J-vs-T goes Java

I just ported the Jabber -vs- Twitter bridge to Java.

That was a point on my todo list for a long time, because I hate the hacked stuff from the improvised Perl solution. And in the end I finally did it ;-)

You can find the new XMPP to Twitter bridge with the name XTB in my sidebar. It’s now written in nice Java code, easy to understand and much easier to work with! So feel free to give it a try!

End of announcement! :P

IonHunter

Some days ago IonHunter came into the world!

IonHunter is the tool I’m actually developing to receive one of these diplomas. It’s is a software to identify biomarkers in a huge number of LC/MS runs. IonHunter is able to preprocess mass spectrometry data, to merge multiple runs of the same sample and also to correct retention time shifts to align various experiments.

The whole software is modularly designed and easy to extend with further plugins. So developers feel free to join my development!

Currently it isn’t published, but since it’s written in Java it will run on nearly all operating systems. We focused on usability and comfort for mass spec scientists, who will use the tool.

This is just a small announcement for the recently launched website, you might want to take a look at it!? (-;

Small hint for my faithful readers: Subscribe to IonHunters newsletter to stay informed and miss no release!

Presentation using two screens

Yesterday I attended a presentation of a colleague, but unfortunately during his speech the PDF viewer on his laptop crashed.

His supervisor told him to use pdf_presenter_console . Don’t know whether you’ve already heard about this tool? It’s able to display the current slide on the beamer-screen while you can see the next slide on your real screen. Generally a nice idea, but the software seemed to be a bit unstable ;-)

Anyway, I always wanted to find a solution to see some notes for a single slide while the slide is active, and today I set to work.

I searched for tools that are able to open two different PDF’s at once, I tried impressive, some vnc hacks, and so on, until I realized that there is already a smart solution on my laptop using the lightweight PDF viewer XPDF!

XPDF has a nice remote feature, if you run it like

xpdf -remote SOMEID presentation.pdf &

you can use your terminal to send some commands to the viewer. For example to go to the next slide try the following (see the COMMANDS section of XPDFs man page):

xpdf -remote SOMEID -exec nextPage

Great, isn’t it!? (if you receive the error error: "nextPage" file not found scroll down to XPDF is buggy)

I think the rest is clear, open two different XPDF-instances, one for the notes and one for the presentation itself:

usr@srv % xpdf -remote NOTES notes.pdf &
usr@srv % xpdf -remote PRESENTATION presentation.pdf &

and define some keys to scroll through the PDFs. You could use xbindkeys to bind the keys to the commands, for example I use F9 to go to the next slide and added the following to my ~/.xbindkeysrc :

"xpdf -remote PRESENTATION -exec nextPage && xpdf -remote NOTES -exec nextPage"
    m:0x10 + c:75

After running

xbindkeys -f ~/.xbindkeysrc

I’m able to go to the next slide by pressing F9 . To find the keycodes for some keys you may use xbindkeys -k or xev . Take a look at the documentation for more information (GER). Of course presentation.pdf and notes.pdf should have the same number of pages ;-)

XPDF is buggy

The -exec flag didn’t work for me, returning the following error:

usr@srv % xpdf -remote SOMEID -exec nextPage
error: "nextPage" file not found

I tried version 3.02 and also 3.03. The problem is located in the XPDF wrapper script, located in /usr/bin/xpdf . If you take a look at the contents you’ll find the following lines (in my case it’s 25ff):

while [ "$#" -gt "0" ]; do
    case "$1" in
    -z|-g|-geometry|-remote|-rgb|-papercolor|-eucjp|-t1lib|-ps|-paperw|-paperh|-upw)
        cmd="$cmd $1 "$2"" && shift ;;
    -title)
        title="$2" && shift ;;
    -m)

They simply forgot to define the -exec parameter to take an argument. So nextPage is not seen as argument for -exec and XPDF tries to find a file called nextPage that is obviously not present. To patch this you just need to add -exec like:

while [ "$#" -gt "0" ]; do
    case "$1" in
    -z|-g|-geometry|-remote|-rgb|-papercolor|-eucjp|-t1lib|-ps|-paperw|-paperh|-upw|-exec)
        cmd="$cmd $1 "$2"" && shift ;;
    -title)
        title="$2" && shift ;;
    -m)

or just use xpdf.real directly and skip the wrapper:

usr@srv % xpdf.real -remote SOMEID -exec nextPage

Since modifying files in /usr/bin isn’t a good idea I recommend to just substitute xpdf for xpdf.real in your ~/.xbindkeysrc .

That’s it for the moment, I wish you a nice presentation ;-)

Compress Google's Reader

If you are using Google’s Reader to aggregate news feeds you might have recognized that Google re-engineered its feed-reader to fit into the styles of other Google-services.

The new interface slimmed a bit and is more lightweight, but I’m arguing about the large white-spaces! Too much space is unused and to less information is presented. Such disadvantages are also discussed at other places.

First I thought I’ll get used to it, but now I decided to change it on my own. So I created a small user script for the Firefox extension Greasemonkey. Here you see the difference (click the images for larger versions):

Reader w/o modification
Reader w/o modification
Reader w/ modification
Reader w/ modification

So you see, there is less space at the top of the page and single entries got closer together. The script is available in the download section, all you need is the browser Firefox and its extension Greasemonkey. If you have both installed just click the following link to the download and Greasemonky will ask you to install my short script. That’s it for the moment ;-)

Update 22.11.2011: Updated the UserScript to support googles new layout.

Download: JavaScript: Google Reader Whitespace Remover (Please take a look at the man-page. Browse bugs and feature requests.)

Sharing a Wifi connection

Due to different circumstances I had to figure out how to share a wireless connection with some wired clients. And what should I say, that’s a very simple task ;-)

The scenario

With your notbook you are able to connect to an AP with access to the internet, but other machines within your network infrastructure don’t have access to the outside world, and you want your local machines to also use this wireless connection of your notebook. Figure 1 visualizes this use case.

The setup

First of all I have to admit I don’t know which software needs to be installed. Since I previously did some network hacks with this notebook I didn’t have to install something that wasn’t actually present, but I think you’ll need something like network-manager-gnome , dnsmasq-base and dnsmasq-utils . And of course you also need a Linux notebook (e.g. with a Debian or an Ubuntu) with wifi hardware, an AP with internet connection and a RJ45 Ethernet port on the notebook for the wired connection to other PC’s.

The first thing you should do is to connect to the AP, so your notebook will be able to access the WWW.

The next step is to connect another machine to your notebook using a network cable. This machine needs to be configured as a DHCP-client. (Since this might be any operating system of your choice I don’t describe the configuration, but most systems should already be configured correctly)

Now you have to setup a shared connection on your notebook. Right-click the network indicator icon in your systems panel (next to your clock) and choose Edit Connections…, compare to figure 2.

This will open a new window with connections you still configured. In the Wired tab click Add to install a new shared connection, see figure 3.

You’ll see another window to configure this new connection. Just give it a name like share and choose the method Shared to other computers in the IPv4 Settings tab, as shown in figure 4.

Last but not least open a terminal and add a new entry to the nat-table:

sudo iptables -t nat -A POSTROUTING -j MASQUERADE

That’s it, using this newly created connection you’re able to connect your clients behind your notebook through your wireless connection.



Martin Scharm

stuff. just for the records.

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