BioServices.net

SnipClip

noreply@blogger.com (Martin Szugat) — Tue, 16 Sep 2008 12:36:00 +0000

SnipClip is the name of my new venture. SnipClip is a platform for online scrapbooks. It is not officially launched yet, but you can register for it here.

This is definitely my last post on this blog. I now fully focus on our company and dropped out of my Master studies on Bioinformatics. SnipClip has less to do with computational biology at first glance. However, we will use a lot of data mining techniques to provide our users the best recommendations for their favourite digital collectibles, so some learnings from my studies go into our product :)

Have a good time!

Martin

This blog will be closed (sooner or later)

noreply@blogger.com (Martin Szugat) — Tue, 12 Feb 2008 14:38:00 +0000

If you are interested in what I'm doing next, visit paid content is back.com.

3rd place

noreply@blogger.com (Martin Szugat) — Tue, 18 Sep 2007 13:48:00 +0000

... is the result of our effort to win the start2grow competition! We are very happy!

start2grow

noreply@blogger.com (Martin Szugat) — Wed, 29 Aug 2007 23:36:00 +0000

start2grow is the name of a business plan competition we participated in and, hey, we are invited to join the final round, together with twenty other teams. Ten teams will get a price. So wish us luck!

BioWeka 0.7.0 released

noreply@blogger.com (Martin Szugat) — Tue, 24 Apr 2007 20:50:00 +0000

This release contains some important changes and bug fixes:

We changed the architecture of the alignment packages. The new aligner classes are found in packages which refer to the source of the underlying algorithm code (e.g. bioweka.aligners.jaligner.SmithWatermanGotohAligner).
The new release solves a problem when using the "supply test set" option with BlastClassifier or SimpleAlignmentClassifier, which lead to incorrect results in previous releases (other options like cross-validation or percentage split were not affected).
The interface of the BlastParser and the converter classes for sequence-based data formats have been updated.

ScieCon 2007

noreply@blogger.com (Martin Szugat) — Thu, 05 Apr 2007 20:33:00 +0000

For my German readers:

Biothursday: "ScieCon 2007 - Firmenkontaktmesse für Life Sciences

Biowissenschaftler und Mediziner haben hier die Möglichkeit, Kontakte zu Unternehmen aus der Biotechnologie, Pharmaindustrie und Medizintechnik zu knüpfen und sich über die aktuellen Trends der Branche zu informieren. Rahmenprogramm mit Vorträgen, u.a. von Leibniz-Preisträger Prof. Dr. Patrick Cramer, Genzentrum München. Nähere Informationen unter: www.sciecon.info

Termin: Mittwoch, 16.Mai 2007 10:00 - 18:00

Ort: Marchionistraße 15, 81377 München, Klinikum Großhadern, Hörsaaltrakt"

BioWeka - extending the Weka framework for bioinformatics

noreply@blogger.com (Martin Szugat) — Wed, 21 Mar 2007 11:38:00 +0000

Now it's official - the paper about BioWeka is published in the current issue of Bioinformatics: BioWeka--extending the Weka framework for bioinformatics -- Gewehr et al. 23 (5): 651 -- Bioinformatics

What a surprise

noreply@blogger.com (Martin Szugat) — Thu, 15 Mar 2007 22:25:00 +0000

I still can't believe it: we are one of the ten teams that were honoured at the Science4Life Venture Cup for their business plan. A great thanks to

the Science4Life team, especially Christiane Wohlers, for the perfect organisation
our coach Wolfgang Schmidt for valueable feedback on our business plan
the unknown jury members for sending us their assessments
the speakers for the interesting presentations about business development, patents and law issues
Sanofi-Aventis and Bundesland Hessen for the sponsoring of this event
everybody else for their input and the exciting discussions!

Hope to see you again soon!

BioServices.net rocks at Science4Life Venture Cup 2007

noreply@blogger.com (Martin Szugat) — Thu, 01 Mar 2007 13:56:00 +0000

We, that is Feline Benisch, Bianca Künnecke, Kerstin Hoder, Moritz Sebastian Wurfbaum and myself as well as the research and development team from the Bioinformatics unit of the LMU, participated in the Science4Life Venture Cup 2007 (concept phase) with our business idea BioServices.net. We are one of twenty teams that are now invited to a workshop in Berlin next month to improve our business plan.

We like to thank the UnternehmerTUM GmbH for their support, especially for the course "Businessplan-Grundlagen" and for the opportunity to participate in the program Manage&More.

Connotea: basic integration with Word

noreply@blogger.com (Martin Szugat) — Wed, 14 Feb 2007 06:50:00 +0000

Create feature:

Word 2007 has some built-in support for bibliographies and citations. It's pretty basic and has some, um, issues, but by using it you can get your Connotea bookmarks into Word fairly quickly.

Read the whole story: Flags and Lollipops - Bioinformatics Blog: Connotea: basic integration with Word

Extending the Weka Framework for Bioinformatics

noreply@blogger.com (Martin Szugat) — Fri, 19 Jan 2007 23:37:00 +0000

An application note about BioWeka was published by Bioinformatics: BioWeka - Extending the Weka Framework for Bioinformatics by Jan E. Gewehr, Martin Szugat, and Ralf Zimmer.

