Presentation slides from the IB-conference in Cambridge online (dg)

Thu 2010-04-01 10:00

The slides from the International Symposium on Integrative Bioinformatics (IB 2010) are now online. Please have a look at our and the other presentations at: http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib2010/prog.php

Support forum added at the SF project page

Wed 2010-03-31 15:00

We have added a Forum to the sourcefoge project page where users can ask questions about the project and can make feature requests as well. Here is the Link to the Forum.

Bioscanners paper has been published in JIB (dg)

Thu 2010-03-25 13:00

Our paper "Data integration using scanners with SQL output - The Bioscanners project at sourceforge." has been published in the Journal of Integrative Bioinformatics, 7(3):122, 2010. See here: http://journal.imbio.de/index.php?paper_id=122 for a PDF verion of this paper. Pubmed entries will follow soon. Please use this paper for citations.

Bioscanners project will be presented in Cambridge next week (dg)

Mon 2010-03-15 10:00

The International Symposium on Integrative Bioinformatics (IB 2010) will be held from March 22th to October 24th, 2010 in Cambridge, UK. In the afternoon session on Monday the Bioscanners project will have a presentation of 25 minutes. The complete program of the conference can be seen here. After the conference the paper to the talk will be published in the "Journal of Integrative Bioinformatics".

BLASTXMLScanner Version 0.1 released (dg)

Wed 2010-03-10 15:00

We released today an new Scanner for BLAST-files generated with the "-m 7" option, i.e. XML-files. The scanner can be used like the BLASTScanner for text files and the BLASTM8Scanner for M8-output files. The source code and binaries for Win32, Linux, OSX, OSF1 and Solaris are available at the Download-section.

BLASTM8Scanner Version 1.1 released (dg)

Wed 2010-03-10 14:00

We released today an new version of the BLASTM8Scanner which translates BLAST-files generated with the "-m 8" output option into database code. In this version the score column wasd renamed to bit_score to be in sync with the BLASTScanner and the BLASTXMLScanner. Files releases are available at the Download-page.

BLASTScanner Version 1.3 released (dg)

Wed 2010-03-10 13:00

We released today an bugfix version of our BLASTScanner. For long query sequences more than 1000 character slong, the scanning process would fail. This bug was fixed an furthermore the score column was renamed to bitscore, the frame column was more specifically named query_frame, the hit_frame column for (blastx and tblastx) was introduced. See the Download-Section for getting the latest binaries and source code.

dgScannerRunner Version 0.4 released (dg)

Mon 2010-02-22 15:00

We released today an improved version of our dgScannerRunner. Mainly the perfomance was improved. You can now load data tables with 100.000 rows and 10 columns within a few seconds, sorting by clcicking on the table headers is also done within a few seconds. See the Download section for you binary. Please note that this application can be also used as a simple SQLite data browser with exceptional performance.

TargetPScanner Example added (mf)

Thu 2009-12-17 16:00

We added a new example page on how to scan results files from the TargetP-predictor into database code TargetPScanner here. Informations about the cellular localization predictor TargetP can be found here. http://www.cbs.dtu.dk/services/

BioBash 1.1 released (dg)

Fri 2009-12-11 16:00

In some case programming a full fledged scanner is just overkill, often it is enough to just write a short shell function which can translate the input with some commands into a tabular output. That output can feeded afterwards wiht the column defintions into the generic TabCsvScanner to create the database code required to fill the database. Our BioBash.sh script contains some examples which can be used to perform your own scanning procedures or as a leraning aid to create you own scanner functions.

TabCsvScanner 1.10 released (dg)

Thu 2009-11-05 14:00

We released TabCsvScanner 1.10. It now uses the column definitions for deciding of quoting or not quoting the columns in the SQL-insert statement. Currently INT, BIGINT, INTEGER, SMALLINT, FLOAT, DOUBLE and REAL-types are recognized as numerical types. A hash (#) being the first character in a row can be used to comment lines in a file as those lines will be ignored. Furthermore the column count for each line is now checked. If there are to many or to few columns an error will thrown and the program exists. The downlaods are available from the Download-page.

TabCsvScanner 1.9 released (dg)

Mon 2009-10-26 13:00 updated Wed 2009-10-28 18:00

We uploaded a new Scanner to the Sourceforge-download area. TabCsvScanner is a scanner which can translate tabulated files on the fly into database code. Often a dataformat might e easily converted into a tabulated format wiht a few shell commands. The output of those tools might be easily imported afterwards into your database using this scanner. Read more on the README-page. Binary builds for Win32 and Linux32 as well as the source code can be downloaded from the Downloads-page. Form version 1.8 on wards the Tab-format is the default one.

Bioscanners project will be presented in Leipzig (dg)

Mon 2009-10-19 17:00

The World Conference on Regenerative Medicine (WRM) will be held from October 29th to October 31st, 2009 in Leipzig. In the Bioinformatics session on Friday October 30st the Bioscanners project will have a presentaion of 30 minutes. You are welcome. The complete program of this session can be seen here.

dgScannerRunner Version 0.3 released (dg)

Wed 2009-10-14 14:00

We released today the dgScannerRunner application version 0.3. it contains some bugfixes regarding help page loading and now we have binaries for Solaris-sparc, Linux-32 and 64bit, Win32 as well as a port for the Mac-OSX/Darwin with X11. The aqua-port currently unfortunately does not work. We will look into this. See the Download section for you binary.

