Where to submit your manuscript?

I was recently made aware of an online tools called JANE (Journal/ Author Name Estimator), which helps you to decide where you should submit a recent paper you are working on. Essentially you copy and paste your abstract into the online tool and it spits out a ranked list of journals where you should submit your paper. It seems to work pretty well. If you test it with abstract of recently published papers, the journal where the paper is actually published almost always comes up in the top 3 choices. JANE also has other functionality of potential use, like finding citations or authors related to your abstract.

This is where it gets interesting.

I read a little more about how the program works. It basically pulls all published abstracts from pubmed and then text mines them for keywords found in your abstract. Now say you’ve written a manuscript; you run it through JANE and it tells you that the best fit is “American Journal of Botany”. But secretly, you hoped that your manuscript would go into a higher profile journal like say “Genetics”. Should you give up all hopes and submit it to AJB? Of course not! What you should do is go look at abstracts published in Genetics and AJB and find out what are the key differences between them. Often, they are surprisingly subtle and by making slight modifications to your abstract, all of a sudden it can become a great fit for Genetics!

So this online tool can actually be very useful to write abstract in the style of the journal you wish to submit to. In addition, I know at least one senior editor at a high profile journal who uses this tool to guide decisions to send manuscript out for review. This is probably not a good decision on their part, but at least now you can use it to your advantage!

Old lab PC – new Ubuntu computer

I’ve installed the latest version of Ubuntu (12.04) on the old PC lab computer:

-Username, computer name and password are written on the computer itself, if needed.
-I’ve also installed on it a few of my favorite programs (LibreOffice, Inkscape, Gimp, R, Chrome).
-It boots in about 35 seconds, not bad for an “old piece of junk”!

Feel free to use it!


AWK (Seb)

What is awk?

AWK is a language for processing files of text. A file is treated as a sequence of records, and by default each line is a record. Each line is broken up into a sequence of fields, so we can think of the first word in a line as the first field, the second word as the second field, and so on. An AWK program is of a sequence of pattern-action statements. AWK reads the input a line at a time. A line is scanned for each pattern in the program, and for each pattern that matches, the associated action is executed.” – Alfred V. Aho

Why awk?

1.AWK is simpler to use than most conventional programming languages.
2. It is fast.
3. It has string manipulation functions, so it can search for particular strings and modify the output.
4. A version of the AWK language is a standard feature of nearly every modern Unix-like operating system available today.

Simple examples on how to use AWK:
Continue reading