Category Archives: Software

Many, many maps

Ever since I created a linkage map of the human genome with old-fashinoned crimap, we are talking about “mapping” diseases and genes. GIS mapping also ever increases – see the interesting first monday article Many, many maps: Empowerment and online participatory mapping, that has a lot of details about grassroots initiatives building on Keyhole/Google technology. I learned also about Common Census – looks like grassroot epidemiology.

Powerpoint slides in wordpress

I have tested several programs for their usefulness of showing Powerpoint slides on the web- some packages create standalone pages only while others have major problems with figures, graphics or transitions (or are quite expensive).

A rather simple method works at least in part – loading a .ppt file in Open Office Impress and exporting it to .swf. The flv player, however, creates a messy display as it doesn’t use the full display area.

Another option is to export all pages as 800×600 .jpg files and mount them in File Show Maker to a standalone flash film – as seen below in a talk that I have given in 2006:

To bookmark or not to bookmark

Instead of bookmarking I am printing instead with PDFcreator and let GDS later index these files. Pages (in particular supplements and news stories) are frequently vanishing while printing into a file lets me store a local copy. Printing to a PDF file is only one click away if you use the following “save” options:
pdfcreator.png

Undocumented Thunderbird function – help needed

For documenting a research project I want to insert quick links to previous emails. Clicking a link should kickstart Thunderbird and go directly to a known message. Mozilla.org says

Athough Google desktop is able to do it, there is no clear API to instruct Thunderbird to display a given email stored in its mail box (knowing the folder & message ID)

Here is how Google Desktop Search (GDS) links to an email

gsdurl.png

What I have found out so far by comparing different links

(1) is the fixed parameter relating to my hard disk??
(2) is a variable parameter relating to the physical location of my \daten\Mail\thunderbird\imap\INBOX file??
(3) is the unique Message-ID that may be seen in Thunderbird with the View Header plugin
(4) the variable salt/seed value that is stored in the registry at HKEY_CURRENT_USER\\Google\\CustomSearch\\Google Desktop Search\\Url which may be retrieved with a 2 line perl script.

So I am ready to construct URLs that link to an email by using GDS. This is, however, not very elegant. Isn’t there any other way (maybe by a Thunderbird extension) to construct and follow links directly to emails? Can somebody trace with Sysinternals Process Explorer what GDS spits out and follow it up at XUL planet ?

At its heart

43 folders writes:

Remember that your blog is only incidentally a publishing system or a public website. At its heart, your blog represents the evolving expression of your most passionately held ideas. It’s a conversation you’re holding up with the world and with yourself — a place where you can watch your own thoughts take different shapes and occasionally surprise you with where they end up…

wow – couldn’t say that in a better way.

Human genome variation

Being a former curator for a genetic disease database, I received a PM that explained why the foundation of the Human Genome Variation Society did not include most of the HUGO Mutation Database Owners — most did not join as they found it difficult to pay for membership. This reflects the overall frustration in obtaining funds for databases projects that are between research and service. Now, a new initiative for the Human Variome Project (HVP) is started to create a focus pulling the whole vision together and to assist in fundraising. Meeting details are at www.humanvariomeproject.org. I strongly support this initiative. All genetic variation databases are sharing a high interest in the community but zero interest at funding bodies (more). I have a dream…

the flyer…
humvariomeproj.png

Anything better than impact factors?

Here is a nice inside view from the BMC journals – you can watch how often your own papers are being downloaded.

bmc.png

Hopefully these hits are not only generated by search engine spiders, yea, yea.

Laptop stolen – phoning home

Scientists are frequent travellers – hopefully you have always your harddisk encrypted. There are many companies that offer to trace your computer like Computrace(R), zTrace(R), LapTrak(R), BoomerangIt(R), LoJack(R) and PC-Guardian(R). Save your $/€ for your next experiment, here is the trick: During the next boot your laptop will send out a http request to any server you like. You simply need to watch the server logfile if your stolen laptop is phoning home…
For installation please download LaptopService.cmd, LaptopService.reg and two small binaries from the windows ressource kit. Adjust path and server name before running LaptopService.cmd. Voilà, that’s it – for a good joke look at Slashdot.

