the microbiology of the built environment talk for #sequencingcity by @phylogenomics

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microBEnet: microbiology of the Built Environment network

!Jonathan A. Eisen

University of California, Davis !

May 6, 2014 IBM Sequencing the City Meeting

2010

• The Alfred P. Sloan Foundation announced calls for proposals for a new “Indoor Environment Program”

• One project would be to “… establish an interdisciplinary network of researchers and practitioners that will build the community, operate community web resources, and organize specialized workshops …”

Paula Olsiewski

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http://www.microbe.net/


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Meetings &

Workshops

Citizen Science

Digital &

Social Media

Information (Overload)

Education

Openness &

Sharing

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Meetings &

Workshops

Citizen Science

Digital &

Social Media


Education

Openness &

Sharing

microBEnet

Goals !

• Knowledge dissemination • Networking • Catalyzing collaboration • Gap filling • Producing resources • Teaching openness

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Meetings &

Workshops

Citizen Science

Digital &

Social Media


Education

Openness &

Sharing

microBEnet

Meeting Examples • 2011 Session at Indoor Air • 2011 Citizen Microbiology • 2012 Session at Lake Arrowhead

Small Genomes • 2012 Session at Healthy

Buildings • 2012 VAMPS/QIIME • 2013 Citizen Microbiology at ASM • 2013 QIIME Workshops • 2013 GSC13 • 2014 Publish or Perish

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Meetings &

Workshops

Citizen Science

Digital &

Social Media

Education

Openness &

Sharing

microBEnet

Future Plans/Ideas !

• Animals in the BE • Microbial Eukaryotes in the BE • Closed ecosystems • Culture collections and reference

genomes • Building Science Education • Antimicrobials in the BE • Software Carpentry • Bioinformatics workshops • Ideas wanted

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Meetings &

Workshops

Citizen Science

Digital &

Social Media


Education

Openness &

Sharing

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Digital and Social Science

New Paper

Blog Post

Twitter

Facebook Page

LinkedIn GroupPubmed

CommonsMendeley

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New Paper Twitter

Facebook Page

LinkedIn GroupMendeley

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om/url?Rachel Adams

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Meeting

Storify

Twitter

Facebook Page

LinkedIn GroupBlog

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Allison Fish

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Monthly Newsletter

• Summary of blog posts

• “Resource of the Month”

• “People Behind the Science” video series… “Project of the Month”

• Recent and upcoming meetings

Mary Jo Seminoff

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People Behind the Science

Holly Bik Amy Pruden

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News Tracking

Brooke Borel

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Blog Post About News

Holly Ganz

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Meetings &

Workshops

Citizen Science

Digital &

Social Media


Education

Openness &

Sharing

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New Paper

Blog Post

Twitter

Facebook Page

LinkedIn GroupPubmed

CommonsMendeley

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Social Reference Collections

