BGI training lecture: Scott Edmunds - Science 2.0, why new developments on the web will make you a better scientist!
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BGI training lecture: Scott Edmunds - Science 2.0, why new developments on the web will make you a better scientist!

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Training lecture for BGI staff, June 23rd 2011.

Training lecture for BGI staff, June 23rd 2011.

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BGI training lecture: Scott Edmunds - Science 2.0, why new developments on the web will make you a better scientist! BGI training lecture: Scott Edmunds - Science 2.0, why new developments on the web will make you a better scientist! Presentation Transcript

  • Scott Edmunds
    Science 2.0 and beyond:
    how new developments on the web will make you a better scientist!
    ?
    (“Everything you wanted to know about social networks but were too afraid to ask…”)
  • What is?
    “Science 2.0 uses the technologies of web 2.0 to conversations between researchers, let them discuss the data and connect it with other data that might be relevant. Blogs, wikis and such permit users to make information available in ways that create a conversation. Web 2.0 permits scientists to create digitized conversations that provide context for the data.”
    (+ Semantic Web)
  • Open-Science
    Open-access (PLoS/BMC)
    Open-source (github/sourceforge/googlecode)
    Open-data
  • Open-Science
    For
    Against
    Allows crowdsourcing.
    Better for Science.
    Fairer (public money).
    More use (=citations)
    Scooping?
    Patents/publications?
    Time/effort.
    Data deluge?
  • Open-Science
    Sharing Detailed Research Data Is Associated with Increased Citation Rate.
    Piwowar HA, Day RS, Fridsma DB (2007) PLoSONE 2(3): e308. doi:10.1371/journal.pone.0000308
  • Daphnia Genome Consortium
    wFleabase: Mar 2006
    Genome release: July 2007
    Genome Published: Feb 2011
    >58 companion papers
    https://daphnia.cgb.indiana.edu/Publications
  • Open Lab Notebooks
  • Faster scientific communication
    FUTURE
    PAST
  • Why is it important for Chinese research?
  • SPEED
  • SRA Closure
  • SRA Closure
  • Online sources of scientific information
    Databases/portals of traditional media
    Blogs (networks/aggregators)
    Social Networks:
    Open Notebook Science
    Wikis
    Forums/Other
  • Traditional media 2.0
    Science databases: general
    Subject specific
    Journal content: browse
    eTOCs
    RSS
    • Newspapers/television:
  • Science Blogs
    Some good examples:
    Tree of Life (Jonathon Eisen): http://phylogenomics.blogspot.com/
    Bad Science (Ben Goldacre):http://www.badscience.net/
    A Blog around the Clock (Bora Zivkovic): http://blog.coturnix.org/
    Not Exactly Rocket Science (Ed Yong): http://blogs.discovermagazine.com/notrocketscience/
    Genetic Future (Daniel MacArthur): http://www.wired.com/wiredscience/geneticfuture
    OMICS, OMICS! (Keith Robison): http://omicsomics.blogspot.com/
    Bacpathgenomics (Kat Holt): http://bacpathgenomics.wordpress.com/
  • Science Blogs
    Group blogs:
    Open Helix (Genomics news): http://blog.openhelix.com/
    Genomes Unzipped (Personalized Genomics): http://www.genomesunzipped.org/
    Blogging Networks:
    PLoS Blogs: http://blogs.plos.org/
    Nature Network: http://network.nature.com/
    Scientific American: http://www.scientificamerican.com/blog/
    Discover Blogs: http://blogs.discovermagazine.com/
    Science Blogs: http://scienceblogs.com/
    Occam’s Typewriter: http://occamstypewriter.org/
  • Science Blogs
    Blog Aggregators:
    Science Blogging: http://scienceblogging.org/
    Research Blogging: http://researchblogging.org/
    Honorable Mention:
    NCBI ROFL: http://blogs.discovermagazine.com/discoblog/category/ncbi-rofl/
    Urologe A. 2005 Dec;44(12):1473-5.
    Inappropriate use of a titanium penile ring. An interdisciplinary challenge for urologists, jewelers, and locksmiths.
    Wiedemann A, Müller H, Rabs U.
    Psychol Rep. 2011 Feb;108(1):43-4.
    National anthems and suicide rates.
    Lester D, Gunn JF 3rd.
  • Social Media
    Good for events
    Good for networking
    Good for groups
  • Using Twitter for Science
    James Darcy: “Researchers need to get themselves onto Twitter pronto because it is fast becoming the place to find out the breakthroughs in your research field.”
