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[csj_Elst.pdf](https://mdr.nims.go.jp/filesets/1b65530f-77f5-45e0-aa15-09c8a717fa98/download)

## Creator

[TODOROKI, Shin-ichi](https://orcid.org/0000-0003-3986-1900)

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[Manuscript writing support system for researchers based on hypertext list of their achievements](https://mdr.nims.go.jp/datasets/fe1a65bd-dc4a-481f-aee8-1d7707f18ffa)

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Manuscript Writing Support System for Researchers Based on Hypertext List of Their AchievementsManuscript Writing Support System for ResearchersBased on Hypertext List of Their AchievementsS. Todoroki∗August 4, 2008AbstractA method is presented for shortening the time needed to prepare research papers and slides.The key is to enhance the searchability of related documents previously written by the author andstored in a PC. It is achieved by employing a hypertext list of the author’s achievements, eachitem of which includes links to related files and web sites. Such a list was constructed with theaid of reference management software (BIBTEX) and a scripting language (Ruby). Automaticincorporation in the author’s home page makes it easy to disseminate the author’s achievements.1 IntroductionWhen writing a manuscript on PC, you may often want to cut and paste something from a file thatyou made previously but cannot find. How can this problem be overcome? Some people may open allthe folders and search them one after another, and others may use a full-text search software in theirPCs such as Google Desktop.Recently, I found a better way to deal with such a situation. The left window in Fig. 1 shows alist of my research papers displayed on a web browser. It is different from a conventional list becauseeach item includes links to local files and web sites on the net. The clue to finding the target file isto remember that the file was used in a previous article or presentation. Although the idea is quitesimple, I have found it to be an indispensable support system when publishing my research results.This paper outlines the approach.Hypertext list of research achievements• What is the benefit?• How is it constructed?• How does it promote information dissemination?2 Useful functionsPromoting reuse of past documentsWe can easily find target files by using our memory of our publications. This is because your memoryis directly related to your list of research achievements and we researchers always focus on this listNational Institute for Materials Science, JAPANhttp://www.geocities.jp/tokyo 1406/1http://www.geocities.jp/tokyo_1406/Hypertext List of Research Achievements / S. TodorokiFigure 1: Typical pages of my hypertext list of research achievements. Each page is displayed on adifferent web browser. Left: List of research papers already published. Right: List of paper submis-sion deadlines.when applying for jobs, promotion and funding. Our primary mission is to increase the items in thelist. Thus, most of the files we make are related to the list. We can remember our own list in detail.Finding target files quickly means you have many chances to reuse your past documents. Thisreuse saves you time and provides extra time for polishing your document. To my surprise, thissystem also helps me find graphics files. In most cases, the clue to finding them is also my memoryof my publications, i.e., “The figure I want was included in a certain paper or presentation”. The listis also the best place to store links to photographs taken during conferences.Impromptu presentation for visitorsPresentation slides are still useful after you have returned to your lab because they can be used topresent your message visually to your guests. You can make a good impression on them if you canquickly find appropriate slides in your PC based on the visitor’s interest. For this purpose, I preparedtopic-specific hypertext lists including links to my presentation slides in order to be ready to makeimpromptu presentation in my lab.Scheduling of document preparationIt is possible to make a list of future goals in a similar manner to that described above. The rightwindow in Fig. 1 shows a list of deadlines in order of date on a certain day. I always open this page2Hypertext List of Research Achievements / S. Todorokiwhen I start to write a manuscript, because it provides links to the files to be finished and relatedweb pages. The latter is particularly useful when we prepare a photo-ready manuscript whose styleis announced at a conference site, or make plans for a business trip by referring to an interactivemap service such as Google Maps. Collecting related information in one place is a basic strategy forcreative work.Adding links to your list of achievements helps you• to find files in your PC and to save time by reusing them• to show appropriate slides promptly to your guests• to manage manuscript and presentation deadlinesYou may agree with me that such lists are useful, but who will make them for me given the timeand effort that would involve? It is completely impractical unless the lists are compiled automatically.The next section outlines how to construct them.3 Construction policyDesignThree types of list are presented in the previous section: (1) lists organized by media (journals, inter-national conferences, patents, etc...), (2) lists organized by subject, and (3) lists of things to be done(deadlines). It is impractical to construct these lists one by one manually. Thus, we must registerall the items using a reference management software with unique identifiers, and retrieve the itemsneeded to make one of these there types of list. All we need to do is to prepare recipes that contain aset of identifiers (see Fig. 2). To make a list of deadlines, we collect items containing future dates.For example, the third item in the right window of Fig. 1 shows the deadline for this article(original version in Japanese[1]). This item is registered in the reference management software asshown in Fig. 3. Todoroki07BCSJ is its identifier under which its bibliographic data is stored. Thehomepage field contains the homepage address of the journal and the draft field the path of themanuscript file in my PC. These fields are the source information of the links in the hypertext listshown in Fig. 1.Recipes:to specifythe orderJournals• Todoroki06JCSJ709• Inoue06JNCS632• Todoroki05ASS• Konishi05ASS• Todoroki05OEX9248...Recent activities1. Fiber fuse• Todoroki06OCS• Todoroki06NG• Todoroki06Eglass• Todoroki05OEX9248...Deadlines• List future itemsin order of dateReferencemanagementsoftware⇓ ⇓ ⇓HTML:����Hypertext listof achievements(Left of Fig. 1)����My homepagehttp://www.geocities.jp/tokyo 1406/node2.html�� List of Deadlines(Right of Fig. 1)Figure 2: The procedure for making hypertext lists of achievements.3http://www.geocities.jp/tokyo_1406/node2.htmlhttp://www.geocities.jp/tokyo_1406/node2.htmlHypertext List of Research Achievements / S. Todoroki@Article{Todoroki07BCSJ,author = ”S. Todoroki”,title = ”E-list of research papers”,journal = ”Ceramics”,year = 2007,volume = 42,number = 7,homepage = ”http://www.ceramic.or.jp/ihensyub/index j.html”,draft = HOME#”/-d/07/0704/csj elst/csj elst.pdf”,annote = ”070410: Deadline”, }Figure 3: Example of an item registered in reference management software (The third item in theright window in Fig. 1.)Required softwareA search using any of the net search engine will show that many types of reference management soft-ware are available. What choices should you make when constructing this hypertext list of researchachievements? My criteria are as follows.Is the software compatible with your PC and software for manuscript writing? The softwareshould be in harmony with your writing environment, not only with your operating system (OS;Windows, Mac, Linux etc...) but also your manuscript writing software (MS Office, OpenOffice,LATEX etc...), in order to avoid any reduction in performance.Is it possible to export stored data for future migration? The lifetime of software is generallyshorter than that of data, especially your research achievements. In the event that further developmentof the software is abandoned, you should have the skill needed to handle data stored in the softwarefor future migration.Is it possible to extend its functionality for customization? The style of the output list must becustomizable. Specifically, you need to embed links in the output. If this is impossible, you haveto modify the output by using other software. Such a cooperative process should be controlled byone of the programming languages. Some languages, called “glue language”, are very useful for thispurpose, including Perl, Python, and Ruby.Can you obtain the required output automatically? Since the final hypertext list is used for thedaily tasks of searching files in your PC, the list should be always ready for updating at short notice.The updating process should be completed automatically just after you have typed the required data,such as bibliographic data about your article, the addresses of related web sites, and the deadline ofyour manuscript. Otherwise, you have to repeat this tiresome procedure every time and thus becomeimpatient with the updating procedure.A model case of mineI always use LATEX2e for writing manuscripts. Thus, BIBTEX is the most suitable reference manage-ment software. Since BIBTEX’s output is not HTML, LATEX2HTML is used to obtain the final HTMLoutput. As shown in Fig. 4, these two types of software are combined by Ruby script, which readsa recipe, requests BIBTEX to obtain a required list, and converts it to HTML. However, you have tomodify the format of BIBTEX output beforehand in order to embed links in it.All these software are available free of charge. I believe TEX-related software can be expected tosurvive for more than a decade since user and developer populations are sufficiently large. Since theonly user of this customized hypertext list is the list’s owner, I do not think that in the near future Ineed to abandon the present system and migrate to a new one. In fact, 20 years has passed since I4Hypertext List of Research Achievements / S. TodorokiRecipeReferenceManagementSoftwareRuby scriptHypertext Listof Achievements LaTeX2HTMLBIBTeXFigure 4: Data flow in the procedure for compiling a hypertext list of research achievements.began to use LATEX. However, there may be a better choice for those who are willing to construct theirown system.Procedure for making hypertext list of research achievements• Register all your research achievements using reference management software.• Configure the software to obtain lists with links to related resources.