Eisen Lab Blog

For those who missed it: "Science as an open enterprise" from Royal Society

This will be of interest to many I think: Science as an open enterprise – Report | Royal Society

It is a comprehensive report from the Royal Society with links to videos, text, previous meetings, references, EPUBs, and more relating to a report that was released a few days ago.  From the web site:

Six key areas for action are highlighted in the report:

  • Scientists need to be more open among themselves and with the public and media
  • Greater recognition needs to be given to the value of data gathering, analysis and communication
  • Common standards for sharing information are required to make it widely usable
  • Publishing data in a reusable form to support findings must be mandatory
  • More experts in managing and supporting the use of digital data are required
  • New software tools need to be developed to analyse the growing amount of data being gathered

Definitely worth a serious browsing/reading.

For more on this see …

——–
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.

——–

"More than a freezer" – #microbes in funny ad for Thermo Scientific freezers

I don’t normally post about ads but this one is quite well done. From Thermo Scientific – “More than a freezer”.

——–
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.

——–

Best. Microbiology. Video. Ever.

Well, I could say so so much about this.  But it speaks for itself.  Funny.  Gross.  Cute.  And more.  Just watched it – like – seven times in a row.  Best. Microbiology. Video. Ever.

From Jennifer Gardy.

——–
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.

——–

Science Magazine Special Issue on H5N1 #Links #Microbes

"As a service to the community, AAAS is also making these articles free to the public. "

Would be nice to make ALL of Science available to the public but AAAS is a dinosaur of sorts. Anyway — at least these are available. (Thanks to Eileen Choffnes for the links).

H5N1: Bruce Alberts

Science 22 June 2012: 1521

http://www.sciencemag.org/content/336/6088/1521.full.pdf

Benefits and Risks of Influenza Research: Lessons Learned: Anthony S. Fauci and Francis S. Collins

http://www.sciencemag.org/content/336/6088/1522.full.pdf

Implementing the New U.S. Dual-Use Policy:Carrie D. Wolinetz

http://www.sciencemag.org/content/336/6088/1525.full.pdf

Evolution, Safety, and Highly Pathogenic Influenza Viruses:Marc Lipsitch, Joshua B. Plotkin, Lone Simonsen, and Barry Bloom

http://www.sciencemag.org/content/336/6088/1529.full.pdf

Influenza: Options to Improve Pandemic Preparation : Rino Rappuoli and Philip R. Dormitzer

http://www.sciencemag.org/content/336/6088/1531.full.pdf

Perspectives

Regulating the Boundaries of Dual-Use Research – Mark Frankel http://www.sciencemag.org/content/336/6088/1523.full.pdf

Securing Medical Research: A Cybersecurity Point of View : Bruce Schneier http://www.sciencemag.org/content/336/6088/1527.full.pdf

Airborne Transmission of Influenza A/H5N1 Virus Between Ferrets (2012). Sander Herfst et al. http://www.sciencemag.org/content/336/6088/1534.full.pdf

· Materials/Methods, Supporting Text, Tables, Figures, and/or References Download Supplement

The Potential for Respiratory Droplet–Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host. Colin A. Russell et al. (2012). http://www.sciencemag.org/content/336/6088/1541.full.pdf

· Materials/Methods, Supporting Text, Tables, Figures, and/or References Download Supplement

Major lesson from #ASM2012 meeting: microblogs & microbiology go together well

Well without a doubt the biggest surprise to me of the American Society for Microbiology General Meeting was the massive increase in the use of Twitter compared to previous years.  Microbiologist are clearly just way way ahead of the curve compared to other scientists on this.  The tweets and retweets and discussion of tweets was so extensive that #ASM2012 was a trending topic on twitter for much of the time during the meeting:

For those not familiar with Twitter – this abbreviation w/ the # is known as a hashtag – and if everyone at a meeting uses this hashtag in their posts about the meeting then it is easy to keep track of all the meeting posts by searching for posts with that hashtag.  Such searches can be done in real time with various Twitter clients or via the Twitter website.

And if you followed in real time the #ASM2012 you were treated to a broad real-time coverage of pretty much the whole meeting.  At most broadly focused science meetings I have been at recently – even ones with 1000s of people like #AAAS – the use of Twitter has been relatively limited at best.  Sometimes a single session is covered well but very rarely is the whole meeting covered.  So this ASM meeting was indeed different.

