Ported two posts

Author: egonw

_posts/2009-05-21-bioclipse-beta5-really-last-one-now.markdown

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+---
+layout: post
+title:  "Bioclipse beta5: really the last one now"
+date:   2009-05-21
+blogger-link: https://chem-bla-ics.blogspot.com/2009/05/bioclipse-beta5-really-last-one-now.html
+doi: 10.59350/6xj82-qag38
+tags: chembl bioclipse cdk
+image: /blog/assets/images/starlite.png
+---
+
+[Bioclipse beta 5](http://bioclipse.blogspot.com/2009/05/bioclipse-20-beta5-released.html) was just released by Ola, and the team had
+some bad days over an [problem](http://chemicalrcp.blogspot.com/2009/05/eclipse-spring-export-problem-uses.html) that happened after
+a merge of [an important branch](http://jonalv.blogspot.com/2009/04/i-just-came-up-with-yet-another-way-of.html) regarding the
+managers we are using to allow scripting of Bioclipse.
+
+![](/blog/assets/images/starlite.png)
+
+In the end, [Jonathan](http://jonalv.blogspot.com/) found a workaround for the problem, even though we still have no clue what was
+the exact cause. Additionally, Arvid implemented one of the last missing features of the JChemPaint editor, being the ability to
+draw bonds in any arbitrary direction, and the ability to create a new bond to an already existing atom. This really seems to be the
+last beta before the 2.0 release candidate. So, head over to [SourceForge](http://sourceforge.net/projects/bioclipse) as it is
+now time to report this smaller things you like to see improved.
+
+The beta has many really nice features, and we will have much to write about in later blogs. One thing I particularly like, is the
+support for (really) large SD files; the above screenshot is a 800MB file with [StarLite structures](http://chembl.blogspot.com/),
+though we also tried files larger than 1GB. There is a *2D-Structure* tab, which will zoom in on the structure in a regular
+JChemPaint editor.
+
+For the Bioclipse scripting, I can just encourage you to browse this blog for example scripts.
+
+There are many extensions currently being developed, around the globe, which will extend the basic Bioclipse workbench towards
+particular use cases. While surely these will get blogged about in detail later, I do want to briefly mention them. In the works
+are features for: QSAR, Decision Support, Speclipse (NMR and MS spectrum handling), Resource Description Framework, a StructureDatabase,
+Metabolomics, Medea (MS spectrum and fragmentation prediction), XMPP, and much more.
+
+Focus of Bioclipse 2.1 will be towards bioinformatics: sequence handling, BLAST, better PDB/CIF support for protein structures,
+and who knows.

_posts/2009-06-17-no-pdfs-really-do-suck.markdown

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+---
+layout: post
+title:  "No, PDFs really do suck!"
+date:   2009-06-17
+blogger-link: https://chem-bla-ics.blogspot.com/2009/06/no-pdfs-really-do-suck.html
+doi: 10.59350/dv8xh-5dk63
+tags: publishing
+---
+
+A typical blog by Peter MR made (again), [The ICE-man: Scholary HTML not PDF](http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=2102),
+the point of why PDF is to data what a hamburger is to a cow, in reply to a blog by Peter SF, [Scholarly HTML](http://ptsefton.com/2009/06/11/trip-report-visit-to-microsoft.htm#id3).
+
+This lead to a [discussion on FriendFeed](http://friendfeed.com/petermr/767254d7/ice-man-scholary-html-not-pdf).
+A couple of misconceptions:
+
+**"But how are we going to cite without paaaaaaaaaaaage nuuuuuuuuuuumbers?"**<br />
+We don't. Many online-only journals can do without; there is DOI. And if that is not enough, the legal business has means of
+identifying paragraphs, etc, which should provide us with all the methods we could possibly need in science.
+
+**Typesetting of PDFs, in most journals, is superior than HTML, which is why I prefer to read a PDF version if it is available. It is nicer to the eyes.**<br />
+Ummm... this is supposed to be Science, not a California Glossy. It seems that
+[pretty looks is causing major body count](http://shirleywho.wordpress.com/2009/05/11/an-open-letter-to-oprah/) in
+the States. Otherwise, HTML+CSS can likely beat any pretty looks of PDF, or at least match it.
+
+**As I seem to be the only physicist/mathematician who comments on these sort of things, I feel like a broken record,
+but math support in browsers currently sucks extremely badly and this is a primary reason why we will continue to use
+PDF for quite some time.**<br />
+HTML+[MathML](http://www.w3.org/Math/) is well established, and default FireFox browsers have no problem showing mathematical
+equations. For years, the [Blue Obelisk](http://en.wikipedia.org/wiki/Blue_Obelisk) [QSAR descriptor ontology](http://qsar.sourceforge.net/dicts/qsar-descriptors/index.xhtml)
+has been using such a set up for years. If you use TeX to author your equations, you can
+[convert it to HTML](http://silas.psfc.mit.edu/mathmltalk/) too.
+
+**We can mine the data from the PDF text.** Theoretically, yes. Practically, it is money down the drain. PDF is particularly
+nasty here, as it breaks words at the end of a line, and even can make words consist of unlinked series of characters
+positioned at (x,y). PDF, however, can contains a lot of metadata, but that is merely a hack, and unneeded workaround.
+Worse, hardly used regarding chemistry. PDF can contain PNG images which can contain CML; the tools are there, but not
+used, and there are more efficient technologies anyway.
+
+I, for one, agree with Peter on PDF: it really suck as scientific communication medium.