2009 post: Free, easy, quick, great PDF creation: Try OpenOffice

keywords: free software, opensource, OpenOffice, grantwriting

I try to give credit where credit is due.

I have written before about using OpenOffice (version 2.4) for “real professional work.” In an earlier post, I wrote about successfully writing an entire grant application using OpenOffice for wordprocessing and figure creation in conjuntion with Zotero for references (and the grant was funded, so…).

PDF creation from OpenOffice (use “Export to PDF” in the File menu) simply works great. It is very fast and the pdf quality is excellent. One note – it does not open the pdf automatically – it just stores the file – so pay attention to this. This works much better than printing to a pdf using the Adobe PDF printer or using the Microsoft Office 2007 export to pdf functions (which, besides being slow, caused Microsoft Office to crash occasionally on my machine).

Also, before I forget, I really like OpenOffice Draw for scientific figure creation – I use it a lot in my work and I have been quite happy with it. I’m using Microsoft Office a fair amount now, but I still use draw to make figures. I’ve used Zotero and Draw for well over a year now, with fairly intense use.

Note: This is almost entirely based on using OpenOffice 2.4. The current version is 3.0, which I just downloaded.

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2008 post: Bioinformatics: Sequence Alignment Is Central…?

Keywords: Illumina, Sequence Alignment, algorithms, teaching, next-generation sequencing

I haven’t posted in a while; I have been busy teaching bioinformatics. I do receive an occasional email or question about learning bioinformatics, so why don’t I just write what I taught here?

Here, at least, was my thinking on the subject. Remember that I was teaching second year students with a variety of backgrounds.

The first point is that sequence analysis/alignment is the heart of bioinformatics. Ok, you can argue with me on this. But I think that sequence alignment is, without question, a major – if not THE major – success in bioinformatics. Why do I say this?

1. Sequence alignment is non-trivial.

2. Sequence alignment approaches derive from a solid mathematical basis.

3. There are well worked out statistics for sequence alignment.

4. Sequence alignment is extremely prevalent and popular as an application of bioinformatics – not least of which is evolutionary studies of gene change and, of course, analysis of the rapidly growing number of fully sequenced genomes (or even partially sequenced ones, for that matter).

5. New situations that are variants/subsets/offshoots of sequence alignment are emerging that have already produced new algorithmic/computational frameworks. So, although this is arguably a fairly mature area of study (I think so), there is new work being done. Specifically, I am thinking of new sequence alignment approaches for next-generation sequence data (esp. short reads like Illumina, ABI) and (probably) also for metagenomics data. In the case of next-generation sequencing, mostly we want to align near-perfect reads – optimizing this for tens of millions of reads is non-trivial. Some recent work that looks good is ZOOM! in Bioinformatics 2008 24:2431 and SeqMap in Bioinformatics 2008 24:2395. (But note that I have not used either at all yet).

As a route to teaching bioinformatics, I also like sequence alignment because it touches on major topics in bioinformatics/biology: alignment itself, evolution of sequence (including phylogenetic tree construction), hidden markov models (profile HMMs, pair HMMs, PAM for alignment), etc. So just by examining sequence alignment, I end up introducing major “techniques” in bioinformatics (note that this point is certainly not original; you see it in the famous Durbin et al. book Biological Sequence Analysis and in other books like Mount’s text Bioinformatics).

2008 post: Free Multiplatform Reference Management? Try Zotero

So 2009… remember? So a lot of this is probably out of date, sorry!

Mark Bieda zotero references computer software citations

You use Endnote, refman, or one of the others. You want a free alternative because (1) you don’t want to worry about licensing issues (like buying a new copy for each computer) (2) you want something that will run under windows, linux, and mac os x (3) you just don’t want to pay or (4) you want to move your references from place to place without having to adapt to the local software choice (i.e. some places will have Endnote, others will have RefMan, others will have other solutions) or (5) you just believe stuff like this should be free.

So: I have been using Zotero for over a year. Zotero is great for everyday web stuff, but here I will just talk about it as a reference manager.

As with my other software comments, this is based on my real experience. I recently wrote an entire grant using Zotero as my only reference manager. And it worked well.

A key thing:
Zotero is heavily and institutionally supported (see the webpage). From the forum comments, you can see that many users are in academe. So it should only get better

Problems/Weaknesses:
(1) This is clearly still in development. But, as I said, I wrote a grant with it – and it worked well for me, but it is not as smooth as EndNote in many ways.
(2) There are a limited number of citation styles, but this number is growing – and you can define your own. For things like grants, usually you get to choose a style. For a typical paper, you won’t have a large number of references, and a little manual editing. Still, because of this, Endnote really still has a big edge.

Getting it:
(1) Zotero is a firefox extension and, when you go to the site, seems more geared toward web-based research.
(2) Installation is superfast and easy. Firefox is the way to go. No internet explorer version.
(3) You will also need to download plug-ins for either Microsoft Word or Openoffice Writer. I used OpenOffice Writer for my grant.

Basics:
(1) There is a tutorial on the website, unfortunately oriented mostly toward the MS Word usage. The same rules apply.
(2) IF you are using OpenOffice Writer, here is something to be careful with: don’t save your files in .doc (MS word) format. I usually do, because I need to send files to colleagues, all of who have MS word but not OpenOffice Writer. If you do this, you will lose the ability to handle your citations.

Getting going:
download and install Zotero from the Zotero website
download and install the appropriate word processing plugin

To get citations:
(1) you can import from many, many sites – like Pubmed, notably.You just click on a button when you find something you like and it gets imported into Zotero.

Recommendations:
(1) When I last looked (about April, 2008), the documentation for Zotero was generally very good, but the documentation for the citation/reference aspects was very poor. So I strongly suggest that you download a few references and play with a pretend, test document to get a sense of how zotero works and your results. I did this and it really helped me use it. Only took a few minutes of playing around.