nodalpoint.org - blog - Comments

forum posts?

dalloliogm — Fri, 19 Oct 2007 09:54:35 -0400

Well.. and what about referencing forum posts in a thesis/article?

Examples of good forums on biology/bioinformatics:
- http://www.protocol-online.org/forums/index.php
- http://molecularbiology.forums.biotechniques.com/forums/index.php
- http://www.biology-online.org/biology-forum/
- http://nodalpoint.org/forum
- http://www.molecularlab.it/forum/

Blog citation index

Neil — Fri, 19 Oct 2007 00:00:03 -0400

The NCBI now have guidelines for citing blogs

That's cool! Now all we need is a way to record when someone cites our blog, then we can build the blog citation index ;)
Oh wait, this is the brave new world, not an attempt to mimic the old one.

NCBI guidelines

alf — Wed, 17 Oct 2007 10:41:04 -0400

The NCBI now have guidelines for citing blogs.

OneNote alternative

glh — Fri, 12 Oct 2007 15:04:31 -0400

A OneNote alternative that I've seen mentioned is a Java application called Memoranda: http://memoranda.sourceforge.net/overview.html

I haven't tried it personally so I don't know how well it works but it does look interesting. It gives you a place to create notes as well as track tasks, meetings and resources (links to related files). Everything appears to be organized by projects, which may or may not work for your needs.

Interesting, but...

lbbros — Thu, 11 Oct 2007 17:51:58 -0400

It is definitely interesting, however not applicable to my case as I have stopped using Microsoft's OS since two years ago. The other post about ELN looks interesting as well, and I'll give it a try if I can.

Microsoft OneNote 2007

glh — Thu, 11 Oct 2007 11:53:24 -0400

The latest version of OneNote has the capability to organize notes into notebooks with some of the capabilities of a wiki. OneNote is an electronic notebook that you can organize into notebooks, sections and pages in whatever way works best for you. With the latest version notebooks can be shared on a network, but a local copy is cached to your hard drive. If you connect with a laptop you can work offline and when you connect to the network again the two versions are automatically merged (unless you specify otherwise). Editing by multiple users is also supported. Links can be made between information on multiple pages so you can navigate between related information in much the same way you do in wiki. They have also added some very nice integration with Outlook (2003 or later) that provides the ability to create links from meetings, tasks and emails that link to the related notes in your OneNote notebook. Outlook tasks and meetings can also be created directly from OneNote.

OneNote also has a built in print driver that can be used to "print" documents such as PDF files directly to to OneNote. By default text is extracted from images using the built in OCR capabilities to make these searchable. Here is an example from another blog of someone that uses this for keeping track of journal articles: http://missionarygeek.blogspot.com/2007/07/using-onenote-for-academic-jo....

OneNote pages can also have freehand notes written on them using a mouse if you're on a regular PC, or with a stylus if you are using a tablet PC. This way you can add comments or highlight text on PDF files, presentations or other documents imported into OneNote without worrying about reformatting the original document. The ideal situation is to have a small tablet PC that you can take with you everywhere so you always have your notes with you and you can add new notes, although I haven't had a chance to try this yet. Most of the features mentioned require OneNote 2007 and Outlook 2003 or later.

ELN Option

imtechnology — Thu, 11 Oct 2007 07:37:40 -0400

I have been developing a website which has an ELN component to it in addition to a LIMS component. It might be what you are looking for. have a look here:

http://www.yourlabdata.com

Once you create an account and login you will see some new links appear in the menu titled "Write ELN Entry", "Show Your ELN" and "e-mail your ELN". I haven't got the email your ELN part working perfectly yet but its nearly there. Have a look it might be what you are looking for.

blog and wiki

jcbradley — Wed, 10 Oct 2007 15:11:45 -0400

Neil - indeed the combination of a blog and wiki is perfect for a notebook system. We use Blogger and Wikispaces for well supported hosted free solutions.

Jean-Claude Bradley
Associate Professor of Chemistry
Drexel University
http://usefulchem.wikispaces.com
http://usefulchem.blogspot.com

File System, text, MSoffice

seidel — Wed, 10 Oct 2007 14:15:07 -0400

I use the file system to organize projects, and keep groups of files together. I often share bioinformatics stuff with lots of non-computational people, so I bit the bullet and decided the benefits of MS office outweigh the pitfalls. I use MS Word as a main document or journal for each project, because it can hold text, pictures, and tables, and it has a nice feature of being able to insert headers that can be automatically assembled into a table of contents/outline at the beginning of the document. Thus upon opening it, one can see an outlined trail of my intellectual journey down some path. If there are bits of shear code and unix commands, I tend to put those in a text file (something I can easily access from the command line), and I may refer to it in the Word document. Other bits of code I want to discuss, I can paste into the word document from my favorite editor and they are nicely syntax colored. All the figures are then also easily accessible for programs like powerpoint. Thus the project has a standard name, the word document in the project directory has a standard name, and associated code documents also have a standard name. Thus one can easily peak into my directory structure, see that I've worked on X projects, enter any directory and open an analysis document that describes everything about the project, etc. And I can always print my main analysis doc for a project to pdf. The idea of using a wiki as a personal CMS is attractive, but using the directory structure to organize, Word to handle formatting and multimedia, and text files for results and non-discussed code bits allows freedom in a rich interface (the OS) that is not all through a web browser.

Pers comm

chris — Fri, 05 Oct 2007 21:59:25 -0400

fwiw, I like the pers. comm. approach. Add a footnote with the blog post URL, rather than including it in the formal reference list. I wouldn't play this card too often, though - it might give the right impression :-)

another option..

pwnedd — Fri, 05 Oct 2007 14:11:57 -0400

If it's something you want to share with other people, then a blog is a pretty
good way to go. If you are looking more for something to keep personal notes,
Google notebook is pretty useful since you can access it from any machine.

Wiki's are nice, but only if that is what you need. If you want to either have something
that other people can edit, or just for keeping track of different versions of documents,
then a Wiki is a good option.

Keith

I will probably wait for the

nuin — Fri, 05 Oct 2007 11:31:40 -0400

I will probably wait for the next concept, or maybe the next new new silverbullet, maybe the uber-bliki-dip-n-licki.

I like SVN+trac, but I find trac a little bit clumsy to use. Any of the wikis are pretty bad and slow to use.

For Windows, I am exploring e that can store histories of files. It is not free though.

Trac could be useful

lbbros — Fri, 05 Oct 2007 10:38:17 -0400

Trac could be useful to track my programs (usually a bunch of python scripts and utilities I write to ease my work), I'll investigate on the use of a Bliki for my own work.

Bliki :)

Neil — Fri, 05 Oct 2007 10:05:32 -0400

I believe some people are turning to a blog+wiki combination for this purpose, or bliki as it's come to be known.

I agree MediaWiki is overkill, but it has some nice extensions of use to researchers (math formulae, latex and so on). When I played with it I found a calendar/blog extension that created dated wiki blog posts (i.e. like a blog post but editable like a wiki entry). Dokuwiki has some similar features.

I've recently turned to SVN + Trac; see most recent post.

Availability

lbbros — Fri, 05 Oct 2007 04:07:13 -0400

I've thought about making my thesis publicly available after it's done. I'm probably going to use one of the print-on-demand services that are around online to publish it (aside offering a PDF for download).