Hello LyX users and developers, my name is Peter Novak and since around 2001 I am a (passionate) user of LyX (as also documented by my bug reports and feature requests at http://www.lyx.org/trac/search?q=walkmanyi), though I did not read the LyX-users mailing lists till now.
To scratch one of many itches of my professional life, I created an unpolished quick-hack LaTeX/LyX package aimed at creation and manipulation of lab books for theorists. I include a motivation for writing the package below and discuss it in the accompanying notes to the package accessible from here: http://www.aronde.net/theolabbook.tar.gz (readme.pdf/lyx) file. Hereby I would like to solicit comments from the LyX users community, which includes also many research professionals, especially in applied mathematics and computer science, which is what I care for myself. The best outcome of this announcement for me would be getting help with improvements of the package - these are also briefly discussed in the readme notes to the package. Below, I am including the motivation for writing the package, which (hopefully) illuminates the problem I want to solve. In the case somebody finds this kind of work useful, I would be happy to give back something to the LyX community as I am definitely grateful to the LyX team for providing this great tool I rely on in my every-day work since many years. Best regards, Peter. ------------------------------------------------------------------------ *** Motivation Keeping a research lab-book is a daily bread for many researchers, such as experimental physicists. It helps them to keep track of their experiments, equipment, results, as well as capture their ideas about the stuff they work on. Typically a researcher, or a team, keeps one lab-book per project. This suits the typical workflow of experimental research, where the evolution of a project can be captured as a (more, or less) linear stream of notes in a lab book. Scientists in more theoretical disciplines, such as (applied) mathematics, or in computer science often deal with several intertwined and related, yet distinct topics at once. In a consequence the evolution of their thoughts from inception to a finished paper is often rather non-linear, rather meandering stream of ideas and notes, which are difficult to order linearly before the idea/project is ripe enough and finally “clicks in”. Yet, due to this non-linearity, researchers in theoretical fields are perhaps even more in a need to capture their research notes so that they do not get lost. There is definitely a need for flexible tools and workflows to help theorists capture, organize and expose their ideas and research notes. Theolabbook is an attempt to solve this problem for users which center their daily life around TeX related tools, which are especially useful when one deals with mathematics. The central requirements driving the development of the theolabbook package are the following: 1.- notes should be media-rich in terms to the extent TeX allows. That is, should easily include math, pictures, figures, etc.; 2.- notes can be scribbled in a linear fashion, their order should be irrelevant; 3.- the package should provide tools for rapid and simple organization and re-organization of the set of notes, result of which is primarily a document, the lab-book instance; 4.- the editing of the notes should be as simple as possible, yet as good as possible. This is a no-brainer, LyX is the editor of choice; 5.- the package should facilitate also publishing of the notes on the web to support the open notebook research (https://en.wikipedia.org/wiki/Open_notebook_science). As of publishing this document, the package implements requirements 1-3 (supported only in Unix environments, for reasons, see the internal philosophy of the package in the readme document), to a large extent also 4 and completely lacks support for 5. By publishing the package as is together with the readme ntroductory text, my hope is to firstly, receive comments, suggestions, and criticism from interested LyX users; and secondly, solicit help with improvements, improving upon the implementation of the requirement 4 and working out 5. The rest of the readme document is structured as follows: after a brief discussion of related work and existing tools for the problem of capturing and organization of a non-linear stream of notes, I explain the guts of the theolabbook package, provide a step-by-step installation instructions, explain included examples and finally discuss its shortcomings and points where I need help from others. *** Related work The observation of non-linearity of research notes in many disciplines is of course a well known issue. Some of the popular solutions to the problem is the use of wikis and blogs (see https://en.wikipedia.org/wiki/Open_research, https://en.wikipedia.org/wiki/Open_notebook_science). While blogs facilitate publication and open discussion of research remarks, their fashion is linear in nature and at the same time require a level of effort to craft the individual notes, essentially essays, or coherent articles, so that they are understandable to a broader audience. Wikis, on the other hand suit well the non-linear fashion of research notes taking and interlinking. They are also a great collaboration tool for research teams. They however still require significant effort in organization of the individual notes, most of the time in hierarchies which can be traversed from the root note. In a case the hierarchy changes over time (the researcher realizes that some of the notes belong to other realms, or previously unrelated notes actually belong together), it is difficult to reshape the organization of such a lab-book. Perhaps the most advanced flavour of wiki utilized for the problem of non-linear research notebook is TiddlyWiki. Because of its interesting features, let me describe it more thoroughly. * TiddlyWiki TiddlyWiki (https://en.wikipedia.org/wiki/TiddlyWiki, http://tiddlywiki.com/) document is a standalone HTML file enhanced with JavaScript to facilitate the interactive parts of the TiddliWiki functionality. TiddliWiki document can be opened in a browser, carries with itself a CSS style sheet (inlined in the HTML), a template (inlined as well) and a number of wiki entries, which are also inlined in the HTML document. TiddliWiki allows adding, editing, deleting and organizing the set of entries in an arbitrary manner, e.g., according to tags, or hierarchies, notes can be linked, dynamically sorted, etc. There exists a large number of extensions which can be installed in the TiddlyWiki document and change its functionality. The philosophy behind a TiddlyWiki can be summarized as a separation of wiki entries from their organization and structure. In result, A TiddliWiki document is a store of a set of unsorted entries and the user can sort and present them as he/she wishes and likes at a particular moment. As useful as they are, all the above discussed tools, however suffer one big disadvantage. That is the problem of editing. This problem is especially a big deal for computer scientists and mathematicians who breath and live with \TeX and many with LyX as well. Editing mathematics for public presentation (e.g., in HTML) is no fun without the right tools, such as LyX. Solutions centered around WYSIWYG editors and jsMath JavaScript plug-ins ease the situation a bit, but cannot compete with workflows centered around LyX editor and TeX/LaTeX tools. Therefore, after quite extensive meddling with TiddlyWiki for almost a year, I set out to create a better tool centered around LyX and TeX. -- Peter Novak, p...@aronde.net, http://peter.aronde.net/
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