あとでよむ - mitsuteru nakao on Diigo

Think of CC0 as the "no rights reserved" option.
CC0 is a single purpose tool, designed to take on the dedication function
3 more annotations...
- PDDC is based on U.S. law, and the enforceability of its dedication function outside of the U.S. is not certain.
- Once you apply CC0 to your work you can’t change your mind later and re-assert copyright or database rights over the work.
- Databases may contain facts that, in and of themselves, are not protected by copyright law.

Bioinformatics is a visual analytics (sometimes) « Freelancing science

Bioinformatics

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visualize 可視化 biology bioinformatics あとでよむ

19 Feb 09

Tips and tricks for software engineering in bioinformatics (talk by Joel Dudley) « I was lost but now I live here

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bioinformatics あとでよむ

08 Feb 09

IA Spectrum: ユーザーエクスペリエンスデザイン成果物リスト（User Experience Deliverables）

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design pattern あとでよむ

01 Feb 09

サービス｜日本発！クラウドコンピューティング情報発信サイト CLOUD news（クラウドニュース）

cloud.manabing.jp/service - Preview

EC2 S3 あとでよむ

23 Dec 08

Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009 -- Galperin and Cochrane 37 (Supplement 1): D1 -- Nucleic Acids Research

nar.oxfordjournals.org/...D1 - Preview

bioinformatics NAR あとでよむ

179 databases

19 Dec 08

viの使い手がvimエディタについて知っておくべき事トップ10 — 名無しのvim使い

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vim あとでよむ

11 Dec 08

Oxford Journals | Life Sciences | Nucleic Acids Research | SUBMITTING TO THE WEB SERVER ISSUE

www.oxfordjournals.org/...submission_webserver.html - Preview

IoA NAR あとでよむ

a summary of web servers produced by Francis Ouellette and his colleagues at the Ontario Institute for Cancer Research.
Authors must contact Dr. Gary Benson at narwbsrv@bu.edu to check the suitability of their proposed submission by 31 December, 2008 at the latest. A maximum one page summary of the web server function should be submitted for this purpose. Proposals sent in before 24 November 2008 will not be reviewed until after that date.
32 more annotations...
- Servers which require access through a separate application program will be rejected.
- MUST include a simple mechanism to try out sample data
- The website MUST contain help pages or a tutorial
- MUST contain, at the top, the following affirmative statement. "This website is free and open to all users and there is no login requirement."
- names
- website address
- emails of all authors
- affiliations
- the processing method
- the output,
- descriptions of the input data
- two to four keywords
- how long the server has been running
- testing
- For proposals given approval, the manuscript submission deadline will be 3 weeks after the date of the approval email or 31 January 2009, whichever is later. (Authors are encouraged to be patient. Proposal reviews take up most of January.)
- The manuscript should include a description of the software including the required input, the range of computations it can perform and examples of the output returned to the user. Submissions should typically be 4-5 printed journal pages in length, but authors are urged to be succinct in their writing, given the tight page constraints of this special issue.
  - 4-5 printed journal pages - on 2009-01-10
  Add Sticky Note
- email addresses of six suggested referees
- the name(s) of the software as the first word(s) in the title of the article
- nclude within the abstract a valid URL
- Manuscripts that contain only a cursory description of the web server
- The software must be completely functional and have been extensively tested at the time of submission.
- who have relevant expertise or who would be likely users of the web server
- References must be in the correct journal format
- The purpose of this software issue is to provide a single location where potential users of web-based software can find out what is available and what the software actually does.
- originality is not necessarily an issu
- A key consideration on acceptability will be whether the software described in the manuscript is useful and whether it actually works over the web as described
- brevity
- The author has stated that the website is free and open to all and that there is no login requirement. Please notify me in your review if this is not the case.
- URLs, u
- should not be cited
- The home page for the software should not be used as a figure
- native language is not English