WolfPScanner released (dg)

Wed 2009-10-07 18:00

We uploaded a first version of the WolfPScanner which is used to scan WoLFPSORT output files (http://wolfpsort.org). Go to the Download page to get the application. You can read the manual at the WolfPScanner page.

Linux32 version of dgScannerRunner uploaded(dg)

Thu 2009-09-27 20:00

We uploaded also the 32bit-Version of the dgScannerRunner, the 64bit-version and a Mac-OSX version will follow in a few days. We then have access again to such machines ;) The download is available in the Download section.

Bioscanners poster at the GCB (dg)

Thu 2009-09-24 14:00

Next week we will present our poster: "The Bioscanners Project at Sourceforge" on the German Conference on Bioinformatics in Halle (Saale)/Germany. You can find more informations about the GCB here: http://www.gcb2009.de Hope to see you at our poster session on tuesday afternoon. For your preparation we put a draft of our poster here as a PDF document.

dgScannerRunner released (dg)

Wed 2009-09-18 14:00 | Add Comment

We recently released dgScannerRunner a graphical tool to simplify the running of our console based scanners like the BLASTScanner and the GoOboScanner. The user can select the scanner and the input and output files. As a database library is included as well we were also providing a database browser to browse and query the database structrue. More information can be found at the dgScannerRunner page. Currently only a windows executable is released, the Linux- and the Mac-OSX version will next week. The download can be accessed from the Download page. BTW: The download counters still does not count :(

GoOboScanner released (dg)

Wed 2009-09-02 13:00 | Add Comment

We recently released GoOboScanner an application which scans Gene Ontology Obo-files Version 1.2 into database code. Databases tested were SQLite, MySQL and PostgreSQL. Details can be found on the GoOboScanner-page. The download will be available from the Sourceforge facilities http://sourceforge.net/projects/bioscanners/files/ soon. Please be aware that for some mirrors it will take time. BTW: Currently the download counters does not count :(

ptlex released (sm)

Tue 2009-08-25 11:00 | Add Comment

We are proud to release the "Potsdam-Tcl-Lexer" a program, which can be used to translate Flex-like input files for the scripting languages Perl, Python, Ruby, and Tcl into standalone applications. Details can be found on the Ptlex-page. The download is available from the Sourceforge facilities http://sourceforge.net/projects/bioscanners/files/ .

BLASTScanner 1.2 released (dg)

Fri 2009-07-31 14:00 | Add Comment

Version 1.1 unfortunately contained a bug if using the prefix argument in a certain order. We fixed this bug and released a new version of BLASTScanner. Sorry for any possible inconvenience. The file is available at the Sourceforge facilities for downloading. In order to download BLASTScanner, either the source code or binaries for various platforms go to the Download page. Details about usage can be found at the BLASTScanner-page.

BLASTScanner 1.1 released (dg)

Thu 2009-07-17 11:00 | Add Comment

We just released a new version of BLASTScanner which supports now shell wildcards as well. WE removed the old getopt library and where further writing a simple arguments parser form command line invocations. It is now possible to translate a bunch of textual files like in this example.

$ BLASTScanner-Windows-x86.exe --infile *.blastp --prefix blastp > sample.sql  

Please be aware that the syntax --infile=filename does not work anymore. We removed the getopt-library as it blows up the standalone c-source files and does not allow shell filename expansion using wildcards. For more details on how to work with BLASTScanner consult the README.

To download BLASTScanner, either the source code or binaries for various platforms go to the Download page.

Abstract from the ISMB in Strockholm (dg)

Thu 2009-07-09 12:00 | Add Comment

At the ISMB at Stockholm we had many interesting discussions about the BLASTScanner and the bioscanners project at sourceforge. The abstract and the poster about the BLASTScanner presented at the ISMB conference are now online available here ....

New Downloads-Section (dg)

Thu 2009-07-09 11:00 | Add Comment

There is a new Downloads section now at the bioscanners project pages available to simplify the finding of the appropiate binaries or sources.

BLASTM8Scanner released (dg)

Mon 2009-05-27 12:00 | Add Comment

A new scanner for translating BLAST-M8 files into database code has been released. Here is a sample session to translate 81 blastm8 files into one go into a sqlite database on a Mac-OSX machine. Time required: 1 second!

groth@palme$ ls | head
blastn_seqs.fasta.1.uniq.fasta.txt
blastn_seqs.fasta.10.uniq.fasta.txt
blastn_seqs.fasta.11.uniq.fasta.txt
blastn_seqs.fasta.12.uniq.fasta.txt
blastn_seqs.fasta.13.uniq.fasta.txt
blastn_seqs.fasta.14.uniq.fasta.txt
blastn_seqs.fasta.15.uniq.fasta.txt
blastn_seqs.fasta.16.uniq.fasta.txt