Posted by: Jonathan Eisen
My Ode to Yolo Bypass
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in UncategorizedFour years – 1461 straight days – of iNaturalist observations
Well, today is a big day I guess. I just posted an observation to iNaturalist of a hummingbird in my backyard.
https://www.inaturalist.org/observations/195397005
Not that big a deal unless you are living in some place where it is really cold and you are jealous we have hummingbirds in our yard in Davis, California on December 31.
But the context here is important.
This entry completes a somewhat crazy run. I have made iNaturalist observations every day for the last four years. That is, every day for the last 1461 days.
It all started in January 2020. Before the pandemic reared its ugly head. I decided it might be fun to try and be more regular about iNaturalist postings. I had gotten into posting my observations there during 2018 and 2019 and then I saw on Twitter some people referring to an iNaturalist "Streak Finder" where you could look up how many days in a row someone posted observations.
And many people were discussing how many they had. And my max # at the time was OK (max of 16) but not particularly high.
And then I kind of forgot about it. But I was inspired by conversations with Laci Gerhart and I decided I would try to do an entry every day for all of 2020.
https://twitter.com/phylogenomics/status/1214614081329487872
And things of course got complicated quickly. First major complication -- I got called for Jury Duty and was selected as an alternate for a pretty serious case that in the end ended up lasting 3-4 weeks.
And I was pretty proud when I got through month 1 - January 2020. I posted a thread on Twitter about this.
I also posted this on my blog here.
One of the reasons I started doing this attempt to post every day was that I was hoping to go on a lot of work trips and to post every day on those trips and this would give me something to do while on the road.
In February I went to the AAAS Meeting in Seattle and on breaks wandered around and took pics and made lots of postings. Plus I got to hang out with an old friend, Carl Bergstrom, and we wandered around one day looking for birds
And things seemed good. Except for one thing. While at AAAS, I decided to avoid indoor crowded places because of the growing reports that this new respiratory disease had shown up in the US. And, well, this would be my last trip involving planes until a few weeks ago. So much for my plan to use iNaturalist as a way to help me not sit in hotels / conference centers while on trips.And there were many many struggles in life generally for me and many others as the pandemic spread. But somehow through this I managed to keep making observations. In fact, I would say without a doubt the mission to make observations helps keep me semi sane during some dark times.
And then I found myself on 12/31/2020. I had done it. One whole year of daily observations.
https://twitter.com/phylogenomics/status/1344873226464161792
And of course lots more happened over the next year. But I made it to 12/31/2021 and had made observations for another whole year.
And fast forward to today. I have made it to four years of daily observations. 1461 days. Through health issues. And the ongoing pandemic. And all sorts of complications. One thing that helped me in life was my mission to make some sort of nature observation I could post every day.
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in UncategorizedNotes on My Meningioma and Gamma Knife Treatment
So - on 9/27 I had Gamma Knife treatment at UC Davis for a posterior fossa meningioma that was first found by MRI about 6 years ago. I am going to be collecting my various posts here on the saga. I am also going to post separate posts here about the saga but just wanted to collect some of the other posts for now.
Day 7 - October 3, 2023.
Day 6 - October 2, 2023.
Day 5 - October 1, 2023.
Day 4 - September 30, 2023
Day 3 - September 29, 2023
Day 2 - September 28, 2023
Day 1 - September 27, 2023.
Posted to many social media channels about my treatment with updates and other details and also got lots and lots and lots of support.
Here are some of the posts.
Twitter:
- https://x.com/phylogenomics/status/1707059212801438207?s=20
- https://x.com/phylogenomics/status/1707169906071085099?s=20
Sept. 26 - Nature Therapy
Sept 25. MRI
Blue sky:
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in UncategorizedSanger DNA sequencing services
Sanger DNA Sequencing Services
So I posted a request to multiple social media sites:
Question - are there good / cheap services out there to do Sanger sequencing (e.g., for 16S / ITS for taxonomic identification of cultures)? The local Sanger operation we were using shut down.
