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Software
 
 
Software Name:SQUAT
Inventors:Li-An Yang, Yu-Jung Chang, Shu-Hwa Chen, Chung-Yen Lin and Jan-Ming Ho
Country:
Date:2018/04–/
Abstract:

A Sequencing Quality Assessment Tool for Data Quality Assessments of Genome Assemblies. https://github.com/luke831215/SQUAT

 
Software Name:WGBS-galaxy
Inventors:Yu-Jung Chang, Wei-Chun Chung, Chung-Yen Lin, and Jan-Ming Ho
Country:
Date:2017/12–/
Abstract:

A customized Galaxy platform for analyzing Whole-Genome Bisulfite Sequencing data. The docker images are currently in beta testing and planning for public online soon. The WGBS-galaxy: http://140.109.16.146:5000/lsnb/galaxy

 
Software Name:HighQ(x)
Inventors:Chih-Hao Fang, Yu-Jung Chang, Wei-Chun Chung, Ping-Heng Hsieh, ChungYen Lin and Jan-Ming Ho
Country:
Date:2017/10–/
Abstract:

Read subset selection for speeding and improving high-depth NGS genome assembly by high-quality percentage. DOCKER image: https://hub.docker.com/r/abnerchang/subset/

 
Software Name:QReadSelector
Inventors:Wei-Chun Chung, Yu-Jung Chang, and Jan-Ming Ho
Country:
Date:2015/12–/
Abstract:

A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce. http://clouddoe.iis.sinica.edu.tw/

 
Software Name:CloudDOE: A Quick and Easy Tool for Setting up Hadoop on Private/Public Clouds and Analyzing High-Throughput Sequencing Data via MapReduce
Inventors:Wei-Chun Chung, Yu-Jung Chang, Chien-Chih Chen
Country:
Date:2013/11–/
Abstract:

Background: Cloud computing provides an on-demand and scalable environment which is capable of processing and analyzing large-scale data. Using MapReduce framework, data and its corresponding workloads can be distributed over all computers in the cloud and execution time can be substantially reduced. MapReduce framework contained in the well-known Hadoop software has been successfully adopted in bioinformatics, including de novo genome assembly, mapping reads to genomes, and finding single nucleotide polymorphisms. Unfortunately, deploying a Hadoop cloud, executing MapReduce programs on it, and extending functionality of the cloud require in-depth computer science expertise and relevant technical skills, thus make practical and available software solutions difficult to obtain.

Results: We present CloudDOE, a platform-independent software package in Java which improves the availability and usability of a Hadoop-MapReduce computing cloud, shortened to Hadoop cloud. Users can be guided by smart graphical wizards to deploy a Hadoop cloud within three steps, to execute available MapReduce programs with a unified interface, and to extend functionalities of an existing cloud. The main purpose of CloudDOE is to encapsulate all technical details and to simplify complicated procedures, and thus free scientists from mind-boggling processes. CloudDOE can guide users with an intuitive user interface for deploying onto private clouds, which may befuddle regular users. Besides that, it also supports public clouds, such as Microsoft Azure and Hinet hicloud, which do not support Hadoop natively.

Conclusions: It is simple and straightforward to manipulate a Hadoop cloud through CloudDOE. CloudDOE reduces the complexity of MapReduce platforms for scientists, and helps promote MapReduce programs for developers, and substantially saves the costs of deployment, execution, enhancement, and management with the help of its smart wizards. CloudDOE is freely available at http://cloudbrush.iis.sinica.edu.tw/CloudDOE.

The CloudDOE paper is under revision (PLOS ONE journal).

