Scott Edmunds

how new developments on the web will make you a better scientist!

Science 2.0 and beyond:

(“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

• Allows crowdsourcing.• Better for Science.• Fairer (public money).• More use (=citations)

• Scooping?• Patents/publications?• Time/effort.• Data deluge?

For Against

Open-Science

Piwowar HA, Day RS, Fridsma DB (2007) PLoS ONE 2(3): e308. doi:10.1371/journal.pone.0000308

Sharing Detailed Research Data Is Associated with Increased Citation Rate.

Daphnia Genome Consortium

wFleabase: Mar 2006Genome release: July 2007

Genome Published: Feb 2011

https://daphnia.cgb.indiana.edu/Publications

>58 companion papers

Open Lab Notebooks

Faster scientific communication

PAST FUTURE

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: generalSubject specific

• Journal content: browseeTOCsRSS

• 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 networkingGood 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 FriendFeed enable 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/

• 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:

1. Eavesdropping: follow informative people to get information and learn

2. Dialogue: exchange, discuss, and debate information3. Broadcast: used by news organizations and businesses to inform

audience about news or products/services4. Data collection: e.g. using Tweeting fishermen to monitor fish

populations.5. Accidental journalism: e.g. landing on Hudson river, Michael

Jackson death, Japan Earthquake6. Mindcasting: following a single story or topic, with links, for a

period of time, e.g. like my ongoing coverage of the #Ecoli at @BGI_Events

Using Twitter for Science

Twitter is good for:

Using Twitter for ScienceTwitter is not so good for:

1. Keep it interesting.2. Keep it short (<140 characters)3. Use links and link-shorteners (bit.ly/t.co/owl.ly)4. Keep it interactive (2-way).5. Use hashtags and twitter ID’s (@xxx)6. Have regular content (RT’s).7. Intersperse tweets.8. Think about timezones (Europe=late afternoon, US=night).

Using Twitter for Science

How it works (‘twetiquette’):People will only read your messages if you have followers or RT’s (re-tweets), so:

BGI Collaborators

Using Twitter for Science

Who to follow:

@Metahit@Genome10K@Assemblathon

#EMP @gilbertjacka@phylogenomics

Science news/blogs@NatureNews @dgmacarthur@Sciencemagazine @Boraz@Biomedcentral @genomesunzipped@genomeresearch @OpenHelix@PLoS @sciencebase@BioITWorld @edyong209

EBI/Sanger @ewanbirney@moorejh@timjph @bffo@Alexbateman1 @deannachurch@lenovere@kamounlab@emblebi@JCVenter

ScientistsHashtags

#pm101 = personalized medicine#OA = open access#microbiome #metagenomics#epigenomics #omics #genomics

ISMB2010 comments July 9-13

ISMB2010 twitter activity

Using Twitter for Science

ConferencesTweets at the ISMB 2010 meeting

Using Twitter for Science

Conferences

Conference: Twitter Feed:Hashtag:

ASHG @geneticssociety#ICHG2011

Society for Neuroscience @SfNtweets#SfN10/#SfN11Plant and Animal Genomes @PAGmeeting #PAGISMB @iscb

#ISMBICSB @ICSB_2011

#ICSB2011HDAACR @AACR

#AACR

Follow the meeting from home:

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

Forumshttp://biology-online.org http://protocol-online.org http://molecularstation.comhttp://biotechniques.com http://seqanswers.comhttp://molbiol.ru (Russian) http://bbioo.com (Chinese)http://www.scientistsolutions.com

Protocols/Workflows/Hubshttp://www.nature.com/protocolexchange/http://www.myexperiment.org/http://main.g2.bx.psu.edu/https://github.com/http://cloudbiolinux.org/

Further reading:

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 Rhttp://nsaunders.wordpress.com/2010/07/20/analysing-the-ismb-2010-meeting-using-r/

Sharing slides from a presentation plus how to do this w/ Slidesharehttp://www.microbe.net/2011/06/15/sharing-slides-from-a-presentation-plus-how-to-do-this-w-slideshare/

Twitter:

Slideshare:

Why is this important to BGI?

Flickr cc: opensourceway

1 Illumina HiSeq 2000 (+Truseq upgrade)

= 600Gb/run (12 days)

X 128 Hiseq = 6Tb/day = >2Pb/year

= ~ 2000 Human Genomes/day

We produce data. (LOTS)

www.gigasciencejournal.com

Large-Scale Data Journal/Database

Editor-in-Chief: Laurie Goodman, PhDEditor: Scott Edmunds, PhDAssistant Editor: Alexandra Basford, PhD

In conjunction with:

Coming soon…

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

Our first DOI:

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.”

www.gigasciencejournal.com

Follow us:

scott.edmunds@genomics.org.cn@SCEdmunds

@gigascience@BGI_Events

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