ODHK.meet.32: Hacking the Human Genome

12079500_1645907945684346_7736685585039988396_nTaking Open Data to the Final Frontier: The Human Genome

Stephens ZD et al. (2015) Big Data: Astronomical or Genomical? PLoS Biol doi:10.1371/journal.pbio.1002195

How big is your data? Stephens ZD et al. (2015) Big Data: Astronomical or Genomical? PLoS Biol doi:10.1371/journal.pbio.1002195


Genomics (DNA sequencing) is a Big Data science and is predicted by some to soon exceed the demands of all other Big Data domains such as astronomy, streaming video, and social media. Hong Kong is at the forefront of this genomic revolution, local researchers making key breakthroughs in circulating DNA based prenatal testing and cancer diagnostics (also predicted to become a multi-billion dollar industry), and hosting the world’s largest sequencing centre in Tai Po (BGI Hong Kong). As we move towards “precision medicine”, all of us as patients will increasingly need to make informed decisions based on how medicines, treatments and lifestyle choices are interact with our genetic background. Despite that, genomic literacy and understanding of the cutting edge work in this rapidly growing field by the Hong Kong public is very poor, with little local awareness as to what it entails, and how it will be soon impacting upon all of their lives. In an era of “direct to consumer” DNA sequencing pioneered by companies such as 23&Me, millions of people now have access to their genome-scale data. Due to perceived ethical issues there can be legal restrictions to what people can do with it, with many in the healthcare industry feeling people should not be trusted to access to their own data.
 Countering this, there are a growing numbers of people taking matters into their own hands, carrying out genome blogging, and citizen lead genealogically/ancestry work (e.g. this PLOS paper). A new generation of tools and platforms such as OpenSNP and promethease are democratising access, citizens are crowdfunding their own projects, and genomic apps are even appearing on the market. Just this week the new DNA.Land genomic data sharing portal launched, and over 5,000 people have posted their genomic data in the first few days. For interested potential “genome hackers” we have a number of people at the forefront of this open genomics revolution presenting at this meetup, including Fiona Nielsen of DNAdigest and Bastian Greshake of OpenSNP . For a preview of what to expect see these previous events from DNAdigest and this interview with Bastian, . We’ll cover the tools and resources any non-biologist hacker can get started with (R-, python, bioconductor, and the databases you can find data). Demonstrating that the personal genomics era is already here, we’ll also have a prize draw so lucky participants can get their alcohol metabolism genes sequenced and presented through a fun new genomic app not yet on the market.
The event will attempt to address questions such as:
What questions can you ask of your genetic data?
How much can you do as a citizen scientist, what activities are reserved for academic researchers?
Sign up to this event via the eventbright link and please submit any questions or suggestions for topics related to “Hacking the human genome”. For more experienced genomics experts, the meet follows an all-day workshop on “How do I find human genomics data to power my research?“. The event is hosted at MakerBay in Yau Tong, and we’d like to thank Fiona and Cesar for their help and support in setting the event up.
Date:
Monday, October 26th, 7:30pm
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Location:
Location: MakerBay, 16 Sze Shan Street, C1 Yau Tong Industrial Building Block 2, Yau Tong, Kowloon
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UPDATE 28/10/15: the great folks at MakerBay did a live stream and we can see the archived video version here.

ODHK.meet.31: Tracking & Transparency

ODHK - meet.31 logoUPDATED 18th September: now including pictures and slides.
ODHK was back on the 16th September after its summer break for our 31st meetup, this month quantifying and throwing light on Open Data and transparency in Hong Kong. Our Mid-Autumn Open Data festival was an interactive affair, as we needed feedback, scrutiny and future participation in two on-going projects: Open Knowledge’s Open Data Index and accessinfo.hk.With the deadline for submissions to the 2015 Global Open Data Index ending on the 20th September, Rob Davidson gave us a quick overview of the index, the various categories we are assessed on, and what is likely to have changed this year (slides here). Anybody currently working on, or would like to contribute to our submission, this is your last chance to provide feedback for the next census. With more categories and datasets under consideration, in the year that it’s data.gov.hk portal finally launched will Hong Kong improve on it’s global ranking of 59th? Helping provide useful scrutiny and pressure on the government to keep improving in their access to “public sector information”, watch this space to see the results. Many other groups around the world will be having events around the census, so check out the handy event guide Open Knowledge have put together on the topic. Check out the portal for more, and with two days to go this is your last chance to start check and contribute to the 2015 census: http://global.census.okfn.org/
The second part of the session was taken over by Guy Freeman who presented on his now up-and-running accessinfo.hk portal. While we had a sneak preview in meet.29 on politics (see the write up), there has been some ironing out of bugs in a soft(ish) launch, and accessinfo.hk is now up to about 30 access-to-information requests. This made it a perfect time to assess how the process is working, how responsive Hong Kong government departments are to these requests (they promise a ten day turnaround), and look to what happens next. With some ideas and goals for longitudinal hacks (watch this space…), Guy gave us insight what can be done in the area of freedom of information and transparency, and how in the absence of Open Data there are things we can to do gather our own. Check out his slides here or embedded below.
Screen shot 2015-09-10 at 11.05.20 PM

Date:
Wednesday, September 16th, 7:30pm
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Location:
Location: Good Lab Cheung Sha Wan. L1, The Sparkle, 500 Tung Chau Street
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ODHK.meet.30: Open Mapping Data & Research Data Management Policy

