Meeting Reports

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<a name="#2042352430"></a>Pan-Asia SNP Bioinformatics (PASB)<o:p></o:p>

Initiative Bioinformatics working group meeting<o:p></o:p>

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▶ Date : August 18-19. 2005 <o:p></o:p>

▶ Place: International Center, Cheju National University, Korea <o:p></o:p>

▶ Co-Host : <st1:personname w:st="on">NGIC</st1:personname>, NGRI/Korea <o:p></o:p>

▶ Co-organizers : <st1:personname w:st="on">NGIC</st1:personname>/Korea, DDBJ/Japan <o:p></o:p>

▶ Sponsor : Cheju National University <o:p></o:p>

Ins. of Medical Science/Korea <o:p></o:p>

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　Program <o:p></o:p>

<a name="#1423561266"></a>Date<o:p></o:p>	Time<o:p></o:p>	Topic<o:p></o:p>	Lecturer<o:p></o:p>
8.18(Thur.)<o:p></o:p>	13:00∼13:20<o:p></o:p>	Opening & welcome speech by host country, <st1:place w:st="on"><st1:country-region w:st="on">Korea</st1:country-region></st1:place> <o:p></o:p>	Dr. Kyuchan Kimm<o:p></o:p> (NGRI)<o:p></o:p>
	13:20∼13:40<o:p></o:p>	Introduction of members<o:p></o:p>	Dr. Jong Bhak<o:p></o:p> (<st1:personname w:st="on">NGIC</st1:personname>)<o:p></o:p>
	13:40∼14:00<o:p></o:p>	Reconfirmation of the <st1:place w:st="on"><st1:city w:st="on">Mission</st1:city></st1:place> and Task of Asian SNP Project<o:p></o:p>	<o:p></o:p>
	14:00∼14:20<o:p></o:p>	The outline of the task of this group<o:p></o:p>	<o:p></o:p>
	14:20∼14:40<o:p></o:p>	Break<o:p></o:p>	<o:p></o:p>
	14:40∼15:00<o:p></o:p>	Presentation 1<o:p></o:p> (Korea SNP research activities)<o:p></o:p>	Dr. Kyuchan Kimm<o:p></o:p> (NGRI)<o:p></o:p>
	15:00∼15:20<o:p></o:p>	Presentation 2<o:p></o:p> (Singapore SNP research activities)<o:p></o:p>	<o:p></o:p>
	15:20∼15:40<o:p></o:p>	Presentation 3<o:p></o:p> (India SNP research activities)<o:p></o:p>	Dr. Partha P. Majumder<o:p></o:p> (Indian Statistical Institute)<o:p></o:p>
	15:40∼16:10<o:p></o:p>	Break<o:p></o:p>	<o:p></o:p>
	16:10∼16:30<o:p></o:p>	Presentation 4<o:p></o:p> (Taiwan SNP research activities)<o:p></o:p>	Dr. Chien-Hsiun Chen <o:p></o:p> (Institute of Biomedical Sciences)<o:p></o:p>
	16:30∼17:10<o:p></o:p>	Presentation 5<o:p></o:p> (The current progress of Affymetrix activities<o:p></o:p>	Dr. Kennedy<o:p></o:p> (AFFYMETRIX, INC)<o:p></o:p>
	17:10∼19:00<o:p></o:p>	Break and Dinner<o:p></o:p>	<o:p></o:p>
	19:00∼19:50<o:p></o:p>	Database standardization format talk<o:p></o:p>	<o:p></o:p>
	19:50∼20:40<o:p></o:p>	Database server, Analysis algorithms, <o:p></o:p> platform selection discussion<o:p></o:p>	<o:p></o:p>
	20:40∼21:30<o:p></o:p>	Administration: Publication issues, credit, funding, Summary and Future work. Next meeting. Concluding 1.<o:p></o:p>	<o:p></o:p>
8.19(Fri.)<o:p></o:p>	09:30∼10:30<o:p></o:p>	Concluding 2. Misc issues. Local meetings (for each national and inter-national discussions) <o:p></o:p>	Dr.Gojobori<o:p></o:p> (DDBJ, NIG)<o:p></o:p>
	10:30∼11:00<o:p></o:p>	Writing up the summary and action progrean<o:p></o:p>	Dr.Jong Bhak<o:p></o:p>
	11:00∼11:30<o:p></o:p>	Free discussion<o:p></o:p>	<o:p></o:p>