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@echo off
if "%1" == "stop" goto stop

echo.
echo installing...
"c:\programme\poweroff\instsrv.exe" LaptopService "c:\programme\poweroff\srvany.exe"
echo.
echo editing registry...
regedit LaptopService.reg
echo.
echo start service...
net start LaptopService
goto end

:stop
echo Stop...
net stop LaptopService
echo.
echo deinstalling...
"c:\ntreskit\instsrv.exe" LaptopService remove

:end
pause

XP system crash

I had to manage a system crash this weekend – where even the rescue console did not work. I learned that (1) my old Knoppix CD could neither write to the hard disk nor (2) read access a truecrypt partition. (3) Too late, I should have spent some money on ghost(r) or true image(r)! I further learned on the next day that (4) Bart PE does not work with OEM versions, (5) truecrypt versions are not compatible and (6) a grml iso is not helpful at the system prompt. Ultimately I came across (7) sysresccd that includes

  • GParted: partition resize tool
  • GNU Parted: a text tool for editing disk partitions
  • Partimage: a partition image tool
  • Plenty file systems tools allow you to format, resize, and debug an existing partition of your hard disk
  • Ntfs3g allows you to mount your partition and get a full read/write access to the NTFS partition
  • Sfdisk allows you to backup and restore your partition table

wow, simply a lifesaver.

Science of course and effective too

Most people in the field search Pubmed but there is another site that I frequently visit – the European patent database that often have more concise information. Look at current allergy patents – the last one will definitely work you may also use a big plastic bag ;-)

patents.png

Be aware that being cynical is probably bad for your heart.

Biomedical journal search – a small gift

Pubmed often leads you to dead ends – journal citations without a link to the journals’ home. Google helps sometimes but is always time consuming. As a little gift for you, I have written a small bookmarklet that will scan the Regensburg library files – just left click on the

bookmarklet

link below and move it to your browser toolbar. With just a mouse click you can then locate the journals homepage.

Addendum

Another approach – the LibraryLookup Bookmarklet Generator.

Playing with your browser

Some blog authors are nuts about protecting their web site from copying files. There are many ways to protect your site – but only one really good (publish nothing). I often see small javascripts that disable the ability to right-click where javascript.about.com has a much simpler solution:

<body oncontextmenu=”return false;”>

Please try a right click now…
If you are fooled by a web author in such a way, what could you do? tech-recipes has the answer: Of course, we can use javascript to turn it back on.

When visiting the offending website, type the following into the URL bar of your browser:
javascript:void(document.oncontextmenu=null)

Happy browsing, yea, yea.

Photoshopped

How to recognize photoshopped pictures? This will be a routine task for future editorial process (BTW I already recognized a faked gel gel picture where the edges and density of the bands looked somewhat artifical). However, with the ever increasing technical capacities we probably need non-destroyable, watermarked pictures from professional scanning and digitizing equipment.
In the meantime, check Wikipedia and the links there. I believe that the majority of the faked pictures could have been detected by splitting up color channels and looking at non-continous transitions of hue (“Farbton”), saturation (“Sättigung”) and brightness (“Helligkeit”) or grey value. This will even work with scanned figures although I would recommed to check original computer files (that may always be electronically stamped by previous publishers). Don´t miss the website of the mp3 developers).

gelfake1.png

gelfake2.png

Addendum

Here is another examples how to recognize photoshop spoof:

set the hue to a low setting, the saturation to a higher setting, and mess with the light and look for blotches of color that don’t follow the rest of the image

22-2-07: The JBC has now adopted an explicit policy

“No specific feature within an image may be enhanced, obscured, moved, removed, or introduced. The groupings of images from different parts of the same gel, or from different gels, fields or exposures must be made explicit by the arrangement of the figure (e.g. using dividing lines) and in the text of the figure legend. Adjustments of brightness, contrast, or color balance are acceptable if and as long as they do not obscure or eliminate any information present in the original. Nonlinear adjustments (e.g. changes to gamma settings) must be disclosed in the figure legend.

11-9-07 Hamin Farid has developed tools to detect digital tampering.