• 149 members • 950 papers • Curated Tags

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Author Contacts

Google Scholar PagesTagging

Blog Journal Club

New People’s Starting Point

RSS Feeds

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Journals Publishing MoBe work35th International Conference on Environmental Systems (ICES); 8th European Symposium on Space Environmental Control Systems (ESSECS), Rome, Italy, July 11, 2005.; 39th COSPAR Scientific Assembly. Held 14-22 July 2012, in Mysore, India. Abstract PE.1-2-12, p.2076; ADVANCES IN APPLIED MICROBIOLOGY; AIHAJ : a journal for the science of occupational and environmental health and safety; AIR QUALITY MONOGRAPHS (AMSTERDAM), VOL. 2. HEALTH IMPLICATIONS OF FUNGI IN INDOOR ENVIRONMENTS; INTERNATIONAL WORKSHOP, BAARN, NETHERLANDS, NOVEMBER 9-13, 1992; AJN The American …; APMIS : Acta Pathologica, Microbiologica, et Immunologica Scandinavica; ASHRAE Transactions; ASM News-American …; ASTM Special Technical Publication; Abstracts of Papers of the American Chemical Society; Abstracts of the General Meeting of the American Society for Microbiology; Acta Allergologica; Acta Astronautica; Acta Dermato Venereol; Acta astronautica; Acta tropica; Advanced Materials Research; Advances in Applied Microbiology; Advances in Space Research; Advances in applied microbiology; Advances in preventive medicine; Aerobiologia; Aerosol Science and Technology; Aerosol and Air Quality Research; Aerospace medicine; African Journal of Biotechnology; African Journal of Microbiology Research; African health sciences; Aiha Journal; Air & Water Borne Diseases; Air Quality Monographs (Amsterdam); Allergie und Asthma; Allergologie; Allergy; Allergy (Copenhagen); American Environmental Laboratory; American Industrial Hygiene Association Journal; American Industrial Hygiene Conference on Industrial Hygiene in the World of Tomorrow, Orlando, FL (USA), 13-18 May 1990; American Journal of Epidemiology; American Journal of Infection Control; American Journal of Respiratory and Critical Care Medicine; American Scientist; American Water Works Association; American journal of epidemiology; American journal of industrial medicine; American journal of infection control; American journal of respiratory and critical care medicine; Anales de Biologia; Ann Agric Environ Med; Annali dell'Istituto superiore di sanità; Annals of Agricultural and Environmental Medicine : AAEM; Annals of Allergy; Annals of Allergy, Asthma, & Immunolology; Annals of Occupational Hygiene; Annals of agricultural and environmental medicine : AAEM; Appl Microbiol Biotechnol.; Appl. Environ. Microbiol.; Applied Biochemistry …; Applied Mechanics and Materials; Applied Occupational and Environmental Hygiene; Applied and Environmental Microbiology; Applied and environmental microbiology; Applied and …; Applied microbiology and biotechnology; Applied occupational and environmental hygiene; Arch. Intern. Med; Archives of Environmental & Occupational Health; Archives of Environmental Health; Archives of Environmental Health.; Archives of Internal Medicine; Archives of environmental & occupational health; Archives of environmental health; Archives of oral biology; Asian Pacific Journal of Tropical Disease; Astrobiology; Atmospheric Environment; Atmospheric Environment Part B Urban Atmosphere; Atmospheric Research; BMC bioinformatics; BMC biology; BMC infectious diseases; BMC microbiology; Biocontrol Science; Biocontrol science; Bioengineered; Biofilms; Biofouling; Bioinformatics; Bioinformatics (Oxford, England); Biological Reviews; Biologija; Biologist; Biosafety; Bioscience, biotechnology, and biochemistry; Biosecurity and bioterrorism : biodefense strategy, practice, and science; Biosensors & bioelectronics; Brazilian Journal of Microbiology; British Microbiology Research Journal; Bromatologia i Chemia Toksykologiczna; Building and Environment; Bulletin de la Societe Francaise de Mycologie Medicale; CANADIAN JOURNAL OF MICROBIOLOGY; CLEAN - Soil, Air, Water; California and western medicine; Canadian Journal of Civil Engineering; Canadian Journal of Microbiology; Canadian Medical Association journal; Canadian journal of microbiology; Canadian respiratory journal : journal of the Canadian Thoracic Society; Chemical Engineering Journal; Chemosphere; Chest; Clean - Soil, Air, Water; Clean – Soil, Air, Water; Clin. Microbiol. Rev.; Clinical & Experimental Allergy; Clinical Infectious Diseases; Clinical Microbiology Newsletter; Clinical Microbiology Reviews; Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology; Clinical and translational science; Community health studies; Continental J. Medical Research; Critical reviews in microbiology; Critical reviews in toxicology; Current Microbiology; Current Opinion in Biotechnology; Current allergy and asthma reports; Current microbiology; Current opinion in biotechnology; Czech Mycology; Diagnostic microbiology and infectious disease; Ecological Indicators; Ecological applications : a publication of the Ecological Society of America; Electronic Journal of Biotechnology; Emerging Infectious Disease; Encyclopedia of environmental microbiology; Encyclopedia of microbiology; Energy and Buildings; Environment India; Environment International; Environment international; Environmental Engineering and Management Journal; Environmental Forensics; Environmental