I posted to the following sites:
These are the places that were recommended the most
These had single suggestions
- Macrogene
- MR DNA
- Integrated Genomics
- Functional Bio
- U Az.
- CosmosID
- Laragen
- Retrogen
- IMR
- Functional Biosciences
These are how the suggestions mapped to the different sites:
- Eurofins
- McLab in south SF
- QB3
- Macrogene
- MR DNA
- Laragen
- Retrogen
- IMR
- Functional Biosciences
- Eurofins
- Quintara
- Functional Bio
- Gene Wiz (now Azenta)
- UC Berkeley
- U Az.
- Blue Sky
- Mastodon
- McLab
- Quintara
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in UncategorizedAnd today in one of the stranger uses of my work … "130 Academic Words Ref from "Jonathan Eisen: Meet your microbes | TED Talk""
Well, this is certainly a bit wacky.
I was, well, Googling myself today and found this.
130 Academic Words Ref from "Jonathan Eisen: Meet your microbes | TED Talk"
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in UncategorizedResponses to requests for suggestions for quiet air filter for daughter’s California dorm room
So I posted a request for suggestions on various social media sites:
"Wanted - recommendations for good / not too expensive / not too loud air filter to get my daughter for her for a small dorm room in California (and thus to filter out pathogens, allergens and smoke ...)"
I am going to compile responses here
Wanted - recommendations for good / not too expensive / not too loud air filter to get my daughter for her for a small dorm room in California (and thus to filter out pathogens, allergens and smoke ...)
— Jonathan Eisen (@phylogenomics) July 23, 2023
Mastodon
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in UncategorizedSummary of responses to request for examples of data sets of microbial genomes with associated phenotypic data
Wanted - dataset(s) to test bacterial genome analysis / annotation methods. Ideally has many genomes from collection of [interesting] bacteria with associated experimental phenotypes / metadata.On Linked In:
- Jonathan Jacobs:"
- All the reference genomes in the ATCC Genome Portal are freely available for non-commercial research purposes. They are also fully authenticated and traceable to physical production lots in our biorepository, and produced under ISO quality management. I’m biased, but I think we’re producing the quality microbial genomes I’ve ever seen on a regular basis - so you might want to look there. We’re producing about 100-150 new genomes every month - and many of them (about ~1/3rd) are for organisms with no preexisting genome. We have about 3,300 microbial genomes now (bacteria, viruses, fungi, protists), and all bacteria and fungi are sequenced kn both Illumina and Nanopore. Drop me an email or DM if you want to learn more or collaborate or something. Here’s a link: https://genomes.atcc.org (and here’s a link to a comparative genomics paper we published in mSpheres earlier https://journals.asm.org/doi/full/10.1128/msphere.00077-22)"
- And then "I should also add that we have tons of metadata and I’ve hired a full time data curator to help bring metadata we have in our historical records warehouse into our digital records (ie phenotypic data from routine QA/QC testing going back to the 1920s…) "
- Natalie Ma wrote
- Joint Genome Institute may have this (if you're fine with an environmental microbes focus). Adam Deutschbauer has done several Tnseq libraries for the bugs and characterized their phenotypes.
- Eoin Brodie pointed to https://fit.genomics.lbl.gov/cgi-bin/myFrontPage.cgi
- Amy Lee wrote: https://twitter.com/minisciencegirl/status/1666186747733061640
- Would something like this help? http://m.genome.cshlp.org/content/early/2017/03/15/gr.213363.116 All the genomic data have been deposited and phenotype data in supplementary tables (not in PDF version).