I tried to create a “Storification” of all the Tweets from the meeting but Storify seems to crash when one includes so many tweets so that did not work.

So I tried to create my own archive via Twitter – by copying and pasting the posts from each day (some got left out here but it is decent coverage).   It is not as pretty as Storification but it works.  Still working on a full archive but Twitter makes it kind of difficult to do alas.

One thing missing however was the use of microbiology related hashtags for topics.  Seems we really need to get some coordination here to make it easier to search through and find tweets of interest.  Here are some I have used in the past and may be worth using if you want more people to notice your tweets.

#microbes
#bacteria
#archaea
#microbiology
#pathogens
#rRNA
#Antibiotics
#viruses
#yeast
#microbiome

Anyway – keep up the good work all you microbe-focused tweeters.  And though microblogging (i.e., Twitter and related things) is great – don’t forget to blog too.  See my growing list of microbiology related blogs and please add to it – either if you know of ones I missed – or by creating your own.

——–
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.

——–

Ooh – cool – got to get this "Illustrated Children’s Book Introduces Invisible World Of #Microbes"

Just saw this news story: Illustrated Children’s Book Introduces Invisible World Of Microbes.  This looks like a potentially good addition to the list of books that could be called “Microbiology for Kids.”  I have made a collection at Amazon of examples in this area.  Any other suggestions for microbiology books for kids? //ws-na.amazon-adsystem.com/widgets/q?ServiceVersion=20070822&OneJS=1&Operation=GetAdHtml&MarketPlace=US&source=ac&ref=tf_til&ad_type=product_link&tracking_id=thtrofli-20&marketplace=amazon&region=US&placement=1469985713&asins=1469985713&linkId=HLADZ63WT64INEJC&show_border=true&link_opens_in_new_window=true

——–
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.

——–

Quick summary of session at #ASM2012 on “The Great Indoors” #microBEnet

 The session at the ASM 2012 meeting on “The Great Indoors” seems to have gone well. I will be writing up a more detailed report but here is a quick summary done via “Storify”.

http://storify.com/phylogenomics/asm2012-microbenet.js[<a href=”http://storify.com/phylogenomics/asm2012-microbenet” target=”_blank”>View the story “Session at #ASM2012 on The Great Indoors: Recent Advances in the Ecology of Built Environments ” on Storify</a>]

——–
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.

——–

Lab meeting, June 20th, 2012

Holly Bik will be presenting for this week’s lab meeting.
We’ll be meeting in room 5206 of the genome center from 1:30 to 3:00pm.

Some notes from GSC13 session on microbiology of the built environment #microBEnet

At the GSC13 meeting a few months ago there was a session on microbiology of the built environment which was sponsored by my microBEnet project.

Posting some details from the meeting here.

Meeting notes and reports

Talk videos:

Paula Olsiewski

  http://www.scivee.tv/flash/embedCast.swf

The Indoor Standards – What Parameters Do We Need to Record? Jeffrey Siegel (University of Texas at Austin, USA)

http://www.scivee.tv/flash/embedCast.swf

Minimal Metadata for the Built Environment: A MIxS Extension Lynn Schriml (University of Maryland, USA)

http://www.scivee.tv/flash/embedCast.swf

The Home Microbiome Project: Unraveling the Relationship Between Human-associated and Home-associated Microbial Signatures. Jack Gilbert (University of Chicago/Argonne National Laboratory, USA)

http://www.scivee.tv/flash/embedCast.swf

The Indoor Virome! Scott Kelley (San Diego State University, USA)

http://www.scivee.tv/flash/embedCast.swf

The Role of VAMPs in the MoBEDAC Initiative Mitchell Sogin (Marine Biological Laboratory, Woods Hole, USA)

http://www.scivee.tv/flash/embedCast.swf

MoBEDAC – Handling Fungal Data From MicroBE Jason Stajich (University of California, Riverside, USA)

http://www.scivee.tv/flash/embedCast.swf

MoBeDAC – Integrated data and analysis for the indoor and built environment Folker Meyer (Argonne National Laboratory, USA)

——–
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.