Good Programmers

noreply@blogger.com (Martin Szugat) — Wed, 10 Jan 2007 14:15:00 +0000

Any fool can write code that a computer can understand. Good programmers write code that humans can understand.

Martin Fowler

Forum Life Science 2007

noreply@blogger.com (Martin Szugat) — Tue, 09 Jan 2007 23:01:00 +0000

14. /15. February 2007, Technische Universität München, Garching:

More than 65 speakers from 11 countries at the 5th Forum Life Science from companies such as BASF, Bayer, Boehringer Ingelheim, Degussa, DSM, Fresenius, GSK, Roche, Siemens, DuPont, Kraft Foods, Nestlé, Valio, Südzucker, Süd-Chemie, Wacker-Chemie, Linde, BRAIN, Genmab, MediGene, ReNeuron, Scil, Sciona or U3 Pharma as well as from universities and research centres from Erlangen, Heidelberg, Munich, Regensburg, Würzburg, Leiden, Lund, Wageningen, Boston and Sydney

Seems to be an interesting event.

ReGenesis

noreply@blogger.com (Martin Szugat) — Mon, 08 Jan 2007 20:08:00 +0000

For my German readers: there is a new TV series on Arte called ReGenesis (every Monday at 20:40). It's about biotechnology, bioterrorism and so on. Not very accurate but quite entertaining.

Happy New Year

noreply@blogger.com (Martin Szugat) — Fri, 29 Dec 2006 17:40:00 +0000

Dear my readers, colleagues and blogger friends, I wish you a happy new year and much success for your projects in 2007!

Biothursday on 18th January at gate, Garching

noreply@blogger.com (Martin Szugat) — Wed, 27 Dec 2006 20:34:00 +0000

We, some students from the TUM (Technical University of Munich), organized the first Biothursday, a self-organized and non-commercial event for people interested in life sciences. The first Biothursday will take place at the Garchinger Technologie und Gründerzentrum on Thursday, the 18th January at about 6:00 pm. Everyone is invited to join us as a listener and/or as a speaker. My presentation is about Life Sciences & Web 2.0. There will be two other presentations. Further information can be found on the corresponding website: www.biothursday.net.

BioWeka 0.6.0 released

noreply@blogger.com (Martin Szugat) — Thu, 23 Nov 2006 23:00:00 +0000

In this release we added a filter under bioweka.filters.universal called AddLastAttributeByName that adds the last attribute (often the class assignments) from a second data set to the current data set by joining the instances by their first attribute (i.e. name attribute).

Further, the release contains these bug fixes:

Calling the toString method on an AvgScoreEvaluator object whose initialize method had not been called leads to a NullPointerException. This bug was fixed.
The default value for the buildCommand property of the BlastClassifier object specified the option "-o T" which tells the formatdb command of the BLAST suite to build an index file for the sequence database. This leads to a better performance. However, as it seems, BLAST behaves differently in different versions with respect to this option, so we decided not to include the option in the default settings.
Under certain circumstances the PsiBlastParser class fails to grep the output of blastpgp. The new releases solves this problem.

BioWeka 0.5.0 released

noreply@blogger.com (Martin Szugat) — Thu, 09 Nov 2006 09:00:00 +0000

The BioWeka 0.5.0 release provides a new filter called AddLastAttributeFrom. This filter can be used to add an attribute, e.g. the class annotation, from an external dataset to the current dataset.

In addition, the new BioWeka version includes two minor bug fixes:

the relation name of a filtered data set does not contain anymore any white spaces or the pipe operator. This change has become necessary because the BlastClassifier uses the relation name as the name for the BLAST database and BLAST uses the database name as the file name for the database. However, Windows ~~permits~~forbids the pipe operator within file names.
the iprscan.xsl stylesheet declares the sequence.name attribute as of type nominal instead of string. This is a workaround for a well-known problem of Weka with sparse instances and string attributes.

BioSchemas at BMC Bioinformatics

noreply@blogger.com (Martin Szugat) — Thu, 09 Nov 2006 06:39:00 +0000

This is the first paper mentioning the open community project BioSchemas: BioMed Central | Abstract | 1471-2105-7-490 | XML schemas for common bioinformatic data types and their application in workflow systems

Is Sun Evil?

noreply@blogger.com (Martin Szugat) — Fri, 13 Oct 2006 08:46:00 +0000

At least this is not kind:

Hi all,

Yesterday our institution, the University of Tübingen, Germany, received
an email from SUN. The email started by saying that SUN is pleased to
see projects written in their programing language "Java" that we provide
at our institution. However, they wanted us to rename our Evoulutionary
Algorithms package "JavaEvA" to something like "JEvA" and our Neural
Network project "JavaNNS" should also be renamed to something else like
"JNNS". The reason for this is that SUN owns a trademark on the name
"Java" and no other institution or company is supposed to use this name
for its own purposes or software packages, even if this is a non profit
and/or open source project as JavaEvA and JavaNNS. We might later even
get a dissuasion letter if we do not follow the instructions in the email.
I do not exactly know how SUN and the BioJava project are connected.
However, in the worst case someday we could also receive a writing like
that.
To summarize: we should be aware that possibly the name "BioJava" has to
be changed to something else like "JBio" or "BioJ" or what ever SUN
might suggest as soon as they recognize our project. If there is already
an agreement with SUN about that, I am not well informed and curious to
know about it. Otherwise you are now informed about what happened to us
in Tübingen.

