Wednesday, October 31, 2012


We'll have some kind of a competition here in the University; something about Science and Art, and how they interact, and how one can be used to express the other, or something like that. I'm not quite sure. Anyway, I decided to participate in the competition, because why not.

This thing will be my submission (pen is given for scale). It's drawn with a sharpie pen, acrylic paints, and a bit of brown colored pencil at the very end. It's probably titled "The known circuitry of Xenopus tadpoles". The circuitry shown here is only partially real; I mean, it's mostly real, and should give a correct idea, even if not being completely 100% accurate. And real tadpoles aren't green of course (they are quite transparent), but green tadpoles just look so much better and watercolorish! But it's definitely art about science - they can't deny that.

Well, we'll see how it goes.

Saturday, October 27, 2012


I love the description:
Superdocs are the suddenly-graying, tired-eyed waifs who you see in the hallway sometimes but never at seminars. Research fellows are non-faculty that get their own lab space (maybe with 1 tech and 1 student). They are usually crying in their offices. (source) 
It's a bit exaggerated, but the imagery is insightful. 

Tuesday, October 23, 2012

Battle of personal wikis: continued

So, my current assumption is that I need a personal wiki to maintain my personal knowledge base. I really like the idea of cross-linking topics. I also really like the idea of keeping sources (papers) as separate entries, and linking my higher-level cards (ideas, objects, concepts) to them. Finally, if I need to write something, I can always create a separate wiki-tree for it, with a contents, and then some "chapters", linking to the "thoughts" created previously. And then, while writing the text, I can go through all these pages, gradually turning them into a text.

I read a wikipedia page on personal wikis, and decided to give a try to wikidpad as an alternative to One Note. Well... The good thing is that it can save to html really nicely. The bad thing is that the interface is not WYSIWYG, but rather a wiki-style coding thing, and it makes everything somewhat harder. But the worst thing is that in this particular program legal wiki entries should have a "CamelCase" format, with capital letters and everything. That's not what I need as many my terms will look like "AMPA" or "notch". Too hard. Won't work.

OneNote can work as a wiki, and you can "Create Linked Pages" from a word you selected, but it wouldn't autolink words for you, and actually even manually linking your words to existing pages is not that simple. If you have a page named mTOR, and then you type mTOR and want it to link to this page, there's no easy way of doing so. You'll have to go and manually find the page, and copy a link to it, and come back, and add it as a hyperlink. And to make things so much worse, while there's a plugin that allows you to export your notes into html, these within-text hyperlinks are not exportable.

So far the most promising personal wiki app is the one called ZIM. It's wysiwyg, exports to html, is simple to operate, and looks neat. Probably I'll give it a try.

Index cards (knowledge base) software

I'm thinking of writing something cool and long, like a review. And it would be nice to do it properly, organization-wise. But I'm not actually sure what would "properly" mean here. I guess the general question is: how to maintain your knowledge database; how to keep in order all those various thing you learn from the literature, and how to make it usable when you need to write something about it.

An ideal system would probably have the following features:

  1. It should look somewhat like a bunch of index card, so that you could put ideas, statements, thoughts, quotes and sources there.
  2. But it should be fully computerized, as I don't want to handle any real paper objects.
  3. Ideally - you should be able to keep both your writing (notes, ideas) and your long-term stuff (quotes, sources) in the same system.

    Then also go some technical considerations:
  4. I should be able to make back-ups easily (have control over the data)
  5. It should work offline (as I'm sometimes too distracted when online)
  6. It should be forward-compatible (it would be silly to start creating a knowledge database in an abandoned obsolete software).
  7. You should be able to "publish" your final text in a readable editable form (as a long Word document or something of this kind).
So far I have the following options as potential solutions:
  1. Scrivener. I kind of like what I hear about it, but I'm not sure it would be good as a knowledge database.
  2. Personal wiki (following this great advice). It provides nice functionality (you can really organize everything properly!), but I'm not sure what software to use for it.
  3. One Note. This Microsoft office tool turned to be really fantastic! And also it is de-facto free, as you get it together with the Microsoft Office, with Word and Excel, that you have to have anyway. It actually combines the index cards look with personal wiki functionality. So far that's the potential winner. There are some drawbacks though: you can not export the whole notebook as one long text document; it is not easy to edit texts longer than 1 paragraph; and most importantly: I'm not quite sure it's going to be supported by Microsoft in the future, as it lies in complete obscurity for several years already. It's really good, so why would not they advertise it more? It's kind of unnerving.
  4. Endnote. Doesn't provide index cards functionality (interface). Also a huge drawback with this one is that I down't own a license (it's expensive, and is provided by the university), and thus I can not really invest into it.
  5. Mendeley. Seems to be a nice free alternative, but the "Notes" field is too hard to access, so - no index card functionality again.
  6. Access (personal database). Seems to be a bulky, but viable solution.
  7. Excel. That's what I'm doing so far. It is scalable, portable, higly visual, and generally very nice. The problems are: you need to keep your notes short if you wan't them to be easily exportable; it's hard to organize a 3-layered structure of "Topic / Idea / Sources" that I envision.
So overall I'm still undecided. I would probably go with a simple text-based personal wiki if only I could be sure about forward compatibility and future support. This thing, this database, would essentially become my external brain and external memory. I don't want to lose it 2-3 years from now for some stupid technical reasons.

Friday, October 12, 2012

Xenopus Tadpole drawing

To make my SfN poster prettier I decided to draw some tadpoles by hand, and include them as some ancor visual elements into the poster design. This one will be the biggest.