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DateFriday, June 12 at 7:00pm
VenueDM Lab, Eliot Hall, The University of Hong Kong
In a world where citizens can 3D map areas with drones, or annotate and improve upon OpenStreetMaps, the HK Lands department still charges “reproduction costs” for PDFs of government maps. It is time for Hong Kong to follow the lead of other countries and open up a resource that will greatly benefit its citizens, far more than charging for these resources.
At this meet we’ll discuss the issue of Open Mapping data, as well as academic research data policy with Professor John Bacon-Shone from The University of Hong Kong.
John is Associate Dean (Knowledge Exchange) of Social Sciences, Director of the Social Sciences Research Centre and will speak on his own experiences of trying to obtain access to HKSARG data for both research and public access, as well as examples of HKSARG data that has been lost. As a long time advocate of Open Access in Hong Kong, he’ll hopefully also cover data management policy in HKU and how to balance research integrity, confidentiality and public good.
Chaired by Darcy Wade Christ, we’ll have data users on hand for an interesting discussion about how to encourage and support the Hong Kong Government to open up their mapping data for free.
This event will be hosted at the Digital Media lab on the ground floor of the JMSC at HKU.
All are welcome!

Also, check out the event on Facebook, and rsvp!

ODHK.meet.29: Open data & transparency for political advocacy

meet29.finalOpen data has many different societal benefits, and in Asia some may be a little nervous pushing it as a tool for transparency and political change, but for meet.29 we threw caution to the wind and tackled that very topic. We had some great visiting and local speakers, helping contrast how activist groups in some parts the world are using open data to strive for political change, with the nascent (and maybe more conservative?) situation here in Hong Kong and China.
IMG_8820We were pleased to have Amanda Meng from the Sam Nunn School of International Affairs as our visiting guest speaker. Amanda is a PhD candidate at the Georgia Institute of Technology where she studies technology and democracy. Her dissertation focuses on the social impact of open government data. Throughout her career as a practitioner and academic she has spent time in the Dominican Republic, India, Ghana, and Nigeria studying or implementing projects in ICT for development or democracy.

Amanda is in Hong Kong conducting a case study on the reuse of open government data. Her investigation includes a qualitative process trace of datasets from government agencies, through civic spaces, and back to public officials as social groups attempt to achieve social or political change. This case study is the first of three to be compared to Chile and the Dominican Republic, and we look forward to hearing her accounts of open data activism. You can get a taster on her research on her recent paper in JeDEM on “Investigating the Roots of Open Data’s Social Impact”. You can see her slides here.

Bringing It All Back Home: FOI and AccessInfo.Hk
After the international perspective, we brought things back to Hong Kong with the second part of the meet focusing on tools we can use here to bring light on the political process, specifically access to information requests and the newly live accessinfo.hk portal. Guy Freeman gave us a quick overview of his handiwork setting up the new platform. With Guy we also had Dr Clement Chen from HKU, a researcher on information rights in China (check out his FOI in China page and see his thesis here), who was on hand for discussion and helped answer questions on the topic of the FOI situation in Hong Kong and Mainland China.

Screen shot 2015-05-07 at 11.18.58 AM
Check out the portal and feed it with questions:
https://accessinfo.hk/

Date:
Tuesday 12th May 2015
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Location:
Delaney’s Wan Chai, One Capital Place, 18 Luard Road Wan Chai.
灣仔盧押道18號海德中心地下及1字樓, Wan Chai.
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ODHK.meet.28: DATA.GOV.HK & OGCIO

Screen shot 2015-04-13 at 10.21.04 PM
For the next ODHK meet we are pleased to cover one of the hot topics in the Hong Kong Open Data scene, the newly launched Hong Kong public sector information portal: DATA.GOV.HK.
We have some of the senior team at the OGCIO (Office of the Government Chief Information Officer) on hand to give us a quick run through of the new platform, and then stick around and answer some of our questions. If there is anything you want to know about the new portal and access to public sector information in Hong Kong, now is your chance to ask. Please bring your questions, or just come along to see the demo, and have a beer and a catch up. Old timers at ODHK may remember some of these presenters from our previous meets, and we’d like to welcome and thank the following OGCIO team members for offering up some of their precious time to present directly to us:
Kimmey Ho
Senior Administrative Officer (Strategy Development)
Jessica Lo
Systems Manager (Strategy Development)
Russell Tang
Executive Officer (Strategy Development)
What public sector information datasets do you want, and do you think is missing? Come to the meet and let OGCIO know.
Screen shot 2015-04-13 at 10.49.54 PM
 
For more on the new data.gov.hk platform see the recent piece in SCMP.

Date:

Tuesday 21st April 2015

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  • Location: Delaney’s Wan Chai, One Capital Place, 18 Luard Road Wan Chai.
  • 灣仔盧押道18號海德中心地下及1字樓, Wan Chai
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ODHK.meet.27: Birthday.2

11096705_10153268335379379_900183058_nThere ain’t no party like an open data party!

Come along to Delaney’s Wan Chai to help ODHK celebrate our second birthday. For our 27th ODHK meet we will celebrate our second anniversary, looking forward to the year ahead, and as well as looking back at the highlights of the last 12 months. We’ll have a have lots of topical things to showcase in our overview of the year (Budget! New Data.Gov.HK portal!), but come expecting cake, drinks, merriment and more. See the pics of last years event to get an idea of what to expect.
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Date:

Tuesday 31st March 2015

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  • Location: Delaney’s Wan Chai, One Capital Place, 18 Luard Road Wan Chai.
  • 灣仔盧押道18號海德中心地下及1字樓, Wan Chai
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