportunities here: a FAIRness evaluation, or how to make data FAIR, and promotion of each component of FAIR. For example, making datasets on DevoZoo more findable by adding tags or other classification tools would help newcomers make the most of our resource.