- Grace Morales wrote https://twitter.com/Ungraceful_Bio/status/1666180695985897474
- Have you looked at using PATRIC/ BV-BRC? Theyve got a ton of different bacterial genomes available and you can search by data you'd like(AMR phenotypes, experiments done). I've pulled data for some AMR prediction work. Link: http://bv-brc.org
- Mike wrote https://twitter.com/mikethemadbiol/status/1666190833064849412
- This will get you a list of every Pathogen Detection isolate at NCBI with a genome and matching AST data https://ncbi.nlm.nih.gov/pathogens/isolates/#property:(%22has%20AST%20phenotypes%22)
- Also from Grace Morales https://twitter.com/Ungraceful_Bio/status/1666480238417829891
- Another one I thought of - PubMLST. (http://pubmlst.org)
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in UncategorizedAnother day to think, to pause, to ponder.
Panorama of Sycamore Park and the memorial to Karim |
A bit over 10 years ago I wrote a blog post that I repost all the time. Entitled "A day to think, to pause, to ponder" it was posted on my dad's birthday and was about the pain of him dying, by suicide, when I was in college. It was meant as a sad, melancholy post but also one about the importance of compassion and how "we can all do a little bit to improve how we treat other." When I reposted this one time a few years ago, someone asked me if I had ever met the "Compassion Guy" who frequented downtown Davis and who had a life's mission of getting people to think about compassion. I told them, yes, indeed I had and I had talked to him on and off over the years about this topic at or near the farmer's market or at his "Compassion Corner" bench area.
And thus, a few days ago, I was devastated when I found out that "Compassion Guy", aka David Breaux, was the person whose body was found April 27 in Central Park in downtown Davis. He had been murdered. And initial reports indicated that the Police did not have any good clues as to what had happened because there were no witnesses.
When I found out that this was David I posted a few things to social media because I wanted to make sure people knew that he was a good person, an interesting person, and was not just some random bit of information.
Very sad and shocking. I talked to David relatively frequently https://t.co/7jLbcMtYme
— Jonathan Eisen (@phylogenomics) April 28, 2023
And I am glad I posted this because many people responded to also say that David had impacted them.
For example:
So senselessly tragic. I saw David for years on 3rd before the compassion bench was built in his honor. A human truly loved by the Davis community. My favorite definition from his book was something like "compassion is sharing your Co-Op chocolate chip cookie with someone else". https://t.co/ENKh9kk0jx
— Vince Buffalo (@vsbuffalo) April 28, 2023
'She recalled meeting Breaux on what she described as a “dark day,” having heard of yet another school shooting in the U.S.
— Ted Hand (@t3dy) April 29, 2023
“I was just feeling very negative,” Tafoya said. “We sat and we talked, and he made me realize that going out there and doing something was compassion.” https://t.co/XIDHNaWjJG
I also posted this to other places, like Facebook, and there I found out that Nat Pearson, who I had known since I was a PhD student at Stanford and he was and undergrad there, had been a first year dorm mate of David's and also had wonderful things to say about him.
I had planned to go visit "Compassion Corner" on Saturday during my regular bike outing to the Farmer's market but alas I could not since I had to go to UC Davis Medical Center for an MRI.
Thanks once again @UCDRadiology for excellent service / care - quick in / quick out - all personnel excellent - and also happy to see mask requirement still in place https://t.co/kEY9gUVM55
— Jonathan Eisen (@phylogenomics) April 29, 2023
Suspect description from Davis PD:
— Zach Boetto (@FOX40Zach) April 30, 2023
- Lightskin male
- Height: 5’7-5’8
- 19-23 years of age
- Long curly loose hair
- Last seen wearing a white hat & a light colored t-shirt
- Riding a bike with straight handle bars@cityofdavispd @FOX40 https://t.co/CIWg3vCDib
And soon we found out that the victim was a UC Davis student - Karim Majdi Abou Najm
Davis Enterprise (via @laurenkeene) is reporting additional details on the fatal stabbing of a 20 year-old male in Sycamore Park in Davis. https://t.co/5KGMmDIFnb pic.twitter.com/QnMsvos82A
— Anthony Volkar (@ucdvolkie) April 30, 2023
This is Karim Abou-Najim. He is the victim in the deadly stabbing at Sycamore Park in Davis. Family friends tell us he was riding his bike home from his award ceremony for his research work. The 20-year-old was graduating in just 10 days from UC Davis. @CBSSacramento pic.twitter.com/BEKmE6xnyT
— Tori Apodaca (@tori_apodaca) May 1, 2023
And this was of course horrific. A second murder in this sleepy town of Davis. And a UC Davis student. And for me, someone who I had multiple direct and indirect connections to. Just horrific.