• Generate lists according to recipes containing the order of items.My hypertext list originated from a set of scripts to simplify the procedure for uploading the listof research achievements to my homepage. After I came up with the idea of embedding links in eachitem, the list grew into the present style and has benefited my homepage. Some of these benefits arepresented below.4 Merits of synchronizing with web siteMaking search engines your spokesmanOnce you have completed a system for making a list of your latest achievements in HTML, it is easyto publish it on your homepage. Then, it is easy for people on the net to access your latest informationthrough search engines. However, you should note that the frequency with which a search engine willvisit your site is proportional to the frequency with which you update it. Thus, it is better to updateyour site as soon as you find something to be renewed. Otherwise, it takes long time for searchengines to retrieve your latest information from your site.Here I report an episode that showed me the prowess of search engines. Just after I had an articlepublished in an academic journal in English[2], I uploaded a Japanese translation on my home pagefor the convenience of domestic readers. I did not expect a quick reaction, but two weeks later, Ifound a blog article introducing the Japanese document written by a graduate student I had never met.At that time, I had synchronized the list and my homepage with a cycle of couple of days. Therefore,the frequency with which the search engine visited my site must have been at least every 10 days. Inaddition, the blog article attracted further readers to my article.Putting forward recommending articlesWe often see lists of research achievements on researchers’ homepages, but most of them provide onlybibliographic data. They may be adequate as a target for search engines, but completely inadequatefor visitors who are guided by search engines. It is surely useful to provide them with links to the5Hypertext List of Research Achievements / S. Todorokicontents, such as specific pages of online journals and manuscript files on your site∗. In addition, theyappreciate seeing the author’s choice of articles organized by subject.I opened some web pages edited using this approach, and the address is shown at the bottom centerof Fig. 2. Sometimes I hear comments stating that this page is interesting. However, it requires mini-mal labor, for example editing recipes, to update the page. The rest of the works is done automaticallyincluding the generation of pages in English and Japanese.Publishing paper list on your area of interestNowadays, most of the research articles we get are PDF files rather than papers. To find requireddocuments among them, I made another hypertext list of these articles in the same way. I have alsopublished this list on the net (see http://www.geocities.jp/tokyo 1406/node3.html) for the convenienceof researchers in my field.Merits of synchronizing hypertext list and homepage• Enhanced access via search engines if your site is updated frequently• Attractive contents with minimal management• Providing expert knowledge source for colleagues5 ConclusionYou may feel that this article is too geeky for ordinary researchers, but the ultimate purpose of mysystem is to enhance the quality of research publications, as pointed out in Section 2. The thoughtfuldelivery of information attracts many people even after it is out of your control. Furthermore, itsometimes has serendipitous consequences[3]. I hope this article will enable readers to recognize mymotivation and try to find their own approach to qualified presentation.For readers in their twenties and thirties, I recommend mastering a programming language thatassists daily writing tasks. At present, you may not need to manage your research achievements, butthe quantity will increase steadily and move out of your control before you notice it. It is important tolearn one programing language thoroughly rather than many languages incompletely. Then, you willfind many daily tasks can be automated. My recommendation? Choose Ruby[4].Never be afraid of a fighter who knows thousands of arts. Be afraid of the fighter who is skilled inone.—A proverb from Chinese martial arts[5]References[1] S. Todoroki: “E-list of research papers — a manuscript writing support system”, Ceramics Japan,42, 7, pp. 520–524 (2007) in Japanese. http://pubman.mpdl.mpg.de/pubman/item/escidoc:33096[2] S. Todoroki, T. Konishi and S. Inoue: “Blog-based research notebook: personal informatics work-bench for high-throughput experimentation”, Appl. Surface Sci., 252, 7, pp. 2640–2645 (2006).[3] S. Todoroki: “Two serendipitous episodes — How I embarked on fiber fuse research” (2007)translated from articles in Japanese. http://pubman.mpdl.mpg.de/pubman/item/escidoc:33124∗It should be noted that few publishers allow the author to publish the final version of pdf files on his/her homepage.6http://www.geocities.jp/tokyo_1406/node3.htmlhttp://www.ceramic.or.jp/ihensyub/index.htmlhttp://pubman.mpdl.mpg.de/pubman/item/escidoc:33096http://dx.doi.org/10.1016/j.apsusc.2005.03.235http://pubman.mpdl.mpg.de/pubman/item/escidoc:33124Hypertext List of Research Achievements / S. Todoroki[4] C. Pine: “Learn to Program (Pragmatic Programmers)”, Pragmatic Bookshelf (2006).[5] R. Matsuda and Y. Fujiwara: “Kenji (manga)”, Vol. 21, Shogakkan (1992). (in Japanese, seeWikipedia for details).7http://en.wikipedia.org/wiki/Kenji_\%28manga\%29