- A monthly newsletter which supports information integration -

BioResource Newsletter  Vol.1  No.5 

” Hot news from abroad No. 4: 

 FIMRe - Federation of International
 Mouse Resources

” Hot news from abroad No. 5: 

 1st International Biocurator Meeting

” Ongoing column vol. 5

 Access Log File Analysis Tool (3)

shigenImage

No.5 2005/05/31  


Download the PDF version of this newsletter here.
 

hot informationHot news from abroad No. 4

 FIMRe - Federation of International Mouse Resources

   The 2nd Mouse Resource Center's Roundtable was held from 21st to 23rd April in Rome's Hotel Mediterraneo which is a few minutes walk from Termini Station. The first conference was held in The Jackson Laboratory in America and was tentatively called International Federation of Mouse Resource (IFMR) at that time. It is now officially named FIMRe and the pronunciation which sounds a little like Italian is "Fiimura".
    FIMRe is a collaborating group of Mouse Repository and Resource Centers worldwide whose collective goal is to archive and provide strains of mice as cryopreserved embryos and gametes, ES cell lines, and live breeding stock to the research community. The workings of this collaboration are intricate and 8 working groups were formed for each of the fields as stated in table 1. Members of the FIMRe are as stated below.


FIMRe members

USAFThe Jackson Laboratory(JAX), Mouse Mutant ResourceRegional Centers (MMRRC:Taconic/SUNY, Harlan/Missouri, UNC,UCD), Mouse Models of Human CancerConsortium (MMHCC),American Type Cell Collection(ATCC),
CANADAFCanadian Mouse Mutant Resource (CMMR),
EUROPEFEuropean Mouse Mutant Archive (EMMA:CNR Instituto di Biologia Cellulare in Monterotondo, Italy, CNRS Centre de Distiribution, de Typage et d'Archivage animal in Orleans, France, MRC:Mammalian Genetics Unit in Harwell, UK,@Karolinska Institute in Stockholm, Sweden, Instituto Gulbenkian de Ciencia in Oeiras, Portugal, GSF:Institute of Experimental Genetics in Munich, Germany, EMBL: European Bioinformatics Institute in Hinxton, UK)
JAPANFRIKEN BioResource Center (RBRC), Center for Animal
Resources and Development (CARD)
AUSTRALLIAFAustralian Phenomics Facility


Table 1

(1) Bioinformatics, (2) Animal Health, (3) Genetic Quality Control,
(4) Procedures,(importation,preservation,distribution,transpotation)
(5) ES cells, (6) Marketing, Training and Education,
(7) Business Plan/International Funding, (8) IP (Intellectual property)


    The conference was hosted by EMMA, the European Mouse Archive. The chairman was the director of CNR, Prof. Tocchini-Valentini and the representative of EMMA, Dr. Martin Hrabe de Angelis, expedited the proceedings.
    The participants were divided into working groups for discussion on the first day, and results of the discussion were presented the next morning, followed by a plenary in the evening and a conclusion on the last day. Out of the 40 participants, 7 of them were from Japan, consisting of 3 representatives from Riken BRC and 4 representatives from CARD Kumamoto University. I attended as a CARD representative, in charge of information and participated in the bioinformatics group discussion. The Jackson Laboratory started IMSR (International Mouse Strain Resource, http://www.informatics.jax.org/imsr/) in July 2004 and the information aspect of FIMRe will start from IMSR.
   The minutes of the proceedings were not publicly released but the main decisions made in the FIMRe meeting are as follows.

(1) Official name of the organization: Federation of International Mouse Resources (FIMRe)
(2) Chairperson: Barbara B. Knowles, The Jackson Laboratory
(3) Vice chairs: North America (Geoff Hicks), Asia (Yuichi Obata), Australia (Chris Goodnow),Europe (Martin Hrabe de Angelis)
(4) Participating institutions (18): All members will sign a memorandum
(5) Host for the next meeting and time: MMRRC.
  MMRRC's annual meeting in Bethesda in October was nominated.
(6) Each working group will compile a written report by the next meeting.