Health Perspectives; Environmental Health.; Environmental Health.Perspectives; Environmental Microbiology; Environmental Monitoring and Assessment; Environmental Research; Environmental Science & Technology; Environmental engineering science; Environmental health : a global access science source; Environmental health perspectives; Environmental microbiology; Environmental monitoring and assessment; Environmental research; Environmental science & technology; Environmental science and pollution research international; Environmental toxicology; Epidemiologie, mikrobiologie, imunologie : casopis Spolecnosti pro epidemiologii a mikrobiologii Ceské lékarské spolecnosti J.E. Purkyne; Ethiopian Journal of Health Sciences; European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery; FEMS Microbiology Ecology; FEMS microbiology ecology; FEMS microbiology letters; FEMS microbiology …; Fems (Fed Eur.Microbiol.Soc) Microbiol.Lett.; Food and Environmental Virology; Frontiers in Microbiology; Frontiers in bioscience (Scholar edition); Fungal Biology; Fungal Genetics and Biology; Fungal biology; Future microbiology; Gefahrstoffe Reinhaltung Der Luft; Genome Biology; Genome research; Gigiena i Sanitariya; Grana; Gravitational and Space Biology; HANDBOOK OF ENVIRONMENTAL CHEMISTRY; HVAC&R Research; Habitation (Elmsford, …; Healthy Buildings 2012; Helsingin Kaupungin Ymparistokeskuksen Julkaisuja; Hokkaido Igaku Zasshi The Hokkaido Journal Of Medical Science; Human molecular genetics; Humans in Outer Space—Interdisciplinary Odysseys; IAF, International Astronautical Congress, 43 rd, …; Igiene Moderna; Immunology; Indian journal of medical microbiology; Indoor Air; Indoor air; Indoor and Built Environment; Industrial Health; Inhalation toxicology; Innovative Food Science & Emerging Technologies; International Biodeterioration & Biodegradation; International Biodeterioration and Biodegradation; International Journal of Astrobiology; International Journal of Current Microbiology and Applied Sciences; International Journal of Food Science & Technology; International Journal of Hygiene and Environmental Health; International Journal of Microbiology Research; International Journal of Scientific and Research Publications; International Journal of Speleology; International Journal of Systematic Bacteriology; International Journal of Systematic and Evolutionary Microbiology; International archives of allergy and immunology; International journal of antimicrobial agents; International journal of environmental health research; International journal of environmental research and public health; International journal of food microbiology; International journal of hygiene and environmental health; International journal of molecular sciences; International journal of occupational safety and ergonomics : JOSE; International …; J R Soc Interface; JAMA : the journal of the American Medical Association; JAPCA; JAPI; JPL Publication 12-12; Journal of Aerosol Science; Journal of Allergy and Clinical Immunology; Journal of Animal Science; Journal of Applied Environmental and Biological Sciences; Journal of Applied Microbiology; Journal of Bacteriology; Journal of Building Physics; Journal of China University of Mining & Technology (English Edition); Journal of Clinical Microbiology; Journal of Cultural Heritage; Journal of Environment and Earth Science; Journal of Environment and Health; Journal of Environmental Engineering and Science; Journal of Environmental Health; Journal of Environmental Monitoring; Journal of Experimental and Integrative Medicine; Journal of Food Safety; Journal of Genetics; Journal of Hospital Infection; Journal of Hospital …; Journal of Infection; Journal of Intelligent Manufacturing; Journal of Medical Entomology; Journal of Medical research and Practice; Journal of Microbiological Methods; Journal of Microelectromechanical Systems; Journal of Occupational and Environmental Hygiene; Journal of Public Health Management and Practice; Journal of Scientific and Industrial Research; Journal of animal science; Journal of applied microbiology; Journal of bacteriology; Journal of basic microbiology; Journal of clinical microbiology; Journal of clinical pathology; Journal of environmental monitoring : JEM; Journal of environmental sciences (China); Journal of exposure science & environmental epidemiology; Journal of foot and ankle research; Journal of forensic sciences; Journal of hazardous materials; Journal of hospital infection; Journal of investigational allergology & clinical immunology; Journal of investigational allergology & clinical immunology : official organ of the International Association of Asthmology (INTERASMA) and Sociedad Latinoamericana de Alergia e Inmunologia; Journal of microbiological methods; Journal of microbiology (Seoul, Korea); Journal of occupational and environmental hygiene; Journal of occupational health; Journal of the Air & Waste Management Association; Journal of the Air & Waste Management Association (1995); Journal of the Formosan Medical Association = Taiwan yi zhi; Journal of the Indian Academy of Wood Science; Journal of the Mississippi Academy of Sciences; Journal of the National Institute of Public Health; Journal of the Royal Society Interface; Journal of the Royal Society Interface the Royal Society; Journal of the Royal Society, Interface / the