Sincerely,
Andreas Dräger

So, to summarize: You, we, nobody is allowed to use the name "Java" for a "software product" like BioJava. Btw: Didn't Sun planned to release Java into the Open Source community?

BioJava 1.5 Beta released

noreply@blogger.com (Martin Szugat) — Fri, 08 Sep 2006 06:36:00 +0000

The BioJava project released the Beta of the next version 1.5. This version also contains the ExternalProcess class.

Here is the full text of Mark's announcement in the BioJava mailing list:

Dear All -

I have prepared a beta distribution of the much awaited biojava 1.5. The
source, binaries and docs for the release can be obtained from the biojava
site at http://biojava.org/wiki/BioJava:Download

The API docs are also available on line at
http://www.biojava.org/docs/api15b/index.html

There are significant new features in this release:

* biojavax, the biojavax packages are extensions to the basic biojava.
They give access to more detailed objects with better functionality. Most
useful to the average user will be the new file parsers (see
RichSequence.IOTools) and the RichSequence object. See the biojavax docs
for more detail (http://biojava.org/wiki/BioJava:BioJavaXDocs).

* Hibernate interaction with BioSQL. The prefered method of interaction
with BioSQL is now via Hibernate. RichSequence and it's associated objects
have hibernate mappings to biosql databases. This provides a number of the
benefits of Hibernates ORM to biojava, especially control over
transactions and the removal of JDBC code. See
http://biojava.org/wiki/BioJava:BioJavaXDocs#BioSQL_and_Hibernate. for
details.

* Genetic Algorithms. A very flexible genetic algorithm library is
available in the biojavax packages. Simple examples are at
http://biojava.org/wiki/BioJava:BioJavaXDocs#Genetic_Algorithms. but much
more powerful things are possible.

* Several new features are available in the Structure package that allow
manipulation of 3D structure files and objects.

* Non HMM Implementations of the NW and SW alignment algorithms are now
available in the alignment package.

* A new package for handling external processes
(org.biojava.utils.process).

* Dozens of bug fixes.

Please take it out for a spin this weekend and let us know how it works.
You will probably find it more reliable than biojava-1.4 even though this
is technically a beta.

Many thanks to all the volunteers who have contributed to biojava!

Best regards,

- Mark

Gene and protein nomenclature in public databases

noreply@blogger.com (Martin Szugat) — Thu, 10 Aug 2006 09:27:00 +0000

The paper covering the creation of the data behind the ProThesaurus-Wiki is now available online on BMC Bioinformatics.

ProThesaurus-Wiki adds GO database and GO evidences

noreply@blogger.com (Martin Szugat) — Thu, 15 Jun 2006 14:45:00 +0000

The ProThesaurus-Wiki contains in its newest release the complete GO database. For each GO identifier/term there is a category page which lists all

parent categories (i.e. GO terms)
subcategories (i.e. subordinated GO terms)
part of-relations
annotated genes/proteins
comments
cross references
synonyms

In addition, each GO annotation for a gene/protein mentions the sources of evidence (e.g. the SwissProt database entry) and the GO evidence code. For each protein/gene name synonym there is also a list of sources.

Finally, the database was updated with the newest database identifiers and synonyms.

.NET-Award

noreply@blogger.com (Martin Szugat) — Wed, 14 Jun 2006 12:31:00 +0000

ProTag participates in the competition for the .NET-Award.

ProTag is a Smart-Tag and Add-In solution for the Microsoft Office applications Word, Excel and PowerPoint, that integrates the web services LiMB, BeThesaurus and ProThesaurus for the recognition of protein namens and database identifiers within Office documents.

The .NET-Award is an initiative of the Software & Support company to promote the .NET software development in Germany, Austria and Swiss. S&S organized formerly the JAX-Award at which the Bioclipse project participates and received the third prize.

BioWeka 0.4.2

noreply@blogger.com (Martin Szugat) — Tue, 23 May 2006 17:00:00 +0000

The new BioWeka release 0.4.2 contains some minor bug fixes and improvements:

The default, internal SMO classifier of the Eclat classifier now returns estimated probabilities (instead of just 0.0 or 1.0) and thus increases the frame prediction accuracy. This affects the components EclatFrameFinder, EclatFrameClassifier and Eclat.
Andreas Dräger provided new versions of his global alignments classes for the BioJava project, which fix some bugs. The BioWeka project incorporates these changes with the newest release.