😢😢😢😢😢😢😢 https://t.co/2jXFSDxIh6
— Jonathan Eisen (@phylogenomics) May 1, 2023
I decided that some NatureTherapy for me and others might be useful.
It is a sad and scary time right now in #davisca and at @ucdavis due to recent murders. I thought some #naturetherapy might be useful for me and others. From the @ucdavis Arboretum https://t.co/lK97RdV8VH pic.twitter.com/cSquRgaaGd
— Jonathan Eisen (@phylogenomics) May 1, 2023
Stunning sight at @ucdavis Riparian Preserve this AM. Male Western Tanager with snack. Some #NatureTherapy for a wounded university at town. #DavisCA https://t.co/FLet4dDzqN pic.twitter.com/FNrKNJZQ09
— Jonathan Eisen (@phylogenomics) May 1, 2023
Really feeling sad about the recent murders in #davisca - thinking of the two people who were killed and all their families, friends, and colleagues - spent a lot of the day in nature thinking of them - here is some #naturetherapy from #yolobypass pic.twitter.com/0cfi5uEEN9
— Jonathan Eisen (@phylogenomics) May 2, 2023
Been a rough few days here in #DavisCA so I spent much of the day out in nature trying to rebalance. At the end of the day I was driving home and took a little detour on a rural farm road in #DavisCA and saw this guy. Blue Grosbeak. Not a bad ending to my day of #NatureTherapy. https://t.co/Hi5ljBOtnu pic.twitter.com/oCzlBNOGiD
— Jonathan Eisen (@phylogenomics) May 2, 2023
And these got some nice responses that indicated they helped some other people out there. And then in the middle of the night we got a phone call and multiple text messages telling us there was a third stabbing.
Just got this alert - report of another stabbing in #davisca pic.twitter.com/ClTQcwC1Ty
— Jonathan Eisen (@phylogenomics) May 2, 2023
And despite a shelter in place order the suspect got away
Third stabbing in Davis — suspect eludes manhunt after shelter-in-place downtown, at UC Davis https://t.co/MmQ8g8tmlE
— Marcos Breton (@MarcosBreton) May 2, 2023
Later we found out that the victim fortunately survived but was seriously wounded.
Meeting is back on.
— KCRA Lee Anne Denyer (@KCRALeeAnne) May 3, 2023
The victim from last night's stabbing, the police chief says, underwent surgery but is awake, alert and talking. She is in critical condition but making progress, he said.
More: https://t.co/z6lU2liJWi @kcranews
And all around town and at UC Davis people were justifiably both devastated and scared. So for the class I am currently teaching, we put into place every measure we could to let students NOT have to come to class in the wake of such incidents. And despite UC Davis focusing on only nighttime safety, some of us also understood that students might be afrain in the day time too (with good reason I might add).
To everyone in the @ucdavis and #DavisCA area, be careful out there. But also, while attacks have happened at nighttime, @ucdavis & @cityofdavispd should also be emphasizing at least some caution and extra protections during daytime until the person(s)responsible are caught https://t.co/4ftKlDf6HL
— Jonathan Eisen (@phylogenomics) May 2, 2023
That morning I went out for some #NatureTherapy again but this time decided to not go to too isolated a place on campus and went off campus:
A little more #naturetherapy from Putah Creek https://t.co/3bZnWJw8Ef pic.twitter.com/FL9yWPoKcj
— Jonathan Eisen (@phylogenomics) May 2, 2023
I then went to "Compassion Corner" to pay tribute to David. I took some pics and posted them.
