Monday, January 21, 2013

Building a personal Knowledge Base: a follow-up post

So, some time ago I wrote about building your personal knowledge base, and how personal wikis can be nicely employed for this purpose. Here's a follow-up post.

TLDR: I tried several, and settled on the... Microsoft Word =)

I started from the Wikipedia list of personal wikis, and then checked those that looked promising. Namely:

  • Pros: while not exactly a Wiki, you can make wiki-style references there. Also it's extremely pleasant to work with, especially if you are a visual thinker, as I am.
  • Cons: easy to delete your work accidentally (as it's a note-taking tool, not a personal Wiki). Hard to make back-ups. While export to html is available (as a third-party plugin), it doesn't export wiki-style cross-references correctly, and is thus mostly useless.

I ended up using OneNote for note-taking, but not for knowledge building. It's actually a really great tool, a serendipitous discovery that made my life much easier! Yet everything you do there is just a bit too ephemeral to use it for knowledge-base building purposes.

  • Pros: it's a personal wiki that works.
  • Cons: It isn't WYSIWYG, which renders it almost unusable (I'll spend most of time editing the Knowledge Base, not reading it, thus the edit mode should look neat and uncluttered)

  • Pros: Works. Has a nice, simple interface. Allows export to html (which I'd really love to have, both for back-up and compatibility reasons), creating a set of linked html files. Also stores the data in a set of plain txt files, which is good, as theoretically even in the worst case, if the tool crashes permanently, one would still be able to read these txt files one by one.
  • Cons: I managed to crash it twice in my test wiki with 20 entries, which is not good. To tell the truth, it happened while I was renaming entries violently, which is a rather esoteric activity, but anyway. Thus decided not to use.

  • Pros: Works. The interface is even neater, almost conceptual. Does really good on-the-fly linking between entries. Exports to html (in a giant cross-linked file, which I actually like even more than a set of separate html files). Renames links nicely.
  • Cons: Strange way of storing data (machine-readable, but not human-readable). Can do synchronization on its own, but it is also not quite transparent. And as my whole life) will, in a way, depend on this knowledge base I'm building, I'm just afraid to entrust it to a system I don't quite understand. When exporting to html, into this giant html file, it cannot order the entries alphabetically, but puts them in the "tree-crawling order". It is a logical thing to do, but it looks strange. Also you cannot have a word "dogs" link to the entry "dog"; it would be two different entries for Tomboy, as the title of the entry is the link to the entry. There seems to be a plugin to fix it, but I have not tried it.

It's not quite a wiki, but rather a structured tree-like note taking system. Yet it has one major flaw that rendered it perfectly unusable: it doesn't work properly with unicode.

Microsoft Word
(On which I have finally settled, at least for my main Knowledge Base)
  • Pros: In Word you can do cross-referencing within a document, from every word to every title. Thus you can create a one-document Wiki. Also you can use the Draft mode with Outline on the left to work with a tree of entires, thinking about your knowledge in a structured manner. And most importantly: you can save or print your document at any moment, as if it were a plain text.
  • Cons: It takes some time to format a link. Also I'm not sure how fast the processing will be when my document grows a hundred pages long or more (right now it is at ~30 pages, and doesn't seem to have problems, so there's a hope).

Friday, January 18, 2013

A non-profit in Florida firing all postdocs with 1 mo notice?

I've just heard that allegedly a Torrey Pines Insistitute in Florida is firing all their postdocs with 1 month notice. Well, all postdocs that don't have a funding on their own (but apparently not many of them have it).

And it's really weird actually, as a friend of mine was just hired there as a postdoc about half a year ago! Didn't they anticipate the funding going dry? Why did they hire them to begin with?

The drama gets even more intense because my friend is on the H visa, and thus doesn't have a grace period: the hour they lose their job they become illegal immigrants in the US, violating all possible laws. In practice that means that they can gamble, and desperately look for a job, but if they don't find one, they spoil their relationships with the US visa machinery for a long time. Alternatively they can buy tickets for their entire family to their respective country, but with 1 mo leadtime these tickets would be quite expensive. So essentially that's a trap.

Not that other people suffer less. As a person from Europe, I was really puzzled by the fact that here in the US, from the majority of jobs, you can fire a person immediately, without a warning, without any explanations at all. In my country it would be unthinkable. But anyway, a one month warning probably doesn't sound that bad in the Unites States. Still, when foreigners are concerned, a one month warning is a disaster, because you can easily screw somebody's career this way, even from purely financial point of view! For a family of 4 it would mean spending ~4 $M on the tickets back home, getting rid of all their belongings, selling a car at a loss, loosing the rental deposit... Probably about $10 000 of instantaneous loss. Even with careful budgeting, not every household living on a ~45 $k/y income would have a cushion to easily survive unforeseen expenses like that.

Thursday, January 17, 2013

Scientific Spam

Each time I get spam about pipetters and RNA in my e-mailbox I  feel guilty.

Because what's the natural reaction to a spam letter? Hitting the "Report spam" button almost automatically! Die, die, you useless spam letter, and burn in the spam filter, so that other good and honest people would be spared of your loathsomeness.

But when I get a spam letter about axon tracing, it's not that easy anymore. What if I actually use this company? Or may use it in the future? If I now put their e-mail in a black list, would I be sorry about it later? What if they were at SfN, and scanned my badge? Does it mean that now I'm obliged to delete their letter calmly and carefully, without cursing it forever? And also, aren't we in the same boat? Like, if I meet them in a bus, I would treat them as a friend, as a colleague, and we'd find something to talk about. They are doing something similar to what I am doing. Aren't we brothers? Aren't we fighting for the same common goal? Like for light of knowledge, and the betterment of the world?

...But still it's obviously a spam letter, shameless and unsolicited...

I am actually surprised how uselessly emotional I get about it, and how I actually start thinking before finally pressing the "report spam" button. It's just crazy. Why would I care? Spam is spam, regardless of the topic! Yet for some bizarre psychological reasons I now hesitate.

The "official best practice" however is still to press the button. Because spam is noise, and noise is evil. If you  send unsolicited communications, you deserve your sales to go down. Period =)

Saturday, January 12, 2013

Update for toad videos

By the way, as I finally managed to watch those wonderful toad neuroscience videos I posted here earlier (those based on work of Jork-Peter Ewert), I realized that they show 3 scientists in this short movie, and all three of them are women. Isn't it nice? It's early 90s, by the way.

Even more reasons to like the guy =)

Tuesday, January 8, 2013

Giant tadpoles in Providence, RI

About a month ago I have drawn this historical painting. Not many people remember these days that in the middle of 19th century giant tadpoles were widely employed as a means of transportation, for both goods and people, here in New England, and generally along the East Coast. Alas, they went extinct since then. Probably a fungal infection, or predatory steam engines: nobody knows for sure.

Friday, January 4, 2013

Neuroethology of toads

It turns out that Youtube hosts a great mini-documentary about those old famous experiments in the toad, in which, depending on what kind of a black shape you show to the animal, it either tries to catch it, or avoids it.

That's the foundation of neuroethology, and a great educational video to show! (I usually give videos as a homework. I guess watching videos is easier than reading papers, and thus makes a more humane homework)

The video is split in 3 parts, and is about 30 minutes in total.

Keywords: worm, antiworm, nucleus isthmus, visually guided avoidance behavior, prey capture, frog, toad.