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<o:p> </o:p>
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Pan-Asia SNP Bioinformatics (PASB)<o:p></o:p>
Initiative Bioinformatics working group meeting<o:p></o:p>
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<o:p> </o:p>
▶ 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>
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Date<o:p></o:p>
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Time<o:p></o:p>
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Topic<o:p></o:p>
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Lecturer<o:p></o:p>
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8.18(Thur.)<o:p></o:p>
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13:00∼13:20<o:p></o:p>
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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>
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Dr. Kyuchan Kimm<o:p></o:p>
(NGRI)<o:p></o:p>
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13:20∼13:40<o:p></o:p>
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Introduction of members<o:p></o:p>
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Dr. Jong Bhak<o:p></o:p>
(<st1:personname w:st="on">NGIC</st1:personname>)<o:p></o:p>
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13:40∼14:00<o:p></o:p>
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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>
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<o:p></o:p>
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14:00∼14:20<o:p></o:p>
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The outline of the task of this group<o:p></o:p>
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<o:p></o:p>
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14:20∼14:40<o:p></o:p>
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Break<o:p></o:p>
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<o:p></o:p>
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14:40∼15:00<o:p></o:p>
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Presentation 1<o:p></o:p>
(Korea SNP research activities)<o:p></o:p>
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Dr. Kyuchan Kimm<o:p></o:p>
(NGRI)<o:p></o:p>
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15:00∼15:20<o:p></o:p>
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Presentation 2<o:p></o:p>
(Singapore SNP research activities)<o:p></o:p>
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<o:p></o:p>
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15:20∼15:40<o:p></o:p>
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Presentation 3<o:p></o:p>
(India SNP research activities)<o:p></o:p>
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Dr. Partha P. Majumder<o:p></o:p>
(Indian Statistical Institute)<o:p></o:p>
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15:40∼16:10<o:p></o:p>
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Break<o:p></o:p>
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<o:p></o:p>
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16:10∼16:30<o:p></o:p>
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Presentation 4<o:p></o:p>
(Taiwan SNP research activities)<o:p></o:p>
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Dr. Chien-Hsiun Chen <o:p></o:p>
(Institute of Biomedical Sciences)<o:p></o:p>
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16:30∼17:10<o:p></o:p>
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Presentation 5<o:p></o:p>
(The current progress of Affymetrix activities<o:p></o:p>
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Dr. Kennedy<o:p></o:p>
(AFFYMETRIX, INC)<o:p></o:p>
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17:10∼19:00<o:p></o:p>
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Break and Dinner<o:p></o:p>
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<o:p></o:p>
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19:00∼19:50<o:p></o:p>
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Database standardization format talk<o:p></o:p>
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<o:p></o:p>
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19:50∼20:40<o:p></o:p>
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Database server, Analysis algorithms, <o:p></o:p>
platform selection discussion<o:p></o:p>
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<o:p></o:p>
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20:40∼21:30<o:p></o:p>
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Administration: Publication issues, credit, funding, Summary and Future work. Next meeting. Concluding 1.<o:p></o:p>
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<o:p></o:p>
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8.19(Fri.)<o:p></o:p>
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09:30∼10:30<o:p></o:p>
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Concluding 2. Misc issues. Local meetings (for each national and inter-national discussions) <o:p></o:p>
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Dr.Gojobori<o:p></o:p>
(DDBJ, NIG)<o:p></o:p>
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10:30∼11:00<o:p></o:p>
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Writing up the summary and action progrean<o:p></o:p>
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Dr.Jong Bhak<o:p></o:p>
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11:00∼11:30<o:p></o:p>
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Free discussion<o:p></o:p>
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<o:p></o:p>
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Participant <o:p></o:p>
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Nation<o:p></o:p>
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Name<o:p></o:p>
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Facility<o:p></o:p>
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Note<o:p></o:p>
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<st1:place w:st="on"><st1:country-region w:st="on">Korea</st1:country-region></st1:place><o:p></o:p>
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Jonghwa Bhak <o:p></o:p>
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<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>
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<o:p></o:p>
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Kuchan Kimm <o:p></o:p>
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National Genome Research Institute, <o:p></o:p>
Korea National Institute of Health<o:p></o:p>
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Hyangsook Yoo<o:p></o:p>
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The Center for Functional Analysis of Human Genome<o:p></o:p>
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Bonghee Lee<o:p></o:p>
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<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>
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Sangsoo Kim <o:p></o:p>
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<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>
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Heekyung Song <o:p></o:p>
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SeouLin Biotechnology Institute(SLBI)<o:p></o:p>
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<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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Wayne Mitchell<o:p></o:p>
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Genome Institute of <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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<o:p></o:p>
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Mark Thomas SEIELSTAD<o:p></o:p>
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Genome Institute of <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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<st1:place w:st="on"><st1:country-region w:st="on">USA</st1:country-region></st1:place><o:p></o:p>
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Giulia Kennedy<o:p></o:p>
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Affymetrix Inc.<o:p></o:p>
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<o:p></o:p>
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Shoba Gopalan<o:p></o:p>
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Affymetrix Inc.<o:p></o:p>
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<st1:place w:st="on"><st1:country-region w:st="on">Japan</st1:country-region></st1:place><o:p></o:p>
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Takashi Gojobori<o:p></o:p>
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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>
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<o:p></o:p>
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<st1:place w:st="on"><st1:country-region w:st="on">Taiwan</st1:country-region></st1:place><o:p></o:p>
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Chien-Hsiun Chen <o:p></o:p>
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Institute of Biomedical Sciences<o:p></o:p>
Academia Sinica<o:p></o:p>
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<o:p></o:p>
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<st1:place w:st="on"><st1:country-region w:st="on">India</st1:country-region></st1:place><o:p></o:p>
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Partha P. Majumder<o:p></o:p>
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Indian Statistical Institute<o:p></o:p>
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<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>
<o:p> </o:p>
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: KR_KR_123456_1_12 <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>
◦ 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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