Nucl. Acids Res. -- Table of Contents (January 2009, 37 [Database issue])

nar.oxfordjournals.org/...index.dtl - Preview

bioinformatics あとでよむ

Michael Y. Galperin and Guy R. Cochrane
Hideaki Sugawara, Kazuho Ikeo, Satoshi Fukuchi, Takashi Gojobori, and Yoshio Tateno
36 more annotations...
- DDBJ dealing with mass data produced by the second generation sequencer
- Petabyte-scale innovations at the European Nucleotide Archive
- Shinichi Morishita
- PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes
- Toutai Mituyama, Kouichirou Yamada, Emi Hattori, Hiroaki Okida, Yukiteru Ono, Goro Terai, Aya Yoshizawa, Takashi Komori, and Kiyoshi Asai
- The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs
- GtRNAdb: a database of transfer RNA genes detected in genomic sequence
- The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
- tRNAdb 2009: compilation of tRNA sequences and tRNA genes
- Takashi Abe, Toshimichi Ikemura, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, and Hachiro Inokuchi
- tRNADB-CE: tRNA gene database curated manually by experts
- The Universal Protein Resource (UniProt) 2009
- InterPro: the integrative protein signature database
- Masafumi Shionyu, Akihiro Yamaguchi, Kazuki Shinoda, Ken-ichi Takahashi, and Mitiko Go
- AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse
- Satoshi Fukuchi, Keiichi Homma, Shigetaka Sakamoto, Hideaki Sugawara, Yoshio Tateno, Takashi Gojobori, and Ken Nishikawa
- The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions
- Miho Higurashi, Takashi Ishida, and Kengo Kinoshita
- PiSite: a database of protein interaction sites using multiple binding states in the PDB
- The GOA database in 2009—an integrated Gene Ontology Annotation resource
- PEDANT covers all complete RefSeq genomes
- DOOR: a database for prokaryotic operons
- HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
- OperonDB: a comprehensive database of predicted operons in microbial genomes
- Hiroyuki Wakaguri, Yutaka Suzuki, Toshiaki Katayama, Shuichi Kawashima, Eri Kibukawa, Kazushi Hiranuka, Masahide Sasaki, Sumio Sugano, and Junichi Watanabe
- Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009
- Ensembl 2009
- The UCSC Genome Browser Database: update 2009
- Yukio Maruyama, Ai Wakamatsu, Yoshifumi Kawamura, Kouichi Kimura, Jun-ichi Yamamoto, Tetsuo Nishikawa, Yasutomo Kisu, Sumio Sugano, Naoki Goshima, Takao Isogai, and Nobuo Nomura
- Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics
- Nobutaka Mitsuhashi, Kaori Fujieda, Takuro Tamura, Shoko Kawamoto, Toshihisa Takagi, and Kousaku Okubo
- BodyParts3D: 3D structure database for anatomical concepts
- Makoto K. Shimada, Ryuzou Matsumoto, Yosuke Hayakawa, Ryoko Sanbonmatsu, Craig Gough, Yumi Yamaguchi-Kabata, Chisato Yamasaki, Tadashi Imanishi, and Takashi Gojobori
- VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts
- Takeshi Obayashi, Shinpei Hayashi, Motoshi Saeki, Hiroyuki Ohta, and Kengo Kinoshita
- ATTED-II provides coexpressed gene networks for Arabidopsis

10 Dec 08

11分30秒でわかる OpenID - まちゅダイアリー(2008-12-06)

www.machu.jp/20081206.html - Preview

openid あとでよむ

09 Nov 08

PLoS Computational Biology: Computational Biology Resources Lack Persistence and Usability

It would seem no longer sufficient to write in a paper that “software is available from the authors upon request” or to publish a Web server that will quickly become obsolete.

www.ploscompbiol.org/...journal.pcbi.1000136 - Preview

あとでよむ bioinformatics

Of 14 methods we attempted to obtain, some over a period of four years, we gained access to six methods (covering the period from 1994 to 2008) that we can run locally or remotely on a consistent basis.
Open sourcing seems to be the most viable solution at this time.
1 more annotations...
- It would seem no longer sufficient to write in a paper that “software is available from the authors upon request” or to publish a Web server that will quickly become obsolete.

21 Oct 08

Rails で MySQL を使うときの注意点 | METAREAL

www.metareal.org/...otes-on-rubyonrails-with-mysql - Preview

rails あとでよむ sql mysql

"select *" が多すぎる
（SQL を EXPLAIN してみて、"using temporary" となっていれば、そういう事態が発生しているサインだ）。
1 more annotations...
- 文字列型がかなり無駄かも

13 Sep 08

Mercurial - Mercurial

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python あとでよむ

11 Sep 08

Access : : Nature

www.nature.com/...nature06862.html - Preview

あとでよむ

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