    Jonathan Eisen:“To do science, you have to know what’s going on…I found Twitter…most useful for becoming informed of what other people are doing in science.”
    “Twitter and other social networks such as FriendFeedenable real-time highlighting and ranking and tracking of what’s going on in the world of science.”
    “Twitter is also useful for networking and finding collaborators.”
    http://deepseanews.com/2010/08/what-is-twitter-and-why-scientists-need-to-use-it/
  • Using Twitter for Science
    Twitter is:
    Microblog: max 140 characters
    (“The SMS of the Internet”)
    Global: 200m users, 190m tweets (1.6b searches)/day.
    Fast: 2,200 new tweets/s! (can fluctuate 3-4x)
    Instant: view global trends/keywords with hashtags #
  • Using Twitter for Science
    Twitter is good for:
    Eavesdropping: follow informative people to get information and learn
    Dialogue: exchange, discuss, and debate information
    Broadcast: used by news organizations and businesses to inform audience about news or products/services
    Data collection: e.g. using Tweeting fishermen to monitor fish populations.
    Accidental journalism: e.g. landing on Hudson river, Michael Jackson death, Japan Earthquake
    Mindcasting:  following a single story or topic, with links, for a period of time, e.g. like my ongoing coverage of the #Ecoliat @BGI_Events
  • Using Twitter for Science
    Twitter is not so good for:
  • Using Twitter for Science
    How it works (‘twetiquette’):
    People will only read your messages if you have followers or RT’s (re-tweets), so:
    Keep it interesting.
    Keep it short (<140 characters)
    Use links and link-shorteners (bit.ly/t.co/owl.ly)
    Keep it interactive (2-way).
    Use hashtags and twitter ID’s (@xxx)
    Have regular content (RT’s).
    Intersperse tweets.
    Think about timezones (Europe=late afternoon, US=night).
  • Using Twitter for Science
    Who to follow:
    BGI Collaborators
    Science news/blogs
    @NatureNews @dgmacarthur
    @Sciencemagazine @Boraz
    @Biomedcentral @genomesunzipped
    @genomeresearch @OpenHelix
    @PLoS @sciencebase
    @BioITWorld @edyong209
    @Metahit
    @Genome10K
    @Assemblathon
    #EMP @gilbertjacka
    @phylogenomics
    Scientists
    EBI/Sanger @ewanbirney@moorejh@timjph @bffo
    @Alexbateman1 @deannachurch
    @lenovere@kamounlab
    @emblebi@JCVenter
    Hashtags
    #pm101 = personalized medicine#OA = open access
    #microbiome #metagenomics
    #epigenomics #omics #genomics
  • Using Twitter for Science
    Conferences
    ISMB2010 twitter activity
    Tweets at the ISMB 2010 meeting
    ISMB2010 comments July 9-13
  • Using Twitter for Science
    Conferences
    Follow the meeting from home:
    Conference: Twitter Feed: Hashtag:
    ASHG @geneticssociety #ICHG2011
    Society for Neuroscience @SfNtweets #SfN10/#SfN11
    Plant and Animal Genomes @PAGmeeting #PAG
    ISMB @iscb #ISMB
    ICSB @ICSB_2011 #ICSB2011HD
    AACR @AACR #AACR
  • Using Twitter for Science
    Conferences
    http://www.slideshare.net/GigaScience/rick-stevens-prospects-for-a-systematic-exploration-of-earths-microbial-diversity
  • Using Twitter for Science
    Conferences
    http://www.youtube.com/watch?v=AlYFa83aCWA
  • Using Twitter for Science
    Aided by: Feed aggregators/Dashboards
  • Science Social Networks
    Genome 10K Networking: http://genome10k.ning.com/
    Science 3.0: http://www.science3point0.com/
  • Forums/Other
    Forums
    http://biology-online.org
    http://protocol-online.org
    http://molecularstation.com
    http://biotechniques.com
    http://seqanswers.com
    http://molbiol.ru (Russian)
    http://bbioo.com (Chinese)
    http://www.scientistsolutions.com
    Protocols/Workflows/Hubs
    http://www.nature.com/protocolexchange/
    http://www.myexperiment.org/
    http://main.g2.bx.psu.edu/
    https://github.com/
    http://cloudbiolinux.org/
  • Further reading:
    Twitter:
    A gentle introduction to Twitter for the apprehensive academic
    http://deevybee.blogspot.com/2011/06/gentle-introduction-to-twitter-for.html
    What is Twitter and Why Scientists Need To Use It.
