UPDATED! Nanome: A Brief Introduction to a Social VR Platform for Exploring Chemistry

Nanome: “The Future of Molecular Design” (VRFocus)

Virtual reality is finding application to many fields, and among them is chemistry. For example, in the spring of 2020, Harvard University used Oculus Quest VR headsets in an undergraduate-level biochemistry class to help students to observe, manipulate, and build molecules and explore the shapes of proteins and drug compounds. (Here’s a link to the recently-published paper in the Journal of Chemical Education. Unfortunately, you’ll have to buy the full-text article, or get a copy via your local public or university library. Remember, librarians are your friends!)

VR use in chemistry is not just for students learning about the basics of chemistry, however; it also has application to research scientists working in the laboratory. A good example of how social VR can be used in cutting-edge, collaborative chemistry research is Nanome, a startup co-founded in 2015 by some engineering students at University of California San Diego, who saw a need for 3D visualization tools to help medicinal and computational chemists and structural biologists reduce their time to market and increase the efficacy of new drugs (a process that can cost billions of dollars per drug).

Nanome recently announced the closure of a successful funding round raising $3 million from several venture capital firms:

“Since our founding, we’ve had a compelling vision about what scientific collaboration should look like and a goal to equip our real-life superheroes — scientists who are discovering ways to combat disease, address climate change and improve people’s lives — with an intuitive virtual interface where they can experiment, design and learn at the nanoscale,” said Steve McCloskey, Nanome CEO and Founder in a statement. “We made huge strides toward realizing that vision in 2020, and this funding gives us firepower to increase our impact, support more research initiatives and continue to revolutionize biotech and scientific research.”

Initially starting as a visualization tool to facilitate research and development by medicinal and computational chemists and structural biologists, Nanome has grown as an open platform for virtual collaboration. During the pandemic organizations have used Nanome’s platform “to assess candidate molecules’ ability to bind viral proteins in 3D,” the company notes.

In fact, Nanome became the first American company to join a coordinated supercomputing project funded by the European Union (EU) Commission to screen chemical libraries for potential activity against SARS-CoV-2, the coronavirus that causes COVID-19! (Here’s the press release.)

Nanome is being used in the search for drugs to fight COVID-19

And the best part is, you can try Nanome out for free! Nanome is free to download for personal use via Steam, Viveport, SideQuest, and the Oculus store, supporting the Oculus Rift, HTC Vive and Valve Index headsets. For academic or commercial use there are various licensing structures; for more details, visit the pricing page on their website.

For more information on Nanome, visit their website or follow the company on social media: Facebook, Twitter, Instagram, LinkedIn, or YouTube. I will be adding Nanome to my ever-expanding comprehensive list of social VR and virtual worlds.

UPDATE July 9th, 2021: Here’s an interesting article about Nanome, from a website called LabCompare: VR for Science: Drug Discovery and More in the Virtual World, with some great illustrations!

Pandemic Diary, June 20th, 2021: Vaccinated, But Exhausted

Late yesterday afternoon, I drove downtown to the Winnipeg Convention Centre to receive my second COVID-19 vaccination (Pfizer). This morning, I am feeling tired and have some muscle aches (a sign that my body is responding to the shot), so I am taking it easy. I have to wait two weeks for the shot to take full effect, and then I can relax my hyper-vigilance somewhat. I just want my pre-pandemic life back!

You will note that I have not been blogging much lately. I have been struggling with severe anxiety and depression these past few weeks. Also, I have barely left my apartment, thinking that it would be tragic if I were to become infected so close to the finish line, with the goal in sight. My self-imposed isolation only fed into my low mood. Overall, I am utterly exhausted.

So, please bear with me. I hope to be back up to full speed soon!

Pandemic Diary, May 27th, 2021: “The Worst COVID Hot Spot in North American Now is Manitoba, Canada”

*sigh*

You know things are really bad when you make the headlines of the venerable New York Times newspaper—and it’s for all the wrong reasons.

The New York Times reporting on Manitoba’s COVID-19 surge (original; archived copy)

The article reports:

The coronavirus is now spreading faster in Manitoba than in any other province or state in Canada, the United States or Mexico, with Indigenous people and people of color hit disproportionately hard.

Figures released on Wednesday show that over the last two weeks, the prairie province in the middle of Canada reported an average of 35 new cases a day per 100,000 population. Canada as a whole is averaging about 10 a day per 100,000; the United States, 7 per 100,000; and Mexico, 2 per 100,000. The next highest states or provinces are Alberta at 16 and Colorado at 15.

Yes, things are that bad.

And yes, I know that most of my blogposts over the past two weeks have been Pandemic Diary entries, as opposed to “news and views on social VR, virtual worlds, and the metaverse”, as the tagline of my blog states. I do apologize for that, but this blog has also been a much-needed place to vent my frustrations at how Manitoba’s response to this pandemic has been largely bungled by Premier Brian Pallister and his Progressive Conservative provincial government.

I am sitting here, having had my first Oxford/AstraZeneca COVID-19 shot, upset and angry because I still do not know when I will receive my second vaccine shot, or even what vaccine I will be getting! Will I get a second AstraZeneca shot? Pfizer? Moderna? Who knows??!? It’s enough to make me tear my hair out in frustration.