——–

Collecting links to blogs that focus entirely or partly on microbiology topics #ASM2012

Making a list of blogs that focus entirely or partly on microbiology topics.  Here are some.  Would love suggestions for others. Obviously not all are of equal quality in terms of the writing or the science but the diversity is impressive.

  1. Aetiology from Tara Smith scienceblogs.com/aetiology
  2. A Flu Diary http://afludiary.blogspot.com/
  3. AIDS.GOV blog.aids.gov/
  4. Antibiotics: the perfect storm from David Shlaes antibiotics-theperfectstorm.blogspot.com/
  5. Antimicrobial Resistance from Miriam Barlow antimicrobial.blogspot.com
  6. Aspergillus Website Blog aspergillusblog.blogspot.com/
  7. Avian Flu Diary afludiary.blogspot.com/
  8. BacterioFiles from Jesse Noar bacteriofiles.blogspot.com
  9. Bacpathogenomics bacpathgenomics.wordpress.com/
  10. Bacteriophage, microbiology and the battle for funding from Philip Skipper phageresearch.blogs.lincoln.ac.uk/
  11. BioBE center Blog: biobe.uoregon.edu/
  12. Blastocystis Blog: blastocystisblog.blogspot.com/
  13. Barf Blog barfblog.foodsafety.ksu.edu/barfblog 
  14. Chimeras chimerasthebooks.blogspot.com/
  15. CoastalPathogens coastalpathogens.wordpress.com/
  16. Contagions from Michelle Ziegler contagions.wordpress.com
  17. Controversies in Hospital Infection Prevention haicontroversies.blogspot.com/
  18. Creepy Deadly Wonderful Parasites parasitewonders.blogspot.com/
  19. Curiosidades de la Microbiología curiosidadesdelamicrobiologia.bl…
  20. Cyanobacterial Adventures cyanobacterialadventures.blogspot.com/
  21. Daily Parasite dailyparasite.blogspot.com/
  22. Daniel Wilson’s Blog blog.danielwilson.me.uk/
  23. Dawn in Antarctica dawninantarctica.blogspot.com/
  24. El buit del temps blocs.mesvilaweb.cat/bloc/view/id/5664
  25. End the Neglect endtheneglect.org/
  26. Epidemonomics www.cddep.org/blog
  27. ERV from Abbie Smith scienceblogs.com/erv/
  28. Food Poison Journal www.foodpoisonjournal.com/
  29. Food Safety and Environmental Health blog www.safefoodsblog.com/
  30. Foraminifera Blog foraminifer.blogspot.com/
  31. Fun with Microbiology (What’s Buggin’ You?) http://thunderhouse4-yuri.blogspot.com/
  32. History of Vaccines www.historyofvaccines.org/blog
  33. HIV This Week http://hivthisweek.unaids.org/
  34. Hospital Infection Control and Prevention hicprevent.blogs.ahcmedia.com/
  35. Human Microbiome Journal Club hmjournalclub.wordpress.com/
  36. Indian Initiative for Management of Antibiotic Resistance save-antibiotics.blogspot.com/
  37. Infection Landscapes infectionlandscapes.org
  38. Infectious Diseases Today bactiman63.blogspot.com/
  39. International AIDS Vaccine Initiative www.iavireport.org/IRblog/default.aspx 
  40. It’s a small world fuckyeahmicrobiology.tumblr.com/
  41. Jason Tetro at the Huffington Post www.huffingtonpost.ca/jason-tetro/ *
  42. JHU Phage Hunters jhuphagehunters.wordpress.com/
  43. Lab Rat blogs.scientificamerican.com/lab…
  44. mBIO mbioblog.asm.org/mbiosphere
  45. Malaria World malariaworld.org/blog
  46. Matryoshka from Jeff Smith matryoshka.org/
  47. Memory Reactivation memoryreactivation.wordpress.com/
  48. Memoirs of a Defective Brain defectivebrain.fieldofscience.com/
  49. microbelog microbelog.wordpress.com/
  50. MicroBichitos blogs.elpais.com/microbichitos
  51. Microbial Diversity from Irene Newton microdiv.blogspot.com/
  52. microBEnet blog from Jonathan Eisen, David Coil, Holly Bik www.microbe.net/microbenet-blog/ 
  53. Microbe Matters from KD Shives http://kdshives.com
