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MachiBase: Drosophila melanogaster 5'-end RNA Transcription DatabaseNo description found
http://machibase.gi.k.u-tokyo.ac.jp/
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MachiBase: Drosophila melanogaster 5'-end RNA Transcription Database | machibase.gi.k.u-tokyo.ac.jp Reviews
https://machibase.gi.k.u-tokyo.ac.jp
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machibase.gi.k.u-tokyo.ac.jp
MachiBase Wiki: Top Page
http://machibase.gi.k.u-tokyo.ac.jp/wiki/Index
Welcome to the MachiBase Web Site. Http:/ machibase.gi.k.u-tokyo.ac.jp/. Machibase Browser: http:/ machibase.gi.k.u-tokyo.ac.jp/.
MachiBase Wiki: About Us
http://machibase.gi.k.u-tokyo.ac.jp/wiki/AboutUs
The fruit fly Drosophila melanogaster. Is a model of development biology with accumulated genetics knowledge. The 1995 Novel Prize. Novel Prize was awarded to Eric Wieschaus. However, despite the absence of prior knowledge of the locations of previously identified genes, the 5-end SAGE. Method has demonstrated efficacy in cataloging high numbers of expressed genes. Following simple modification of adopting the recently developed high-throughput genome sequencer Solexa. Budrul Ahsan (*), Taro L. Saito...
MachiBase Wiki: wiki
http://machibase.gi.k.u-tokyo.ac.jp/wiki/Download
All the Drosophila melanogaster seven development stages transcription data are uploaded as follows. RawTag is archive for all Solexa tags as were collected. It includes. Embryo.dat(tag length 36bp). Larvadat (tag length 36bp). OldFemale.dat (tag length 30bp). OldMale.dat (tag length 30bp). S2dat (tag length 30bp). YoungFemale.dat (tag length 30bp). YoungMale.dat (tag length 30bp). ALL the transcription start site(TSS)s with their expression number determined by alinging 5end tags are.
MachiBase Wiki: Help
http://machibase.gi.k.u-tokyo.ac.jp/wiki/Help
Here, we explain the following tracks related to the MachiBase. This track provides information about displaying genomic region. You can change genomic location by manipulating this track. Some of the values can be changed using drop down menu, where others needed to be input into the parameter boxes (like above image) inside the main window. The details about this method are as follows,. Input the chromosome name e.g., 2L to display. Input the start position of the chromosome to display. To save the pre...
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UTGB Toolkit - Users Manual
http://utgenome.org/toolkit
UTGB Toolkit User's Manual. This page describes the usage of UTGB Toolkit. Drag and drop of tracks is supported in UTGB, and also you can resize the height of tracks by dragging the lower frame border of the tracks. Opens the configuration panel for the track. Adjusts the height of the track. Resizes the track frame height according to the track image size. Minimizes/Restore the height of the track frame. The following keyboard shortcuts are provided for relocating the window location quickly:. These doc...
UTGB Toolkit -
http://utgenome.org/publication.html
UTGB Toolkit for Personalized Genome Browsers. Taro L. Saito, Jun Yoshimura, Shin Sasaki, Budrul Ahsan, Atsushi Sasaki, Reginaldo Kuroshu and Shinichi Morishita. Bioinformatics. In press) (June 2009). Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites. MachiBase: A Drosophila Melanogaster 5'-end mRNA Transcription Database. ACM Portal http:/ doi.acm.org/10.1145/1376616.1376650. UTGB Medaka: Genomic Resource Database for Medaka Biology.
UTGB Toolkit -
http://utgenome.org/download.html
UTGB Toolkit Quick Start. UTGB Shell installer using Java Web Start is available. Open http:/ utgenome.org/toolkit/utgb.jnlp. To install UTGB Toolkit. Downloadable archive for manual installation is also available from here: http:/ maven.utgenome.org/repository/artifact/org/utgenome/utgb-shell/. December 1st, 2011. UTGB Toolkit 1.5.8 released. Upgrade to snappy-java-1.0.4.1, picard-1.5.6, GWT2.4.0. July 6th, 2011. UTGB Toolkit 1.5.7 release. Migration to Tomcat 7.x. June 15th, 2011. April 28th, 2011.