So please stay tuned…I will be returning to my regular coverage of the ever-evolving metaverse marketplace soon. It’s just that things are rather chaotic and a little uncertain at the moment, and this blog reflects that.

Hold tight! We will soon resume our regularly scheduled programming 😉 and in the meantime, thank you for your continued support of this blog.

UPDATED! Pandemic Diary, May 22nd, 2021: Cruel Summer

Photo by Martin Sanchez on Unsplash

Today is officially Day 433 since I began working in self-isolation from home for my university library system. The Victoria Day long weekend marks the beginning of summer up here in Winnipeg, but I am not in a summery mood at all.

Both Winnipeg’s mayor, Brian Bowman, and Manitoba’s premier, Brian Pallister, have called upon the Canadian federal government to send healthcare workers and contact tracers to cope with the worst situation we have been in since the pandemic started (even worse, they are squabbling with each other). This past week, Manitoba has broken records for both the number of those infected with COVID-19 and for those who are in intensive care in hospital. In fact, the circumstances are now so bad that we have begun to ship patients next door to cities in northwestern Ontario and even as far afield as Ottawa (and they are still having troubles of their own in Ontario). Things are pretty fucked up here right now.

The entire province is essentially on lockdown, and I am in a black, despairing mood, stuck in my apartment. The province even sent out an emergency warning to everybody’s cellphones last night (usually only used for child abductions), to sternly warn people to stay home and only go out for essentials. (I would have normally saved it and pasted it into this blogpost for posterity, but why bother?)

I have gone 15 months without a hug, or being in close proximity to anybody but a doctor. I cannot get a straight answer from anyone as to when I can get my second shot of COVID-19 vaccine, or even what brand I will get (my first shot was Oxford/AstraZeneca, but I could receive Moderna or Pfizer for my second shot, or maybe not?). I am losing my psychiatrist, and it is unlikely that I will be able to find a new one who can take me on as a patient. I am angry and tired and just plain FED. UP.

So forgive me if I use this blog, normally about social VR, to vent. This is turning into a cruel summer. I leave you with the following tweet, with which I agree wholeheartedly:

I only want to see one more [Brian] Pallister press conference. At it he will:

1. Ask for forgiveness from Manitobans for the incompetent performance of his government, resulting in far too many avoidable COVID-19 deaths;

2. resign;

3. instruct his successor not to repeat his mistakes.

UPDATE May 23rd, 2021: Today CBC News reported:

When Premier Brian Pallister says Manitobans are living through the darkest days of the pandemic, there are plenty of measures to back that up.

For starters, there are more COVID-19 infections in this province than ever before. On Saturday, the seven-day average daily case count rose to 482, a new pandemic record.

That works out to a daily infection rate of 34.3 new COVID cases each day for every 100,000 people, the highest infection rate among Canadian provinces and U.S. states. Alberta is a distant second, with 20.6.

New infections today lead to more hospitalizations down the road. During this third wave of the pandemic, a greater proportion of COVID hospital patients require intensive care.

The number of COVID-19 patients in Manitoba ICUs hit a record 80 earlier this week and is technically higher now. There were 74 COVID-19 patients in Manitoba ICUs on Saturday and seven more Manitoba patients in Ontario hospitals, some now located as far away as Ottawa.

In living memory, Manitoba has never had to ship ICU patients out of province simply to relieve the pressure on hospitals that are now struggling to deliver basic care. Hence Pallister’s request on Friday for Prime Minister Justin Trudeau to send Manitoba nurses and respiratory therapists.

As well, Winnipeg’s five-day test positivity rate reached a new pandemic record of 16.8 per cent Saturday.

In its analysis, the CBC lays the blame for this situation firmly at Brian Pallister’s feet:

Sadly, Manitoba can not vaccinate its way out of an immediate hospital crisis. The time for long-term solutions ended in early April, when COVID-19 cases in this province began an exponential rise.

When the top priority in this province would appear to be staunching the spread of COVID-19 in Winnipeg, the epicentre of the pandemic, non-essential businesses remain open, office workplaces are not compelled to allow their employees to work from home and manufacturers are not taking a break to give the alleged circuit breaker more teeth.

Only the province could order such measures, which were implemented in part during an April 2020 first wave that turned to be a ripple in Manitoba.

Instead, the province has opted against the most effective measures at its disposal during its greatest time of need.

…Manitoba’s premier is throwing shade at a U.S. president — and asking the Canadian prime minister for help — while this province declines to do everything it could to combat a third wave that’s been gaining momentum for eight weeks.

There were many voices calling for a short, sharp lockdown weeks ago, calls which Brian Pallister and his ministers ignored. And yet he has the gall to suggest that it is Manitobans themselves who are to blame. Countless Manitobans have become sick, and some have died, due to Brian Pallister’s ineptitude.

I am absolutely incandescent with anger this weekend, walled within my apartment to protect my health and safety as one in six Manitobans tests positive for COVID-19. The next few weeks are going to be ugly, and much of it could have been avoided if we had had a truly effective, proactive, competent provincial government.

And I vow that, if I should survive this pandemic unscathed, I will do everything in my power to ensure that the opposition wins the next Manitoba election. Enough is enough.