At Compassion Corner in #DavisCa thinking of David Breaux and the many many many times I saw him here over the years - RIP Compassion Guy pic.twitter.com/5z2Esiy3A5
— Jonathan Eisen (@phylogenomics) May 2, 2023
And also made a video panorama
Video panorama of Compassion Corner pic.twitter.com/Wdu6QpUNhT
— Jonathan Eisen (@phylogenomics) May 2, 2023
Helicopter from @kcranews flying over #DavisCA right now - not sure what it is doing ... pic.twitter.com/ikSbateQjN
— Jonathan Eisen (@phylogenomics) May 4, 2023
Turns out, they were watching overhead as police were questioning a person of interest who had been caught near Sycamore Park and was eventually broungt in to be interviewed.
Person of interest in Davis stabbings detained, police say https://t.co/a7KIa4g8kU
— Jonathan Eisen (@phylogenomics) May 4, 2023
Meanwhile, a fund had been set up in honor of Karim and I donated to it and suggested other do so too.
I encourage everyone to donate to this fund in honor of @ucdavis undergrad Karim Majdi Abou Najm who was killed last week in #DavisCA
— Jonathan Eisen (@phylogenomics) May 4, 2023
Memorial Undergraduate Student Research Award https://t.co/c1gV0ZuCe9
This was when I found out that Nadine Yehya, who I knew from various science communications functions and from Twitter interactions was Karim's mother.
Thank you Johnathan for donating and keeping his legacy alive. Karim is my son who was taken from us all prematurely
— Nadine Yehya, PhD (@yehya_nadine) May 4, 2023
I went back out for more #NatureTherapy for myself and to share
Still spending a lot of time in nature trying to process everything happening in #DavisCA and thinking of the stabbing victims and their families and friends. Tuesday I drove around with my daughter at dusk and got a nice pic of an owl in rural #DavisCA https://t.co/xh5dlDB2Ey pic.twitter.com/g5e0qj0r8l
— Jonathan Eisen (@phylogenomics) May 4, 2023
And I then went to the memorial for Karim in Sycamore Park and tried to get some nice pics there.
I went by the memorial for Karim in Sycamore Park in #DavisCA today. So very sad but also moving. Thinking of Karim and his family and friends today.
— Jonathan Eisen (@phylogenomics) May 4, 2023
Please consider donating the the fund to create a @ucdavis Undergraduate Student Research Award in his honor (see below). https://t.co/uOtIKI2Tzz pic.twitter.com/sTiOUM4DK0
And I also did some iNaturalist observations with the goal of setting up a project in the area in honor of Karim.
When I went to Sycamore Park this AM to visit the memorial for Karim Majdi Abou Najm I also decided to do a little #naturetherapy for myself and to share. It was pretty dark out so pics aren't great but here are a few: bushtit, house finch, Anna's hummingbird, black phoebe. https://t.co/3Ma9lVOWcT pic.twitter.com/0YAn45mFxQ
— Jonathan Eisen (@phylogenomics) May 4, 2023
And then later in the day we found out the promising news:
Breaking news: Davis police will announce arrest in series of brutal stabbings this afternoon. https://t.co/DJDY1GblBc
— The Sacramento Bee (@sacbee_news) May 4, 2023
Well this sounds like amazing news - arrest in #DavisCA stabbings https://t.co/lOCRTMtc6l
— Jonathan Eisen (@phylogenomics) May 4, 2023
And important comment from Nat Pearson
Hope for a Davis community gripped by violence and fear.
