QDP is for everyone.

My sisters in work, Marykutty James and Jincy Devasia, who are X-ray astronomers, have been using QDP tool in the HEASOFT package for generating plots in their publications (Click their names to see their publications). As I was in need of plotting a number of data files, having very similar data, reached one of them to learn QDP.

QDP comes bundled with FTOOLS package from The High Energy Astrophysics Science Archive Research Center (HEASARC). As didn't have an installation of FTOOLS or HEASOFT, thought I would need to generate the plots on the workstation in our lab. But, thank God, it can be installed even if one do not have HEASOFT installed.

QDP (the Quick and Dandy Plotter) is basically a program that reads ASCII files and then calls PLT, an interactive plotting program that is designed to be used by scientists analyzing data. You can get it from http://wwwastro.msfc.nasa.gov/qdp/. Installation instructions and quick help on PLT/QDP are also included in the webpage. Note that, this is not a GUI based plotting program and works probably in linux only.

Latest R and RKWard

Yesterday I got the latest version of R (version 2.14.0 (Great Pumpkin, 2011-10-31)). Later in the day when I opened my favourite R GUI RKWard, it said that it cannot start the R backend.

On reaching the RKWard's sourceforge page, it is seen that my version of RKWard (ver 0.5.4) cannot support R-2.14.0 and I have to add an Inofficial Ubuntu repository to my system's software sources.

As I have been using the CRAN version of R on Ubuntu 10.04 LTS (Lucid Lynx), added the following two lines to the system's software sources.

deb http://ppa.launchpad.net/rkward-devel/rkward-stable-cran/ubuntu lucid main

deb-src http://ppa.launchpad.net/rkward-devel/rkward-stable-cran/ubuntu lucid main

If you have R from default Ubuntu servers, you may need to add the following line to your system's software sources for the latest RKWard.

deb http://ppa.launchpad.net/rkward-devel/rkward-stable/ubuntu lucid main

deb-src http://ppa.launchpad.net/rkward-devel/rkward-stable/ubuntu lucid main

Then I updated the Ubuntu package list and upgraded the rkward package. Now my RKWard is at version 0.5.7 and working perfectly.

More details of latest RKWard binaries can be found here.
If you like the sources, check this page instead.

UPDATE: To rJava/JGR users
You would need to reinstall  JavaGD, iplots, JGR, proto, Deducer packages
Inside R, do the following

install.packages("JavaGD")
install.packages("iplots")
install.packages("JGR")
install.packages("proto")
install.packages("Deducer")

In between if you encounter the following error

configure: error: Cannot compile a simple JNI program. See config.log for details.

you need to reconfigure the Java installation. In the linux terminal issue the following

sudo R CMD javareconf

Google Scribe : Helps you to produce better documents

Google Scribe is an online tool that helps you write better documents. Using information from what you have already typed in a document, Google Scribe's text completion service provides related word or phrase completion suggestions.
It also checks your documents  for incorrect phrases, punctuations, and other errors like misspellings. In addition to saving keystrokes, Google Scribe's suggestions indicate correct or popular phrases to use.

For using Google Scribe visit http://scribe.googlelabs.com/. Detailed help is available at http://scribe.googlelabs.com/static/help.html

The Google Scribe Bookmarklet enables use of Google Scribe anywhere, on any web page. Drag this Google Scribe Bookmarklet to Bookmarks toolbar (or Favorites toolbar depending on your browser). To use Google Scribe on a web page, click on the Google Scribe Bookmarklet. Google Scribe will then enable itself on the active text field on the webpage. Enabled text fields display the icon at top end corner of the active field.

Google Chrome users can use the Google Scribe as an extension to access Google Scribe on any web page. Using the Google Scribe extension is more convenient than using the Google Scribe Bookmarklet - you won't have to click on the Bookmarklet to load Google Scribe.

Google Scribe is supported on PC, Linux, or Macintosh (Mac) and Google Chrome, Firefox 3.5+, Internet Explorer 8+, Safari 5+ browsers.

Mendeley : Bibliography Management Tool

Mendeley is a bibliography management tool and  academic social network that can help you organize your research, collaborate with others online, and discover the latest research. If you have a collection (small or large) of PDF documents, Mendeley can be of great help to you. Especially if you have collection of journal articles and you are planning to write an article or thesis.

Mendeley is available free, as a web service as well as a desktop application -- Mendeley Desktop (Windows/Linux/Mac). It depends on Internet connectivity for account management and retrieval of bibliographic information of the PDFs in your collection.

You can add PDFs to Mendeley Desktop by clicking the Add Document button on the far left of the application toolbar. Alternatively, you can drag and drop PDFs into the content pane. Mendeley will then attempt to detect the document details (bibliographic data or meta data).

Any documents whose details Mendeley is uncertain about will be added to the Needs Review collection for manual verification. You may use Mendeley’s Document details lookup (CrossRef, PubMed, and ArXiv) or Google Scholar Search to complete missing document details.

To lookup document details from CrossRef (DOI), PubMed (PMID), and ArXiv. Just fill in the available document ID in the respective field and click the magnifying glass icon next to it to get the details of the document. These fields are located in the Details tab.

One can import references with a single click from a good number of services/websites including arXiv, NASA ADS, ScienceDirect, Google Scholar, ISI Web of Knowledge, JSTOR, Nature, PubMed, Scirus, SpringerLink, Wiley InterScience, etc.

You can access the details of your collection through the web interface from anywhere in the world and share/collaborate with friends in similar fields of research. It also allows you to store your PDFs online.

You can search for the contents of PDFs in your collection and can annotate/ comment on a part of the document. You can also share your files with your friends.

Once you have made your collection, you can use Mendely to properly insert citations in your journal article or thesis. It includes a number of Bibliographic styles used by nearly all major publishers across the globe. Mendeley plug-in easily integrates with MS Word / OpenOffice inserting citations and generating a bibliography. It also provides means to generate a BibTeX file that can be used in documents typeset in TeX/LaTeX.

More details of usage and feature of Mendeley is available at http://www.mendeley.com. Most of the contents of this post are taken from the Getting Started Guide / FAQ given in the website.

LanguageTool: An Open Source language checker

"An Open Source style and grammar checker for English, French, German, Polish, Dutch, Romanian, and other languages. You can think of LanguageTool as a software to detect errors that a simple spell checker cannot detect, e.g. mixing up there/their, no/now etc. It can also detect some grammar mistakes."

One can download this tool from http://www.languagetool.org/

This can be used as an extension to OpenOffice.org and LibreOffice.

You can even use this as a stand-alone application. Details here
 http://www.languagetool.org/usage/

Converting to Poratble Document Format (PDF)

Many often we need to convert documents in Word or Power Point into PDF.

In Linux there are built-in tools to print a document as PDF. In any application select Print ... from File menu. Select Print to File option. Enter Name, select output folder and output format as PDF. And you are done.


In Windows, irrespective of version, you can install CutePDF (~ 4MB) and Converter (~5 MB) (available at http://www.cutepdf.com/Products/CutePDF/writer.asp). Now a printer named CutePDF will be added and you will be able to print using it, as shown above for linux.

Another excellent option would be to try http://www.web2pdfconvert.com/. It helps to convert webpages into PDF, which could then be used in Google Docs. It can also sent converted documents to your e-mail id.

Another option is available at http://www.freepdfconvert.com/, where you can upload your Word, Excel, PowerPoint, Images, Web Pages and other files and get it converted to PDF in your inbox.