Another 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 t...
Source: The Tree of Life - May 5, 2023 Category: Microbiology Tags: DavisCA UCDavis Karim Majdi Abou Najm David Breaux Kimberlee Guillory compassion Source Type: blogs
Responses to question about functional annotation of metagenomic reads
Posted a question to a few placesHi. 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, 2023Humann suggestion fraggenescan on the raw reads, then use hmmer w/ pfam-A or kegg hmm.EggNog MapperMGRASThttp://mgrast.orgMetawrapYooseph approachhttps://pubmed.ncbi.nlm.nih.gov/27400380/https://pubmed.ncbi.nlm.nih.gov/27585568/mi-faserhttps://bromberglab.org/project/mifaser/ …MGXhttps://micr...
Source: The Tree of Life - April 4, 2023 Category: Microbiology Source Type: blogs
Panoramas from the past ...
In 1997, my then girlfriend (now wife) and I went camping in Death Valley. It was our fourth trip there to camp in grad. school.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 imagesThe only problem was -- I did not know how to do thatBut 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 ...
Source: The Tree of Life - January 20, 2023 Category: Microbiology Source Type: blogs
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:https://www.mdpi.com/journal/microorganismsCool. Cool. Except I never agreed to be on their editorial board. And yet there I am on their web site.https://www.mdpi.com/journal/microorganisms/editors?page_no=3No MDPI Microoorganisms. This is not OK.
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This is from the" Tree of Life Blog "
of Jonathan Eisen, an evolutionary biologist and Open Access ad...
Source: The Tree of Life - December 19, 2022 Category: Microbiology Source Type: blogs
Lake Arrowhead Microbial Genomics Meeting History
Making a page here with information on the history of the Lake Arrowhead Microbial Genomes meeting. Please post in comments any additional links to other information.19981998_arrowhead booklet1998_LakeArrowhead notes1998_Arrowhead booklet version 220002000_arrowhead bookletJonathan Eisen talk from 2000 Jonathan Eisen talk on " Phylogenomics of DNA repair " at Lake Arrowhead Small Genomes Meeting 20002002Jonathan Eisen talk from 2002 Jonathan Eisen talk on " Phylogenomics of Microbes " at Lake Arrowhead Small Genomes Meeting 20022004lakearrowhead2004 bookletJonathan Eisen talk from 2004 Jonathan Eisen talk on "...
Source: The Tree of Life - September 11, 2022 Category: Microbiology Source Type: blogs
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/yKRYU1Gugd1/nhttps://t.co/vD0Cpb795f— Jonathan Eisen (@phylogenomics)August 19, 2022After I posted that, The Chancellor of UC Davis Gary May posted an article with some details of current UC ...
Source: The Tree of Life - August 20, 2022 Category: Microbiology Source Type: blogs
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 seepostings with identifications at iNaturalist.
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This is from the" Tree of Life Blog "
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.
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Source: The Tree of Life - June 6, 2022 Category: Microbiology Source Type: blogs
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 channelThis 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 ...
Source: The Tree of Life - May 16, 2022 Category: Microbiology Source Type: blogs
Endosymbiosis Animations for " Biodiversity and the Tree of Life "
So I am in the midst of co-teachign a very large introductory biology course at UC Davis " BIS2C - Biodiversiy and the tree of Life " . I cover much of microbial diversity in this class and also the large scale structure of the Tree of Life. As always, I spent a lot of time working on slides and such for this class and recently posted some animations based on these slides to Twitter and Facebook and thought I would share some of them here. For today, I am sharing the animations I made on Endosymbiosis. I posted a first version of this to Twitter last week.Endosymbioses are so cool:Some of the images / animations I wil...
Source: The Tree of Life - April 23, 2022 Category: Microbiology Tags: BIS2C tree of life UC Davis Source Type: blogs
A good bye to my beloved Clover
Our adopted cat Clover is pretty sick right now and likely on her last legs. We (my family, and the family of@LoranWyman who were her previous caretakers) are very sad. I compiled some of my Tweets about her herehttps://t.co/JqY1Mijips— Jonathan Eisen (@phylogenomics)April 3, 2022Sadly, Clover is gone. I am 💔. I loved her very very very much.https://t.co/xQ1QXMQ658— Jonathan Eisen (@phylogenomics)April 3, 2022
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This is from the" Tree of Life Blog "
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitt...