Royal Society; Journal of theoretical biology; Letters in applied microbiology; Life Science Journal; Materials Chemistry and …; Measurement; Medical mycology : official publication of the International Society for Human and Animal Mycology; Medycyna pracy; Micologia Italiana; Microbial Ecology; Microbial ecology; Microbiological research; Microbiology and Immunology; Microbiology and Molecular Biology Reviews; Microbiology and immunology; Microbiome; Mikologiya I Fitopatologiya; Mikrobiyoloji bulteni; Molecular and Cellular Probes; Molecular ecology; Mycologia; Mycologia Helvetica; Mycological Research; Mycological research; Mycopathologia; Mycoses; Mycotaxon; N Eng J Med; NASA; NASA Ames Summer High School Apprenticeship …; NASA Technical Reports Server; NATO ASI Series Series 2 Environment; Nature; Nature Methods; Nature methods; Nature reviews. Microbiology; New England Journal of Medicine; New England and Regional Allergy Proceedings; Nihon Ishinkin Gakkai zasshi = Japanese journal of medical mycology; Occupational and Environmental Medicine; Occupational medicine (Philadelphia, Pa.); Origins of Life and …; PDA journal of pharmaceutical science and technology / PDA; PLoS Comput Biol; PLoS Med; PLoS Medicine; PLoS ONE; PLoS Pathogens; PLoS medicine; PLoS pathogens; Pathogens; Pediatric Allergy and Immunology; Pediatrics; PeerJ; Philosophical Transactions of the Royal Society of London - Series B: Biological Sciences; Photochemistry and photobiology; Planetary and Space Science; Plant Disease; PloS one; Plos Computational Biology; Polish Journal of Environmental Studies; Preventive Veterinary Medicine; Proceedings of the ASHRAE conference IAQ '87: practical control of indoor air problems; May; Arlington, VA. Atlanta, GA: American Society of Heating, Refrigerating, and Air-Conditioning Engineers, Inc; Proceedings of the Indoor Air 2002 Conference; Proceedings of the National Academy of Sciences; Proceedings of the National Academy of Sciences of the United States of America; Proceedings of the Royal Society of London. Series B. Biological Sciences; Proceedings. Biological sciences / The Royal Society; Public.Health.Reports; Recent research developments in infection & immunity. Vol. 1. Part I; Research in microbiology; Research in veterinary science; Research in …; Respiratory medicine; Reviews in Medical Microbiology; Revista iberoamericana de micología; Risk Analysis; Roczniki Panstwowego Zakadu Higieny; Roczniki Panstwowego Zakladu Higieny; Roczniki Państwowego Zakładu Higieny; SAE Special Publications; SAE Technical Paper; SAE Technical …; SAE transactions; STUDIES IN SURFACE SCIENCE AND CATALYSIS; Saudi Journal of Biological Sciences; Scandinavian Journal of Work, Environment and Health.; Science; Science (New York, N.Y.); Science of The Total Environment; Science of the Total Environment; Science of the Total …; Scientific Reports; Sick Building Syndrome: In Public Buildings and …; Simpozium IX Mezhdunarodnogo Kongressa po …; Standards in Genomic Sciences; Stress Challenges and Immunity in Space; Systematic and applied microbiology; Taiwan Journal of Public Health; Taiwanese Journal of Agricultural Chemistry and Food Science; Talanta; The 6th International Conference on Indoor Air Quality, Ventilation &Energy Conservation in Buildings (IAQVEC 2007), Sendai, Japan, 28-31 October, 2007; The Analyst; The Annals of Occupational Hygiene; The Annals of occupational hygiene; The European respiratory journal : official journal of the European Society for Clinical Respiratory Physiology; The European respiratory journal official journal of the European Society for Clinical Respiratory Physiology; The FEBS journal; The ISME journal; The International Journal of Tuberculosis and Lung Disease; The Journal Of Allergy; The Journal of allergy and clinical immunology; The Journal of asthma : official journal of the Association for the Care of Asthma; The Journal of experimental medicine; The Journal of hospital infection; The Journal of infectious diseases; The Science of the total environment; The Veterinary Journal; The human equation: health and comfort proceedings IAQ; The new microbiologica official journal of the Italian Society for Medical Odontoiatric and Clinical Microbiology SIMMOC; Thorax; Tidsskrift for den Norske laegeforening tidsskrift for praktisk medicin ny raekke; Toxicology Letters (Shannon); Toxicology and Industrial Health; Trends in Microbiology; Trends in biotechnology; Trends in ecology & evolution; Trends in microbiology; U S Navy medicine; Veterinarnomeditsinski nauki; Virology journal; WJCID World Journal of Clinical Infectious Diseases; Waste management & research; Water Air and Soil Pollution; Water Research; Water science and technology; Water, Air, & Soil Pollution; World Journal of Microbiology and Biotechnology; World Mycotoxin Journ; XIX NORDIC CONGRESS ON ALLERGOLOGY; Zbornik Matice Srpske za Prirodne Nauke; Zentralbl.Bakteriol.Mikrobiol.Hyg.Abt.; Zentralblatt fuer Bakteriologie Parasitenkunde Infektionskrankheiten und Hygiene Erste Abteilung Originale Reihe B Hygiene Krankenhaushygiene Betriebshygiene Praeventive Medizin; Zentralblatt fur Hygiene und Umweltmedizin; Zentralblatt fur Hygiene und Umweltmedizin International journal of hygiene and environmental medicine; eLife; mBio; …; … Meeting of the American Society of …; …Science and Technology; ;

