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Dr. Wang Yi from U C, Berkeley Visits HZAU

On the afternoon of March 30th, Dr. Wang Yi, Assistant Professor from University of California, Berkeley, shared his experience in developing bioinformatics tools with teachers and students of HZAU. Zhang Hongyu, Dean of the College of Informatics, Li Xiangdong, Party Secretary of the College and some professors attended the exchange activity.

Wang Yi has successfully established plant gene intron and exon evolutionary database (PIECE) and online clustering analysis platform of homologous protein (OrthoVenn). Taking these as examples, he elaborated on the complete process of the development of bioinformatics tools. Speaking of the differences between the PIECE database and the OrthoVenn (an online analytical platform), Wang said that the database could provide a friendly interface for the user while the online analysis platform requires users to submit data, and then visual feedback will be given after background calculation. The development of both functional tools has to go through the following steps: analyzing demand, reading literature, writing development documents, designing programming, testing and releasing. He introduced that the design of OrthoVenn’s is based on the OrthoMCL algorithm developed in 2003. After improving the BLAST with DIAMOND, the algorithm speed increased by 10,000 times. “Nearly two hundred users submit data to my site every day, and we often get the feedback that the site is easy to operate from users. Of course, they also give some suggestions by email”, Wang Yi said. He said that PIECE 3.0 would be released within the following two years.

Finally, Wang Yi stressed 3 issues worthy of concern. The first is the version. Special attention should be paid to software version used in the development process and the upgraded version in the later debugging process. The second is the permission. The server usually is weak in security, and the server permissions are different from the users’ rights (the former is stricter than the latter). Therefore, we should be very careful when setting permissions. Last but not least, it is necessary to discuss with potential users, because they are more sensitive users and have higher demand, and may come up with better suggestions.

(By Zuo Xiaoling)