 
Software Name:FontCloud: Build your own font from personal handwriting and present your articles in your own writing style
Inventors:Shu-Yu Lin, You-Jyun Wang
Country:
Date:2013/10–/
Abstract:

http://gainwisdom.iis.sinica.edu.tw/fontcloud/

 
Software Name:CloudRS: An Error Correction Algorithm of High-Throughput Sequencing Data based on Scalable Framework
Inventors:Chien-Chih Chen, Yu-Jung Chang, Wei-Chun Chung
Country:
Date:2013/05–/
Abstract:

ReadStackCorrector is develped based on mapreduce and the error correction algorithm of Allpath-LG (http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12), an NGS de novo genome assembler.

The software is released under Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) and can be accessed at https://github.com/ice91/ReadStackCorrector.

 
Software Name:CloudBrushPack
Inventors:Wei-Chun Chung, You-Chun Wang, Chien-Chih Chen, and Yu-Jung Chang
Country:
Date:2012/12–/
Abstract:

CloudBrushPack is a installation package of Hadoop and CloudBrush on a computing cluster at user's premise. The project is currently running at http://cloudbrush.iis.sinica.edu.tw/.  Its source code can be accessed at GITHUB in two projects, i.e., CBPHI (a hadoop installer, https://github.com/moneycat/CBPHI) and CBPPI (installer of CloudBrush and other plugins, https://github.com/moneycat/CBPPI). Both are released under Apache License 2.0.

 
Software Name:撈智網
Inventors:Hung Min Hsu, You-Jyun Wang
Country:
Date:2012/10–/
Abstract:

This is a crowdsourcing service focusing on outsourcing collection of ground truth of knowledge and web extraction problems from the web users.

 
Software Name:CloudBrush, A De Novo Next Generation Genomic Sequence Assembler Based on String Graph and MapReduce Cloud Computing Framework
Inventors:Chien-Chih Chen, Yu-Jung Chang
Country:
Date:2012/01–/
Abstract:

State-of-the-art high-throughput sequencers, e.g., the Illumina HiSeq series, generate sequencing reads that are longer than 150 bp up to a total of 600 Gbp of data per run. The high-throughput sequencers generate longer reads with greater sequencing depth than those generated by previous technologies. Two major challenges exist in using the high-throughput technology for de novo assembly of genomes. First, the amount of physical memory may be insufficient to store the data structure of the assembly algorithm, even for high-end multicore processors. Moreover, the graph-theoretical model used to capture intersection relationships of the reads may contain structural defects that are not well managed by existing assembly algorithms.

Further information on the software can be found in the following literature:

1. Yu-Jung Chang, Chien-Chih Chen, Chuen-Liang Chen and Jan-Ming Ho, "De Novo Next Generation Genomic Sequence Assembler Based on String Graph and MapReduce Cloud Computing Framework," BMC Genomics, volume 13, number Suppl 7, pages S28, December 2012, (also in InCoB2012 Conference, BMC, Asia-Pacific Bioinformatics Network (APBioNet), Oct. 2012).
2. Chang Yu-Jung, Chien-Chih Chen, Chuen-Liang Chen, and Jan-Ming Ho, "De Novo Assembly of High-Throughput Sequencing Data with Cloud Computing and New Operations on String Graphs," in Proceedings 5th International Conference on Cloud Computing, IEEE CLOUD 2012, IEEE, Hawaii, USA, June 2012, Acceptance rate = 17%.
3. Yu-Jung Chang, Chien-Chih Chen, Chuen-Liang Chen and Jan-Ming Ho, "CloudBrush: A String Graph Approach of De Novo Assembly for High-Throughput Sequencing Data with Cloud Computing," Proceedings the 10th Asia Pacific Bioinformatics Conference, pages 1, IEEE, Melbourne Australia, January 2012.

The software is released under Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) and can be accessed at https://github.com/ice91/CloudBrush.