Participant <o:p></o:p>

<a name="#2041304216"></a>Nation<o:p></o:p>	Name<o:p></o:p>	Facility<o:p></o:p>	Note<o:p></o:p>
<st1:place w:st="on"><st1:country-region w:st="on">Korea</st1:country-region></st1:place><o:p></o:p>	Jonghwa Bhak <o:p></o:p>	<st1:place w:st="on"><st1:placename w:st="on">National</st1:placename> <st1:placename w:st="on">Genome</st1:placename> <st1:placename w:st="on">Information</st1:placename> <st1:placetype w:st="on">Center</st1:placetype></st1:place>, <o:p></o:p> <st1:place w:st="on"><st1:country-region w:st="on">Korea</st1:country-region></st1:place> Research Ins. of Biotechnology & Bioscience<o:p></o:p>	<o:p></o:p>
	Kuchan Kimm <o:p></o:p>	National Genome Research Institute, <o:p></o:p> Korea National Institute of Health<o:p></o:p>
	Hyangsook Yoo<o:p></o:p>	The Center for Functional Analysis of Human Genome<o:p></o:p>
	Bonghee Lee<o:p></o:p>	<st1:place w:st="on"><st1:placetype w:st="on">Institute</st1:placetype> of <st1:placename w:st="on">Medical</st1:placename></st1:place> Science, <o:p></o:p> <st1:place w:st="on"><st1:placename w:st="on">Cheju</st1:placename> <st1:placename w:st="on">National</st1:placename> <st1:placetype w:st="on">University</st1:placetype></st1:place><o:p></o:p>
	Sangsoo Kim <o:p></o:p>	<st1:place w:st="on"><st1:placename w:st="on">Soongsil</st1:placename> <st1:placetype w:st="on">University</st1:placetype></st1:place><o:p></o:p>
	Heekyung Song <o:p></o:p>	SeouLin Biotechnology Institute(SLBI)<o:p></o:p>
<st1:place w:st="on"><st1:country-region w:st="on">Singapore</st1:country-region></st1:place><o:p></o:p>	Wayne Mitchell<o:p></o:p>	Genome Institute of <st1:place w:st="on"><st1:country-region w:st="on">Singapore</st1:country-region></st1:place><o:p></o:p>	<o:p></o:p>
	Mark Thomas SEIELSTAD<o:p></o:p>	Genome Institute of <st1:place w:st="on"><st1:country-region w:st="on">Singapore</st1:country-region></st1:place><o:p></o:p>	<o:p></o:p>
<st1:place w:st="on"><st1:country-region w:st="on">USA</st1:country-region></st1:place><o:p></o:p>	Giulia Kennedy<o:p></o:p>	Affymetrix Inc.<o:p></o:p>	<o:p></o:p>
	Shoba Gopalan<o:p></o:p>	Affymetrix Inc.<o:p></o:p>	<o:p></o:p>
<st1:place w:st="on"><st1:country-region w:st="on">Japan</st1:country-region></st1:place><o:p></o:p>	Takashi Gojobori<o:p></o:p>	DNA Data Bank of <st1:place w:st="on"><st1:country-region w:st="on">Japan</st1:country-region></st1:place>, <o:p></o:p> National <st1:place w:st="on"><st1:placetype w:st="on">Institute</st1:placetype> of <st1:placename w:st="on">Genetics</st1:placename></st1:place><o:p></o:p>	<o:p></o:p>
<st1:place w:st="on"><st1:country-region w:st="on">Taiwan</st1:country-region></st1:place><o:p></o:p>	Chien-Hsiun Chen <o:p></o:p>	Institute of Biomedical Sciences<o:p></o:p> Academia Sinica<o:p></o:p>	<o:p></o:p>
<st1:place w:st="on"><st1:country-region w:st="on">India</st1:country-region></st1:place><o:p></o:p>	Partha P. Majumder<o:p></o:p>	Indian Statistical Institute<o:p></o:p>	<o:p></o:p>

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Meeting Summary <o:p></o:p>

The Korean meeting on PASNP Bioinformatics (PASB) tried to agree on some practical issues in bioinformatics area.<o:p></o:p>

We agreed on the basic file name format and also a detailed DB schema was proposed.<o:p></o:p>

There were several important points discussed to make the bioinformatics effort fruitful.<o:p></o:p>

PASB meeting’s outcome can be extended to more general bioinformatics collaboration in Asian region.<o:p></o:p>

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Here are the points we discussed at the jeju meeting (Pan Asia SNP Bioinformatics meeting). <o:p></o:p>

① PASB will use a new protocol of handling SNP data collected from Affymetrix chip experiments. <o:p></o:p>

② Both raw and processed data will be deposited and processed by PASB. <o:p></o:p>

③ Affy chip Q/C parameters = 90% Calling at 0.25 P-value <o:p></o:p>

④ Once enough data are gathered PASB freezes the database and analysis will be initiated. <o:p></o:p>

⑤ Both local and central bioinformatics groups will carry out the analyses in parallel <o:p></o:p>

⑥ The Affy chip file name we decided has a format example: <a href="http://biocc.ngic.re.kr/PASbase/Mediawiki/index.php/National_code">KR</a>_<a href="http://biocc.ngic.re.kr/PASbase/Mediawiki/index.php/Ethnic_code">KR</a>_<a href="http://biocc.ngic.re.kr/PASbase/Mediawiki/index.php/Unique_serial">123456</a>_<a href="http://biocc.ngic.re.kr/PASbase/Mediawiki/index.php/Experiment_serial">1</a>_<a href="http://biocc.ngic.re.kr/PASbase/Mediawiki/index.php/Technology_serial">12</a> <o:p></o:p>

⑦ Data table scheme will be determined by bioinformatics group <o:p></o:p>

◦ The use the minimal number of fields → Dr Chen will give me a draft for it <o:p></o:p>

◦ IRB documentation will be necessary for <o:p></o:p>

<a name="#80000000"></a>◦ e-mail + mailing list will be set up for future communication <o:p></o:p>

⑧ DB format : MySQL DB format is recommended <o:p></o:p>

⑨ Four countries will mirror the data. The four countries should be able to reliably maintain the hardware & DB servers + ftp, etc. <o:p></o:p>

⑩ Enforcement of the format usage is necessary <o:p></o:p>

⑪ List of the actual depositing institutes and the personnel will be necessary <o:p></o:p>

⑫ Previsously produced data need to be integrated into the new system <o:p></o:p>

⑬ Next meeting → around Oct. 21th, <st1:place w:st="on"><st1:country-region w:st="on">Singapore</st1:country-region></st1:place> <o:p></o:p>

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