  54. Microbiology Bytes from AJ Cann microbiologybytes.com/blog
  55. Microblogology from Lorraine Cramer  microblogology.com/
  56. Microbiology Stories bacteriastories.blogspot.com/
  57. Mike the Mad Biologist mikethemadbiologist.com/
  58. Miss Parasitos missparasitos.blogspot.com/  AND missparasitesinenglish.blogspot.com/
  59. Monotreme’s Blog monotreme1000.wordpress.com/ *
  60. MyChrobial Romance from David Baltrus mychrobialromance.blogspot.com/
  61. Mycorant mycorant.com
  62. MycorWeb Fungal Genomics mycor.nancy.inra.fr/blogGenomes
  63. Mystery Rays from Outer Space www.iayork.com/MysteryRays/
  64. Not Exactly Rocket Science from Ed Yong blogs.discovermagazine.com/notrocketscience/
  65. Of Bacteria and Men from Robin Tecon ofbacteriaandmen.blogspot.com/
  66. One in Seven People http://oneinsevenpeople.co.uk/
  67. Outbreak News outbreaknews.com/
  68. Parasite of the Day dailyparasite.blogspot.com/
  69. Parasites http://www.rosemarydrisdelle.com/
  70. Pathogens, Genes and Genomes pathogenomics.bham.ac.uk/blog
  71. Pharmaceutical Microbiology by Tim Sandle pharmig.blogspot.com/
  72. Public Health Matters from the CDC blogs.cdc.gov/publichealthmatters/
  73. Rapid Microbiology Methods rapidmicromethods.com/ 
  74. RRResearch from Rosie Redfield rrresearch.blogspot.com
  75. Rule of 6ix from Connor Bamford ruleof6ix.fieldofscience.com
  76. Russell’s Blog from Russell Neches vort.org/
  77. Safe Food from John Brooks foodsafetywithjaybee.blogspot.com/
  78. Skeptic Wonder skepticwonder.fieldofscience.com
  79. Skewed Distribution skeweddistribution.com/
  80. Small Things Considered schaechter.asmblog.org/schaechter
  81. Smaller Questions www.smallerquestions.org/
  82. Sociobiology sociobiology.wordpress.com/
  83. Spirochetes Unwound spirochetesunwound.blogspot.com
  84. Superbug wired.com/wiredscience/superbug
  85. Superbugs and Drugs superbugsanddrugs.blogspot.com/
  86. Stringent Response stringentresponse.blogspot.com/
  87. Symbionticism from Seth Bordenstein symbionticism.blogspot.com/
  88. The Artful Amoeba blogs.scientificamerican.com/art…
  89. The Febrile Muse febrilemuse-infectious-disease.blogspot.com/
  90. The Genome Factory thegenomefactory.blogspot.com/
  91. The “Germ Guy” Blog: germguy.wordpress.com/
  92. The Hyphal Tip by Jason Stajich fungalgenomes.org/blog
  93. The Intestinal Gardner intestinalgardener.blogspot.com/
  94. The Loom from Carl Zimmer blogs.discovermagazine.com/loom
  95. The Oceloid from PSI Wavefunction blogs.scientificamerican.com/oceloid
  96. The Parasite Diary parasitediary.wordpress.com/
  97. The Tree of Life from Jonathan Eisen phylogenomics.blogspot.com
  98. Ultraphyte from Joan Slonczewski ultraphyte.com/
  99. We Beasties from Kevin Bonham scienceblogs.com/webeasties/
  100. The View from a Microbiologist from Samantha Price theviewfromamicrobiologist.fieldofscience.com/
  101. Viroblogy from Ed Rybicki http://rybicki.wordpress.com/
  102. Virology Blog from Vincent Racaniello virology.ws
  103. Viral Bioinformatics from Chris Upton athena.bioc.uvic.ca/blog/
  104. Worms and Germs www.wormsandgermsblog.com/
  105. Zoonotica zoonotica.wordpress.com
Podcasts and Videocasts


Not screened yet but considering adding to the above list

To add to list

Other stuff about microbes but not quite bloggy enough for my list above

Microbiology related blogs that are appear to be no longer active or very rarely active

Twitter lists
Paper.lis
Scoop.It
Science Blogs Networks that might have some microbial content not listed above
——–
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.

——–