   Further information on FIMRe is available at http://www.fimre.org



hot information Hot news from abroad No. 5

 1st International Biocurator Meeting

   Following up to our article in BioResource now! Vol.1(1), the First International Biocurator Meeting will be held from 8th to 11th December 2005 in Asilomar Conference Center, America. The goal of this meeting is to create a forum for curators and developers of biological databases to discuss their work and swap information such as methodology and new technology and also to promote collaborations to achieve better database architecture.



   Plenary speakers for the meeting are Rolf Apweiler (EBI: UniProt annotation), Russ Altman (Stanford University: Knowledgebases, Simulations) and Mike Tyers (Mount Sinai Hospital: GRID). For each session stated below, there will be 3 or 4 guest speakers.
   1 : Literature collection, curation tools and methods,
   2 : Genome sequence and comparative genomics annotation
   3 : Curation of large-scale functional genomics data
   4 : Ontology development and implementation


   The organizing committee of this meeting is comprised of database developers from each country. Representing Japan, Prof Takashi Gojobori (DDBJ : http://www.ddbj.nig.ac.jp/, H-invDB: http://hinvdb.ddbj.nig.ac.jp/) is the chairman of session 2 and is in charge of giving a lecture.


   I (Oryzabase: http://www.shigen.nig.ac.jp/rice/oryzabase/) am also on the organizing committee so do not hesitate to ask me questions about this meeting. For futher information, refer to http://biocurator.org/

(Author : Yukiko Yamazaki)



Information Technology  Vol. 5

 Access Log File Analysis Tool (3)


   In the previous issue, I explained about the contents of an annual access analysis graph of "Webalizer". In this issue, I will introduce the functions of a monthly analysis and its graphs.

   Picture 1 shows the daily access analysis graph. The headings are similar to those explained in the previous issue and information such as number of hits, number of pages, number of files and total visitors can be obtained from the daily analysis.



Picture 1: Daily access analysis graph


   The daily analysis can also display the ranking of the results. Picture 2 - 5 shows various ranking graphs.


Picture 2: Hit ranking graph

Picture 4: Agent ranking graph

Picture 3: Host ranking graph

Picture 5: Country ranking graph


Hit Ranking Hit ranking sorted by page. It can also be grouped by URL. You can find out which page is the most popular.
Host Ranking Sorted by the name or IP address of host which was in the access ranking and their access total. Info on frequent users can be obtained
Agent Ranking Ranking sorted by agent (browser version).The type of browser (IE, NN, Safari, etc) and OS (WIndows, Mac, Linux, etc) used can be known
Country Ranking Calculated from the host's domain name (co.jp, com, etc).However, if the country of the domain is not specified (org.net), it will be grouped as unknown.

   As shown in the table above, much information can be obtained from these rankings. However, there are a few things that you need to be careful with. An error page will also be counted as a search result and that a great number of accesses from robotic search engine will result in the miscalculation of the correct access total.


 Access Log File Analysis Tool - Summary

There are few drawbacks with the "Webalizer" but if you keep them in mind when referring to the access analysis and ranking information data, you will have a deeper understanding of the needs of the users and therefore will be able to produce better web pages with more attractive contents.


Genetic Informatics Laboratory, Center for Genetic Resource Information
Takehiro YAMAKAWA


 

Editor's notes : It is very interesting to observe how members from different countries put aside their differences to collaborate together. Rome's warm atmosphere and the hospitability of the hosts must have favorably influenced everyone to bond together under this splendid name, FIMRe. I truly felt the importance of the role "information" plays in collaborations. (Y.Y.)

Contact :Yata 1111, Mishima, Shizuoka 411-8640, JAPAN
Center for Genetic Resources Information, National Institute of Genetics
TEL 055-981-6885 (Yamazaki)
E-mailBRnews@chanko.lab.nig.ac.jp