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 [...]

Viewing Large Text Files (like big GFF files) in Windows

I know, I know, many of you will say “just use Linux”. And this is true, but SignalMap from NimbleGen, which is quite convenient for viewing GFF files of ChIP-chip data, is just a windows product (and yes, I did try WINE as an emulator).
So if you try to load a 380,000 line file into [...]

Linux Installation on HP Pavilion Desktop (June 2008 purchase)

Mark Bieda HP Linux install installation
This is just a brief post about my (read: my student’s) experience with installing linux on a new HP Pavilion. This is a standard model available at Futureshop and BestBuy: intel quadcore Q6660 processor, 640 Gb harddisk, 3 Gb RAM. Nice machine, only $899 here in Canada (sure to be [...]

Sqlite (Sqlite3) quick tips: if you know SQL already

Mark Bieda SQL Sqlite Sqlite3
I’m a long-time MySQL user, but recently I’ve been using sqlite (sqlite3).
This is a sqlite tutorial, in a sense, if you know SQL.
As with my other stuff, this is based on my real experience of using this system
Why use sqlite?
The basic thing is that it installs super fast (unbelievably, you just [...]

NCBI GEO submission: howto hints

Ok, NCBI GEO submission of data can be a pain. I mean a big pain.
But there are a few simple things that can make it less painful.
here are my hints and a few steps:
1. Don’t assume that you will get the submission right the first time; it’s easy to have errors.
2. DO assume that NCBI [...]

TAMALPAIS: howto open files

key words: TAMALPAIS, NimbleGen, Mark Bieda, ChIP, server
Background:
TAMALPAIS is the webserver that I created to analyze NimbleGen ChIP-chip data (note that it is not for promoter data). You can find it at:
http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/tamalpais.cgi
I’ve received queries from a number of people on opening files from my TAMALPAIS server.
Some people have trouble opening the files from the TAMALPAIS [...]

Howto install linux… basic options

Ok, so I have another post on howto install linux.
This is just a short list of the top options – all this stuff is covered elsewhere, so I won’t be boring.
The basic list is: dual-boot windows machine (a favorite of mine), a Mac (ok, it’s FreeBSD, but you could also do linux under parallels), [...]

Howto install linux to a computer… fast

Ok, so I have been in the unfortunate situation of jumping from one computer to another.
The fortunate thing is that, along the way, I’ve had to learn to get linux going quickly.
This entry is about getting linux going fast but temporary. You will want to look at my other post (coming): installing linux… longterm for [...]