Source: The Tree of Life - April 6, 2022 Category: Microbiology Source Type: blogs
The ongoing saga with the UC Health Insurance Pharmacy " Benefits " Via Navitus
Well the saga continues. Here is an update. It all started March 7. See here for a long thread and also responses.Dear@UofCalifornia@ucdavisThis is NOT OK.I just got a notice by letter in mail that my insurance will no longer cover the insulin I have been getting " as of January 1, 2022 " . Letter was dated in February and was received after March 1, 2022.This is NOT OK.— Jonathan Eisen (@phylogenomics)March 7, 2022 See this thread in an easier to read format here:https://threadreaderapp.com/thread/1500934973775249412.htmlWell, in case you missed it. Two weeks ago I posted about the disastrous and dangerous and incompete...
Source: The Tree of Life - March 29, 2022 Category: Microbiology Source Type: blogs
Some links to articles about Diabetes and COVID19
Posted some links to Twitter that I am compiling here too about type 1 diabetes and COVID19 with a focus on recommendations for diabetics in current COVID situationPosting some information about#COVID19 and#type1#diabetes that might be useful to folkshttps://t.co/q9LrTXyrAy"Your Guide to Post-COVID Travel with Type 1 Diabetes"— Jonathan Eisen (@phylogenomics)March 21, 2022"As masks come off, vulnerable Americans feel left behind"https://t.co/WGDJ1eII6x— Jonathan Eisen (@phylogenomics)March 21, 2022COVID-19 Update: The Diabetes Connection, WHO Concerned about BA.2https://t.co/GT9xXPMNX2&mdash...
Source: The Tree of Life - March 23, 2022 Category: Microbiology Source Type: blogs
Lots of useful responses to question " What should high risk people do in face of relaxed masking requirements " ?
So I posted this to Twitter.So - hive mind. A question. If you were at high risk for COVID complications if infected, with the ending of indoor mask requirements, would you just try to avoid large indoor gatherings of people even when you wear a good mask?— Jonathan Eisen (@phylogenomics)March 18, 2022And got lots of useful resposnes. Rather than compile them here if interested people should browse the responses.
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This is from the" Tree of Life Blog "
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.
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Source: The Tree of Life - March 23, 2022 Category: Microbiology Source Type: blogs
The ongoing disaster of the new UC Health Insurance Pharmacy " benefits "
Recently I posted to Twitter about the disastrous new University of California Pharmacy Benefits system.Dear@UofCalifornia@ucdavisThis is NOT OK.I just got a notice by letter in mail that my insurance will no longer cover the insulin I have been getting " as of January 1, 2022 " . Letter was dated in February and was received after March 1, 2022.This is NOT OK.— Jonathan Eisen (@phylogenomics)March 7, 2022In summary, I got a letter in March that warned me of something that was about to happen in January (that is, in the past). And what was about to happen was bad - cutting off coverage of my insulin. And the sy...
Source: The Tree of Life - March 22, 2022 Category: Microbiology Source Type: blogs
Full text of University of California Message about Their Disastrous Pharmacy Benefits System
Recently I posted to Twitter about the disastrous new University of California Pharmacy Benefits system.Dear@UofCalifornia@ucdavisThis is NOT OK.I just got a notice by letter in mail that my insurance will no longer cover the insulin I have been getting " as of January 1, 2022 " . Letter was dated in February and was received after March 1, 2022.This is NOT OK.— Jonathan Eisen (@phylogenomics)March 7, 2022In summary, I got a letter in March that warned me of something that was about to happen in January (that is, in the past). And what was about to happen was bad - cutting off coverage of my insulin. And the sy...
Source: The Tree of Life - March 22, 2022 Category: Microbiology Source Type: blogs