— Nathan Pearson (@GenomeNathan) May 4, 2023
And a reminder: victim David Breaux, longtime friend to many of us there and beyond, would (and tirelessly did) seek #transformativejustice. https://t.co/tPkRu2ezP6 pic.twitter.com/8Me2iTujqB
I responded to it:
I spent about an hour at / near his corner yesterday thinking about David and trying to channel his compassion https://t.co/nRW3ilCmgG
— Jonathan Eisen (@phylogenomics) May 4, 2023
And also noted that I had started making iNaturalist observations there too:
And I also started making @inaturalist observations at that site - seemed like something he would have liked https://t.co/ovAX9jkxTb and I will keep doing them regularly
— Jonathan Eisen (@phylogenomics) May 4, 2023
And some additional details stated trickling out
Important details on #DavisCA stabbing arrest h/t @peiferlabunc https://t.co/Qh5Gbde4ub
— Jonathan Eisen (@phylogenomics) May 4, 2023
See details on the press conference regarding the arrest in the #DavisCA stabbing cases https://t.co/d1YejFKE10
— Jonathan Eisen (@phylogenomics) May 4, 2023
Person arrested is s 21 year old Carlos Dominguez of #DavisCA and was a student at @ucdavis until last week according to the police chief
— Jonathan Eisen (@phylogenomics) May 4, 2023
Well I just want to say - thank you to the @cityofdavispd @UCDavisPolice @FBI and all the witnesses and people who helped catch this person. https://t.co/xgPAIaXxAj
— Jonathan Eisen (@phylogenomics) May 4, 2023
And that is how we get to today.
I went by the memorials for Karim and David this AM and the sun was shining, birds were singing and it felt like some sort of renewal. Here are some pics - more later https://t.co/3Ma9lVOWcT pic.twitter.com/db3VrmGb5Y
— Jonathan Eisen (@phylogenomics) May 5, 2023
I note - I went to see if there was anything in terms of public displays at the site of the third stabbing but did not see anything. The woman who was stabbed is Kimberlee Guillory and I would like to at some point also pay tribute in some way to her.
I made some additional nature observations at each site - going to try to keep doing this regularly as a tribute to both of them - and am posting them to iNaturalist - here is my favorite from from today near Karim's memorial https://t.co/5rDNGhC8ak
— Jonathan Eisen (@phylogenomics) May 5, 2023
Also see https://t.co/cnZ1YRhGlZ
— Jonathan Eisen (@phylogenomics) May 5, 2023
— Jonathan Eisen (@phylogenomics) May 5, 2023
And also made some observations from near Compassion Corner / David's memorial such as this nice mushroom https://t.co/MGDRxWjftK
— Jonathan Eisen (@phylogenomics) May 5, 2023
And this Swainson's hawk was flying overhead https://t.co/GteADTqDuT
— Jonathan Eisen (@phylogenomics) May 5, 2023
Basically, I want to make sure that people do not forget Karim and David. They were wonderful people. They were taken from us too soon in a terrible way. But we can get some good out of this. And I will try my best to contribute to that.
Responses to question about functional annotation of metagenomic reads
Hi. We would like to functionally annotate some metagenomic sequencing reads without doing any assembly or binning or read mapping to reference genomes. Just annotate by searching things like nr, PFAM, COGs, etc. Anyone know of tools that do this?
— Jonathan Eisen (@phylogenomics) March 29, 2023
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in UncategorizedPanoramas from the past …
I brought my Olympus OM1 and did something I thought could be cool with it. I took multiple overlapping pics of landscapes with the idea that I would use Photoshop or some such program to combine them together into large panoramic landscape images
The only problem was -- I did not know how to do that
But when I got home I got the photos developed and scanned them using a scanner I had and merged them with something like Claris Draw. Here is an example - three pics from the Sand Dunes area - and the low res panorama I made - not so bad but - well - not great either
I did the same thing in other places around Death Valley. Snapping pics and then when I got home tried to make the panoramas. This one is of Titus Canyon. Not so great but OK it reminded me of the place
Well, fortunately, I keep everything. And I got pics and slides and negatives scanned with better scanners a while back. And recently I was looking through pics and re-encountered these attempted panoramas. So with Adobe Lightroom I tried again
And, well, the results were pretty fucking nice. Here is a new stitched panorama of the dunes - probably going to get the printed and framed
And here is a remake of the Titus Canyon
I am so glad I kept my old pics in relatively good shape and got them scanned. And even though it did not work out so well at the time, I am also glad I did these "click and pan" collections now that I have better tools for merging them. This one is my favorite so far
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in Uncategorized