UTGB Toolkit -
http://utgenome.org/members.html
UTGB Toolkit is developed at Morishita Laboratory. In University of Tokyo. Taro L. Saito. 169; 2007-2010 utgenome.org. This work is licensed under a Creative Commons Attribution-ShareAlike 2.5 License.
UTGB Toolkit - Project License
http://utgenome.org/license.html
Typically the licenses listed for the project are that of the project itself, and not of dependencies. 169; 2007-2011 utgenome.org. This work is licensed under a Creative Commons Attribution-ShareAlike 2.5 License.
UTGB Toolkit - Silk Format Specification
http://utgenome.org/toolkit/silk.html
Silk Text Format Specification. This document is written by Taro L. Saito. Situations where Silk is useful. Situations where Silk is not useful. Tree node with a text value. Tree node with several child nodes with text values. Escape sequences for the head of a line. Multi-line Block Data Reperesentation. Is a human-friendly and space-efficient text format, designed for describing tree-structured data. Silk is a replacement XML. Silk text format has the following features:. That is, a list of trees.
Taro L. Saito, Ph.D. | xerial.org
http://xerial.org/leo
Taro L. Saito. Taro L. Saito, Ph.D. Software Engineer at Treasure Data, Inc. Language Skills: Scala (current favorite), Java, C/C , Ruby, Perl, R, Scheme, OCaml, Z80, etc. GitHub https:/ github.com/xerial. BitBucket https:/ bitbucket.org/xerial. Tutorial of the Scala programming language. Presentation Slides @ SlideShare. Leo's Chronicle (in Japanese): http:/ leoclock.blogspot.com. Xerial Blog: http:/ voice.xerial.org. April 2005 - March 2007. April 2007 - February 2014. March 2014 - June 2015. MachiBase...
Genome Sciences | xerial.org
http://xerial.org/genome-science
Taro L. Saito. Cluser Computing Platform for Genome Sciences. Personal genome analysis involves massive amount of data analysis: genome sequence alignment, SNP calls, finding desease-related mutations, etc. These data analysis involves tons of data managment (e.g., compression, file I/O, table joins, filtering, etc.) Silk supports running these complex data analysis pipeline in a cluster machine. Genome browsers developed by UTGB. The Primary Transcriptome of. This is due to the high frequency of trans-s...
Publications | xerial.org
http://xerial.org/publication
Taro L. Saito. Taro L. Saito. Toshiya Nishimura, Amaury Herpin, Tetsuaki Kimura, Ikuyo Hara, Toshihiro Kawasaki, Shuhei Nakamura, Yasuhiro Yamamoto, Taro L. Saito. Jun Yoshimura, Shinichi Morishita, Tatsuya Tsukahara, Satoru Kobayashi, Kiyoshi Naruse, Shuji Shigenobu, Noriyoshi Sakai, Manfred Schartl, and Minoru Tanaka. Analysis of a novel gene, Sdgc, reveals sex chromosome-dependent differences of medaka germ cells prior to gonad formation. July 30, 2014, doi:10.1242/dev.106864. Taro L. Saito. Matthias ...
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女性がひとりで生きていくという選択がそもそも日本は出来ない社会なんです 立命館大学准教授 丸山里美さんが語る フィールドワーカーとして女性野宿者と出会い続けた日々. その１ 基礎知識編 本人の主体性の尊重が滞納や失踪を防ぐ 入居支援のプロ 小幡邦暁さんに聞く 生活困窮者に対する入居支援講座. 後編 この声は絶対、拾わなければ 流しのマンガ描き さいきまこさんが語る 私の綱渡りまんが道. 前半 私が新宿ダンボール村に足を踏み入れた頃 講演 稲葉剛さん ほっとプラス記念講演 生活困窮者支援の過去と未来. 非効率だからこそ、誰も取り残さない空間 のじれん 室田大樹さんが語る 渋谷の真ん中で野宿の仲間と野菜を刻みつつ紡ぐ自由. 女性がひとりで生きていくという選択がそもそも日本は出来ない社会なんです 立命館大学准教授 丸山里美さんが語る フィールドワーカーとして女性野宿者と出会い続けた日々. そんな中、その問題へ 女性野宿者 という視点から切り込む研究者に、立命館大学准教授 丸山里美さんがいらっし. 後編 この声は絶対、拾わなければ 流しのマンガ描き さいきまこさんが語る 私の綱渡りまんが道.
MachiBase: Drosophila melanogaster 5'-end RNA Transcription Database
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