The Tree of Life
Blog of Jonathan A. Eisen, Professor at U.C. Davis.
Thursday, January 19, 2023
Panoramas 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
Monday, December 19, 2022
Well, this is about as scammy / spammy as a journal can get ... putting me on an editorial board I did not agree to be on ...
So I got an email this AM from "Microorganisms Editorial Office"
Dear Prof. Dr. Eisen,
We are pleased to inform you that your information has been announced on the
webpage of our journal's board.
Please check that all of your information is correct here:
Cool. Cool. Except I never agreed to be on their editorial board. And yet there I am on their web site.
No MDPI Microoorganisms. This is not OK.
Sunday, September 11, 2022
Lake Arrowhead Microbial Genomics Meeting History
- 1998_arrowhead booklet
- 1998_LakeArrowhead notes
- 1998_Arrowhead booklet version 2
- 2000_arrowhead booklet
- Jonathan Eisen talk from 2000 Jonathan Eisen talk on "Phylogenomics of DNA repair" at Lake Arrowhead Small Genomes Meeting 2000
- Jonathan Eisen talk from 2002 Jonathan Eisen talk on "Phylogenomics of Microbes" at Lake Arrowhead Small Genomes Meeting 2002
- lakearrowhead2004 booklet
- Jonathan Eisen talk from 2004 Jonathan Eisen talk on "Phylogenomics of Microbes" at Lake Arrowhead Small Genomes Meeting 2004
- It's Miller Time - Lake Arrowhead Microbial Genomes Conference -- about to begin
- Morgan Langille Review of Arrowhead Conference
- September 16, 2008: Lake arrowhead notes - UPDATED
- Jonathan Eisen talk from 2008 Jonathan Eisen talk on "Genomic Encyclopedia" at Lake Arrowhead Small Genomes Meeting 2008
- Srijak Bhatnagar: Lessons from 2012: Lake Arrowhead Microbial Genomes
- Storify for Lake Arrowhead Microbial Genomes #LAMG12 Meeting
- Lake Arrowhead Microbial Genomes Meeting 2012 Speaker Gender Ratio #LAMG12
- Lake Arrowhead Microbial Genomes 2012 #Genomes #Microbes #Mountains #Lake #Fun #Wine #MustGo
- Jonathan Eisen talk from 2012 Jonathan Eisen @phylogenomics talk for #LAMG12
- Recorded talks from Lake Arrowhead (#LAMG12); James Meadow, Jason Stajich, Susana Remold
- Lake Arrowhead Microbial Genomics Meeting 2012: Microbiology of the Built Environment Session
- Wakelet: https://wke.lt/w/s/3XFHf
- microBEnet wakelet: https://wke.lt/w/s/0Pvtc
- Save the dates / preliminary program for Lake Arrowhead Microbial Genomes Meeting
- Everything You Wanted to Know about the Lake Arrowhead Microbial Genomes meeting #LAMG14
- [slideshare id=39085737&doc=u00svzw6sd6cmzosdqpq-signature-630f2659b9ee1c26c2aa680828306e8586a48ecd7c2440ecf20af82024ab7966-poli-140915022043-phpapp01]
- Storify Days 1-3
- 2014 meeting wrap up on microBEnet
- Jonathan Eisen talk from 2014. http://www.slideshare.net/phylogenomics/jonathan-eisen-history-of-lake-arrowhead-microbial-genomes
- Lake Arrowhead Microbial Genomics 2014 (#LAMG14) F1000 Site w/ Posters and Talks
- Report and Storify from Lake Arrowhead: Day 3
- Report and Storify from Lake Arrowhead: Day 2
- Report and Storify from Lake Arrowhead Microbial Genomics: Day 1
- Wakelet Day 1-3: https://wke.lt/w/s/EiuMu
- Wavelet Day 3-4: https://wke.lt/w/s/oo5xE
- Wakelet Day 4: https://wke.lt/w/s/GyX32-
- Wakelet Day 5: https://wke.lt/w/s/85aHm
- 21st Annual International Meeting on Microbial Genomes at Lake Arrowhead 9/18-22
- Reports from #LAMG16 Lake Arrowhead Microbial Genomes
- Lake Arrowhead Microbial Genomics #LAMG16: Day 4 and Random Thoughts
- microbiology of the Built Environment session at Lake Arrowhead Microbial Genomes meeting
- microBEnet session wavelet: https://wke.lt/w/s/mYYhh6
- Lake Arrowhead Microbial Genomes #LAMG16: Day 3
- Lake Arrowhead Microbial Genomics #LAMG16 Report: Day 2
- Lake Arrowhead Microbial Genomics #LAMG16 Report: Day 1
- Wakelet Day 1-2 https://wke.lt/w/s/t5u4M
- Wakelet Day3: https://wke.lt/w/s/BvXae
- Wakelet Day 4-5: https://wke.lt/w/s/If2XW
- Eisen Tweets wavelet: https://wke.lt/w/s/WQ4Ud
Friday, August 19, 2022
Wanted - comments on the current @ucdavis COVID plans
So - I have been publicly and privately critical of some of the recent @ucdavis practices regarding COVID. If you want to know more about my areas of concern see for example this Twitter thread which I posted today:
Following up on this I thought I would share the slides I used for my presentation to @Chancellor_May and his leadership group a few weeks ago with my thoughts on the @ucdavis current #COVID response. https://t.co/yKRYU1Gugd— Jonathan Eisen (@phylogenomics) August 19, 2022
After I posted that, The Chancellor of UC Davis Gary May posted an article with some details of current UC Davis COVID plans. See https://leadership.ucdavis.edu/news/checking-in-with-chancellor-may-planning-ahead
What he wrote is below - but rather than comment myself right now, I am wondering - what do people out there (especially those at UC Davis) think of all of this?