 
Software Name:Intelligent Search Portal of Educational Resources
Inventors:DAAL
Country:
Date:2011/12–/
Abstract:

The services locates at http://isp.moe.edu.tw/. The goal of the project is to provide web 2.0 services for K12 teachers to share their educational resouces with other teachers or parents of students. The project starts with design of a standard protocol on exchanging educational resources based on MOE's "Grade 1-9 Curriculum Guidelines" and  IEEE LOM. It provides workflow servcies so that teachers may upload new resouces before they can be reviewed by experts assigned by Education Authorities. It also provides community services for the teacher to record learning paths of the students and to interact with his/her students. It currently hosts more than 150,000 educational objects and has more than 3,000 unique visitors daily.

http://isp.moe.edu.tw/

 
Software Name:The Interactive Platform for Smart Living Interactive Innovation Center V.0.1
Inventors:
Country:TW
Date:2008/01–/
Abstract:

The Smart Living Interactive Innovation Center (SLIIC) project aims to introduce the concept of open innovation to facilitate the digital connection. This is a knowledge-hosting platform that enables interdisciplinary researchers and stakeholders to communicate with each other to foster collaborations between Universities and the Industries in Taiwan.

http://www.uns.org.tw/

 
Software Name:人名權威檔資料著錄系統
Inventors:DAAL
Country:TW
Date:2007/01–2008/12
Abstract:與中央研究院歷史語言所合作,本資料庫的建置適用於傅圖館藏之相關人名權威檔之著錄,目的在於整合傅圖館藏善本圖籍與印記資料中所涉及之各式人名,同步建構其基本生平、傳略資料及作品集等,以提供各種數位典藏之重要考證資料。 管理系統 http://ndweb.iis.sinica.edu.tw/fsnpeople/System/ 檢索系統 http://ndweb.iis.sinica.edu.tw/fsnpeople/Search
 
Software Name:VCenter
Inventors:DAAL
Country:TW
Date:2006/10–2008/12
Abstract:VCenter, a platform for publishing, archiving and broadcasting digital multimedia, was developed by the National Digital Archive Program (NDAP). The platform serves the archives projects of NDAP by preserving the valuable digital multimedia content and broadcasting it by streaming techniques. In addition, the platform allows the general public to upload and share digital multimedia content. http://vcenter.iis.sinica.edu.tw/
 
Software Name:ZooDDD
Inventors:陳昀慶、林文鐽、胡忠銘、蕭崇德
Country:TW
Date:2005/10–2008/12
Abstract:A cross-species database for digital differential display analysis. http://bio301.iis.sinica.edu.tw/~ZooDDDNew/main.php (與細生所合作)
 
Software Name:Bio301
Inventors:陳彥臣、陳昀慶、林文鐽、蕭崇德
Country:TW
Date:2005/08–2008/12
Abstract:An automated functional annotation system for ESTs. http://bio301.iis.sinica.edu.tw/ (與細生所合作)
 
Software Name:E2D
Inventors:李果興、莊乃玉、林文鐽、蕭崇德
Country:TW
Date:2005/07–2008/12
Abstract:A novel tool for annotating protein domains in expressed sequence tags. http://bc03.iis.sinica.edu.tw/LEE/E2D.htm (與細生所、台科大資工所合作)
 
Software Name:A Patch for Windows 98/ME DNS Resolver
Inventors:Jeng-Wei Lin
Country:-
Date:2005/01–2008/12
Abstract:http://resolverw98p.openfoundry.org. This patch helps Chinese Windows 98/ME send correct Chinese domain name strings to DNS servers. (download counter: more than 50)
 
Software Name:StreamMaster v2.0
Inventors:J. M. Ho et al.
Country:TW
Date:2005/01–2005/12
Abstract:e-Learning
 
Software Name:GOBU
Inventors:林文鐽、謝明泰
Country:TW
Date:2004/09–2008/12
Abstract:A browsing utility for manipulating gene ontology. http://gobu.openfoundry.org/
 
Software Name:Octopus: A Chinese Domain Name Resolution System
Inventors:Jeng-Wei Lin,Chih-Chung Huang, June-Yen Huang
Country:-
Date:2004/05–2008/12
Abstract:http://octopus.openfoundry.org/. Octopus is a server-side proxy to facilitate Chinese domain name resolution in multiple character encodings, such as BIG5, GB-2312, and Unicode. (download counter: more than 250)
 