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Reading Specific Journals

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Meetings &

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Citizen Science

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Education

Openness &

Sharing

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Newman M E J PNAS 2004;101:5200-5205

Gaps in the FieldFull Text DB

Co-authorship Networks

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Meetings &

Workshops

Citizen Science

Digital &

Social Media


Education

Openness &

Sharing

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Software CarpentryJenna Lang

Tracy Teal

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Data Carpentry

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QIIME Workshops

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Collaborative Micro Edu/research

Jo Handelsman Tiffany Tsang

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BE Reference Genomes• 7 students • Cultured organisms isolated from a variety

of built environments • Identify, sequence, assemble, annotate,

publish a genome each • 5 papers published so far in Genome

Announcements • All Data released • Student blog

• Brachybacterium muris (Jonathon Lo): • Microbacterium sp (Zach Bendiks): • Curtobacterium flaccumfaciens

(Jennifer Flanagan) • Dietzia sp (Amanda Diep): • Kocuria rosea (Jessica Doctor): • Leucobacter sp (Dakota Bevans,

Hannah Holland-Moritz):

Hannah Holland-Moritz

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Swab to Genome Workflow

Dunitz et al. in prep

Madison Dunitz

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Aquarium Biogeography• Biogeography and

succession • Extensive chemical

“metadata” collected • 16S surveys and

metagenomics • Using MBE tools • Coordinated by Jenna

Lang, David Coil, Matt Haggerty

• Advice from Josh Neufeld & Laura Sauder

• Papers in progress

Undergraduates: •Sabreen Aulakh •Alex Alexiev •Akshay Sethi •Andrew Shaver •Jennifer Flanagan •Lakshmi Bharadwaj High School: •Kevin Yang •In collaboration with Kenneth Kubo at American River College !

Sabreen Aulakh

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Citizen Microbiology

Laura Sauder

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Meetings &

Workshops

Citizen Science

Digital &

Social Media


Education

Openness &

Sharing

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The Rise of Citizen ScienceCaren Cooper

Darlene Cavalier

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Citizen Microbiology Meetings

Darlene Cavalier

Phone Microbiome

Georgia Barguil

Georgia Barguil

Jack Gilbert

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Wild Life of Your Home

Slide from Holly Menninger, CoPI on the project

Holly Meninger

Rob Dunn

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Many Other Citizen Microbiology Efforts

Jessica Richman

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MICROBES

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Meetings &

Workshops

Citizen Science

Digital &

Social Media


Education

Openness &

Sharing

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Teaching and Spreading Openness• Open Access publishing • Repositories and preprints • Open Data release • Data and Metadata

publishing • Open Source Software • CC licenses on digital

products • Recording and posting talks,

slides • Post publication peer review

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Data Papers

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Slideshare

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Altmetrics

Heather Piwowar

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Tracking microBEnet metrics

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How To Use Social Media Holly Bik

Miriam Goldstein

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Meetings &

Workshops

Citizen Science

Digital &

Social Media


Education

Openness &

Sharing

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Meetings &

WorkshopsCitizen Science

Digital &

Social Media


Education

Openness &

Sharing

What Next?

Sustainability

More BE/BS

Press Forward

Wikipedia Integration

RewardsMatchmaking

Network Analysis

Protocols

Training on use

Reporter Guides

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Evolution & Ecology of Microbiomes

Disturbance & RestorationPopulation Biology

Biogeography Phylogenetic Ecology

Community Assembly