Davis campus students are required to be compliant with the UC Vaccine Policy by Sept. 21 either by being up to date on vaccines and boosters or submitting a religious or medical exception request. Students who are not in compliance by Sept. 21 will receive a registration hold on their accounts for fall quarter. Please visit the Information for Students and Families page on the Campus Ready website for additional details about the vaccine policy compliance process. The vaccine policy also applies to employees.
It’s clear that COVID-19 will be with us for some time. UC Davis continues to monitor for the virus through weekly wastewater testing, which helps inform our decision making. We have reviewed the scientific literature and heard from many people, and, at this point, we are not likely to increase the frequency of wastewater testing given that Davis is not a large urban center. Also please note: We have access to daily test results from Stanford’s Sewer Coronavirus Alert Network (SCAN).
We encourage our students, faculty and staff to get tested regularly for COVID-19. The Davis campus testing kiosk — offering free, asymptomatic testing (saliva-based) — remains in operation, although in a new location: Human Resources Administration Building (1050 Blue Ridge Road), across La Rue Road from the ARC. The kiosk is open from 8:30 a.m. to 4:30 p.m. Sunday through Thursday (closed Fridays and Saturdays). Testing is by appointment only through the Health-e-Messaging portal. Please note: Testing appointments are limited from Sept. 13 to 15, due to move-in.
At-home antigen tests are available for free as follows:
- By mail from the federal government.
- From no-charge vending machines around Yolo County. The machines are accessible 24 hours a day at the Mary L. Stephens Davis Branch Library, 315 E. 14th St.; West Sacramento City Hall, 1110 W. Capitol Blvd.; Winters City Hall, 318 1st St.; and Esparto Regional Library, 17065 Yolo Ave. (with one more to be installed in Woodland).
- From Yolo County libraries during open hours.
I would also like to recognize the effects of long COVID and the impact it continues to have on people. We are learning more about it every day, in UC Davis Health’s Post-COVID-19 Clinic, which opened in November 2020; and in our research and clinical studies, including one assessing the risks for children.
Students affected by long COVID should work with the Student Disability Center for resources and support. Employees should work with Disability Management Services. These units are busy, so please reach out to begin the interactive process as soon as you can.
Masking and air filters
I recognize that there is still some anxiety about masking. While the Davis campus does not have a mask mandate in place, we strongly recommend that people wear masks indoors to reduce risk.
Free masks are coming soon. The university plans to distribute one N95 mask to every student and employee this fall quarter, with this one-time distribution to take place in September. For more information about the distribution, students should contact their major departments, and employees should contact their departments or units. See “Directions for departments” on how to acquire mask supplies.
Remember that a proper mask fit is especially important. A 10-minute video is available for students on how to properly use N95 masks, also called respirators. They are rated to filter out 95% of particles.
Employees are required to complete a 10-minute video training about the proper use of N95 masks.
Yolo County also offers video guidance on masking. Further information can be found at Campus Ready and through the California Department of Public Health.
If you’re concerned about air filtration at home, a Corsi-Rosenthal Box is a cost-effective device that can be built with just a few components. The box was co-invented by Richard Corsi, dean of the College of Engineering, and has received acclaim nationwide. Visit this link to learn how to build your own Corsi-Rosenthal Box.
Sunday, June 05, 2022
Best pics from Trip to Monterey - Day 1 - May 25, 2022
Went on a brief trip to Monterey, CA last week. Took lots of pics. Here are some of the better ones. Also see postings with identifications at iNaturalist.
Monday, May 16, 2022
Videos about using the UCSC Genome Browser for analysis of SarsCOV2
These look pretty useful and thought I would post here. Text is from the UCSC Youtube channel
This 5-part video series is for virologists and public health researchers interested in leveraging the UCSC Genome Browser and web interface to UShER (Ultrafast Sample placement on Existing tRees). These tools are a 'one-stop shop' to understand SARS-CoV-2 through genome annotations as well as track variants by placing your samples in a phylogenetic tree with millions of other SARS-CoV-2 sequences. Use the SARS-CoV-2 Genome Browser: http://bit.ly/sarscov2browser Visit our SARS-CoV-2 Genome Browser and UShER quick start page with videos, scripts and more: http://bit.ly/ucsccovidbrowser COVID-19 Research at UCSC: https://genome.ucsc.edu/covid19.html 'The UCSC SARS-CoV-2 Genome Browser' publication: https://www.nature.com/articles/s4158... 'Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic' publication: https://www.nature.com/articles/s4158... UShER documentation, installation, source code:: https://github.com/yatisht/usher https://usher-wiki.readthedocs.io/en/... COVID-19 Genomic Epidemiology Toolkit module "Realtime Phylogenetics with UShER: https://www.cdc.gov/amd/training/covi... Learn more about the UCSC Genome Browser: http://genome.ucsc.edu https://twitter.com/genomebrowser Learn more about the UCSC Genomics Institute: https://twitter.com/ucscgenomics https://genomics.ucsc.edu/
Saturday, April 23, 2022
Endosymbiosis Animations for "Biodiversity and the Tree of Life"
Note - I added music - Mussorgsky - Night on Bald Mountain for drama ... I also posted it to Facebook:
Endosymbioses are so cool:— Jonathan Eisen (@phylogenomics) April 20, 2022
Some of the images / animations I will be using today in BIS2C at @ucdavis (I made a little movie and added music here but will have richer explanations for class) pic.twitter.com/92Eb7PMTjL
OK - updated with modifications based on corrections/comments from @Sergiophyceae @mcsymbiont & @DanStarrUCDavis (note, again, these are extracted from slides with lots of other details including comments about which things don't always happen ...) pic.twitter.com/LNGO8Zs94E— Jonathan Eisen (@phylogenomics) April 21, 2022
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