Software Name:UM Synteny
Inventors:張育榮、廖本揚
Country:TW
Date:2004/04–2008/12
Abstract:The UniMarker method for synteny mapping of large genomes. http://syntenymap.openfoundry.org/ (與生醫所合作)
 
Software Name:P2P Screen Everywhere v1.0
Inventors:J. M. Ho et al.
Country:TW/US
Date:2004/01–2004/12
Abstract:Remote Screen Sharing
 
Software Name:善本圖籍典藏管理系統
Inventors:DAAL
Country:TW
Date:2004/01–2008/12
Abstract:The Fu Ssu-nien Library rarebook system archiving over 20,000 rare books’ metadata and over 1,150,000 pages images. It provides a reliable research environment for Chinese researcher. http://ndweb.iis.sinica.edu.tw/rarebook/System/
 
Software Name:MOZOP
Inventors:DAAL
Country:TW
Date:2004/01–2008/12
Abstract:MoZop is a portal to GIS application on the Web. it collect information on the daily life by network using web mining technology automatically, and integrate into The Fish Database of Taiwan, The Taiwan Malacofauna Database. http://mozop.iis.sinica.edu.tw/
 
Software Name:電子影音資料庫加值應用之研究
Inventors:DAAL
Country:TW
Date:2004/01–2005/12
Abstract:與遠流智慧藏公司合作,以台灣社會人文電子影音資料庫為基礎,發展線上影音剪輯技術與影音線上交易技術。 http://ec-video.iis.sinica.edu.tw/
 
Software Name:Intelligent Transportation Web Services 1.0
Inventors:Da-Chun Su
Country:TW
Date:2004/01–/
Abstract:

Recent years have ushered in an accelerated pace in research, development and deployment of intelligent transportation systems (ITS) in Taiwan and abroad. The increasingly wide deployment of ITS can be easily justified by the tremendous benefits of ITS to individuals and societies, including savings in time and fuel, better utilization and management of resources, and increased safety, especially now advances in computing and communication technologies have made these systems cost-effective. The primary objective of the proposed three-year ITS project is to advance information technologies for intelligent transportation systems. Rather than ITS techniques, methods and components designed to support specific policies and tailored for specific locales, the focus of the project will be on basic algorithms, mechanisms, building blocks, and frameworks that can be easily customized to build diverse systems and support diverse ITS policies and management strategies in diverse environments.

[1] 國道交通資訊服務系統, http://140.109.22.36/itws/

[2] ITWS 專案網站, http://itws.openfoundry.org/

[3] MiniWin 專案網站, http://miniwin.openfoundry.org/

[4] GSPTracker 專案網站, http://gpstracker.openfoundry.org/

 
Software Name:OpenFoundry 1.0
Inventors:OSSF Team Members
Country:TW
Date:2003/07–/
Abstract:

OpenFoundry is a development platform for open source software enthusiasts to discuss, edit, and manage projects.

http://rt.openfoundry.org/

http://www.openfoundry.org/

 
Software Name:遼金元拓片數位典藏
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:與中研院史語所共同發展遼金元拓片數位典藏系統,系統典藏了傅斯年圖書館所藏遼金元碑拓,是遼金元研究上極其寶貴的資料。遼金元三代以契丹、女真、蒙古語為國語,國語與漢語通行並用,因 而遼金元三代文獻既有漢文書寫者,亦有契丹、女真、蒙古文書寫者。傅圖所藏非漢語拓碑數目雖然不多(約200幅),卻是目前罕見的拓本,是研究中古音韻和 遼金元史相當珍貴的史料。 http://rub.ihp.sinica.edu.tw/lcyrub/
 