    http://deepseanews.com/2010/08/what-is-twitter-and-why-scientists-need-to-use-it/
    Science journalism: Breaking the convention?
    http://www.nature.com/news/2009/090624/full/4591050a.html
    Analysing the ISMB 2010 meeting using R
    http://nsaunders.wordpress.com/2010/07/20/analysing-the-ismb-2010-meeting-using-r/
    Sharing slides from a presentation plus how to do this w/ Slideshare
    http://www.microbe.net/2011/06/15/sharing-slides-from-a-presentation-plus-how-to-do-this-w-slideshare/
    Slideshare:
  • Why is this important to BGI?
    Flickr cc: opensourceway
  • We produce data. (LOTS)
    1 IlluminaHiSeq 2000 (+Truseq upgrade)
    = 600Gb/run (12 days)
    X 128 Hiseq= 6Tb/day = >2Pb/year
    = ~ 2000 Human Genomes/day
  • Coming soon…
    Large-Scale Data
    Journal/Database
    In conjunction with:
    Editor-in-Chief: Laurie Goodman, PhD
    Editor: Scott Edmunds, PhD
    Assistant Editor: Alexandra Basford, PhD
    www.gigasciencejournal.com
  • Our first DOI:
    To maximize its utility to the research community and aid those  fighting the current epidemic, genomic data is released here into the public domain under a CC0 license. Until the publication of research papers on the assembly and whole-genome analysis of this isolate we would ask you to cite this dataset as:
    Li, D; Xi, F; Zhao, M; Liang, Y; Chen, W; Cao, S; Xu, R; Wang, G; Wang, J; Zhang, Z; Li, Y; Cui, Y; Chang, C; Cui, C; Luo, Y; Qin, J; Li, S; Li, J; Peng, Y; Pu, F; Sun, Y; Chen,Y; Zong, Y; Ma, X; Yang, X; Cen, Z; Zhao, X; Chen, F; Yin, X; Song,Y ; Rohde, H; Li, Y; Wang, J; Wang, J and the Escherichia coli O104:H4 TY-2482 isolate genome sequencing consortium (2011) Genomic data from Escherichia coli O104:H4 isolate TY-2482. BGI Shenzhen. doi:10.5524/100001 http://dx.doi.org/10.5524/100001
    To the extent possible under law, BGI Shenzhen has waived all copyright and related or neighboring rights to Genomic Data from the 2011 E. coli outbreak. This work is published from: China.
  • E. Coli #crowdsourcing: the first tweenome?
    “On 2 June, Chinese scientists announced that they had deciphered the microbe's entire 5.2-million-base-pair genome and immediately made the DNA sequence available for researchers to download. Scores of scientists all over the world started poring over the data, assembling sequence fragments generated by BGI into a coherent genome, and comparing it to reference genomes for E. coli and other bacteria.”
    “The two announcements came on the second day of a U.K. meeting on applied bioinformatics and public health microbiology. Speakers and other attendees immediately started working on annotating the bacterial sequence provided by BGI. “In less than 24 hours we got the reads, the assembly, and the annotation. A good case study,” blogged Marina Manrique of era7 bioinformatics, a Spanish company that quickly did an automated analysis of the E. coli's genome.“
  • E. Coli #crowdsourcing: the first tweenome?
  • E. Coli #crowdsourcing: the first tweenome?
  • E. Coli #crowdsourcing: the first tweenome?
  • E. Coli #crowdsourcing: the first tweenome?
    “The way that the genetic data of the 2011 E. coli strain were disseminated globally suggests a more effective approach for tackling public health problems. Both groups put their sequencing data on the Internet, so scientists the world over could immediately begin their own analysis of the bug's makeup. BGI scientists also are using Twitter to communicate their latest findings.”
    “German scientists and their colleagues at the Beijing Genomics Institute in China have been working on uncovering secrets of the outbreak. BGI scientists revised their draft genetic sequence of the E. coli strain and have been sharing their data with dozens of scientists around the world as a way to "crowdsource" this data. By publishing their data publicy and freely, these other scientists can have a look at the genetic structure, and try to sort it out for themselves.”
  • Follow us:
    @gigascience
    @BGI_Events
    http://www.facebook.com/pages/BGI/144703072248402
    http://www.flickr.com/photos/bgi_events/
    http://www.youtube.com/user/BGIshenzhen
    scott.edmunds@genomics.org.cn
    @SCEdmunds
    www.gigasciencejournal.com