Software Name:佛教石刻造像拓本檢索系統
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:與中研院史語所共同發展「佛教石刻造像拓本」數位典藏系統,典藏了拓自著名的北魏雲岡、龍門、房山等石窟,還包括許多較少人研究的耀縣造像碑,寶山石窟,及更多原石業已被損毀不見的造像碑。 http://ndweb.iis.sinica.edu.tw/rub_public/System/Buddhist/
 
Software Name:甲骨拓片檢索系統
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:主源於民國十七年(西元1928年)中央研究院歷史語言研究所在河南安陽殷墟的考古發掘,及後來購藏的一批甲骨。考古發掘內容包括第一次至第九次,從民國 十七年秋季到二十三年春季;以及第十三次至十五次,民國二十五年春季到二十六年春季又重回小屯村三次發掘,所得共約兩萬多片有字甲骨。http://ndweb.iis.sinica.edu.tw/rub_public/System/Bone/
 
Software Name:青銅器拓片檢索系統
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:與中央研究院歷史語言研究所共同發展本系統,系統數位典藏青銅器拓片(或稱金文拓片) 約一萬餘件,乃為清至民初著名收藏家所收藏的珍品。除了保存了青銅 器的銘文、紋飾及器形資料外,更記錄了收藏者與鑑賞者的題跋、用印等資訊。http://ndweb.iis.sinica.edu.tw/rub_public/System/Bronze/
 
Software Name:漢代石刻畫像拓本檢索系統
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:與中研院史語所合作發展,本系統以數位化方式管理與呈現漢代石刻畫象拓本約1500餘件,主要出土自山東、河南、四川、江蘇等地,漢代石磚構造之墓室、棺槨、祠堂、墓闕、碑等建築遺存之畫象石或畫象磚。 http://rub.ihp.sinica.edu.tw/%7Ehanrelief/h/
 
Software Name:拓片資料庫管理系統
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:「拓片資料庫管理系統」架構設計以拓片資訊為主、原件資訊為輔,為一整合不同研究領域拓片之資料庫檢索與管理系統,目前整合的項目有青銅器全形拓、青銅器銘文拓片、漢代石刻畫象拓本、佛教石刻造像拓本、甲骨文拓片與遼金元拓片等資料。http://ndweb.iis.sinica.edu.tw/rub/
 
Software Name:漢代簡牘數位典藏管理系統
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:與中研院史語所合作,發展漢簡數位典藏系統,除了提供漢代簡牘典藏品後設資料與影像管理之外,也將利用GIS地理時空資訊技術,提供由地圖查詢漢代簡牘及其遺址相關資料。 管理系統 http://ndweb.iis.sinica.edu.tw/woodslip/ 檢索系統 http://ndweb.iis.sinica.edu.tw/woodslip_public/
 
Software Name:考古資料典藏管理系統
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:與中央研究院歷史語言所合作,主要將考古調查與發掘所發現之遺物、所有過程之記錄與影像檔案,以數位化的方式有效的保存。 管理系統 http://ndweb.iis.sinica.edu.tw/archaeo2/index.jsp 檢索系統 http://ndweb.iis.sinica.edu.tw/archaeo2_public/
 
Software Name:印記資料庫
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:與中研院歷史語言研究所合作,以數位典藏系統管理蓋在典藏品中的印章資料。http://ndweb.iis.sinica.edu.tw/sealdb/
 
Software Name:先秦銅器紋飾資料典藏系統
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:與中央研究院歷史語言研究所合作,發展數位典藏系統以管理先秦銅器紋飾資料。http://ndweb.iis.sinica.edu.tw/decoration/
 
Software Name:缺字
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:This system includes an unencoded character retrieval system and online presentation.Users can search for Chinese characters through our web interface and browse the search results. Our technology also allows unencoded characters as glyph expression to be represented in a web document embedded with specific Java Script code, which will then replace the glyph expression automatically with an image of the character in an appropriate font size when loading these web documents. http://char.ndap.org.tw/
 
Software Name:故宮紋飾權威檔資料庫管理系統
Inventors:DAAL
Country:TW
Date:2003/01–2007/12
Abstract:與國立故宮博物院共同開發建置,以數位典藏系統管理紋飾資料。http://ndweb.iis.sinica.edu.tw/decoration2/
 
Software Name:故宮三處款式印記資料庫
Inventors:DAAL
Country:TW
Date:2003/01–2007/12
Abstract:與國立故宮博物院共同開發建置,整合了故宮書畫處、器物處、文獻處的相關資料,為款識印記資料的查詢平台,系統已技術移轉給國立故宮博物院。http://ndweb.iis.sinica.edu.tw/npmseal/
 
Software Name:故宮人名權威系統
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:與國立故宮博物院合作,以數位典藏系統管理故宮書畫處人名權威資料,系統已技術移轉給國立故宮博物院。 http://ndweb.iis.sinica.edu.tw/people/
 
Software Name:故宮書畫典藏系統
Inventors:DAAL
Country:TW
Date:2003/01–2008/12
Abstract:與國立故宮博物院合作,以數位典藏系統管理書畫資料,系統已技術移轉給國立故宮博物院。 管理系統:http://ndweb.iis.sinica.edu.tw/npm/ 檢索系統 http://ndweb.iis.sinica.edu.tw/npm_public/
 
Software Name:台灣美術展覽檢索系統
Inventors:DAAL
Country:TW
Date:2003/01–2005/12
Abstract:本資料庫為日治時期台灣美術展覽會圖錄資料庫(簡稱台展資料庫),其收集了日治時期十六回台灣美術展覽會。 http://ndweb.iis.sinica.edu.tw/twart/
 
Software Name:多媒體中心
Inventors:DAAL
Country:TW
Date:2002/01–2008/12
Abstract:Digital Image Archiving Technology is the image file management system that supports National Digital Archives Program (NDAP). Its major purpose is not only to preserve valuable antiques and their relevant information with texts, images and videos, but also to integrate with archiving systems to establish related applications. The system is special in that users can upload images of any size through Web-FTP interface. Images can be viewed, rotated, and zoomed out without losing their originality online. Watermark and the size of transformation can be configurable to enhance the DRM function of watermark and the efficiency of images searching. It also provides the functions of file management and system rights management; users can arrange image files at their wish and operate the system at ease. This system is established with professional technologies, centralized and efficient hardware and a large amount of multimedia data. It provides the most efficient mechanism of data management and multi-oriented processing services of multimedia.Our long-term goal is to maintain the stability of the system and to provide users with all essential functions. http://ndmmc2.iis.sinica.edu.tw/
 
Software Name:台灣社會人文電子影音數位博物館影音資料庫
Inventors:DAAL
Country:TW
Date:2002/01–2004/12
Abstract:系統收藏了台北藝大李道明教授所拍攝的台灣社會人文影音三千多小時。並可以進行文字與語音檢索、並已建立符合國際標準的後設資料的電子影音資料,讓特定使用者可藉由本計畫所研發之片庫管理系統,瀏覽並自由選取影音片段儲存於個人片庫,再於網路上進行非線性剪輯,並隨時串流播放。 http://twemovie.iis.sinica.edu.tw/index.html
 
Software Name:List of Systems Developed by Technology Development Team, NDAP and TELDAP
Inventors:DAAL, IIS
Country:
Date:2001/01–/
Abstract:

Systems and Technologies developed by DAAL。

http://daal.iis.sinica.edu.tw/Chinese/System/Project.htm

 
Software Name:技術發展組 核心技術一覽
Inventors:DAAL
Country:
Date:2001/01–/
Abstract:

A list of echnologies developed at DAAL, IIS, Academia Sinica.

http://daal.iis.sinica.edu.tw/Chinese/System/Achievements.htm

 
 
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