Nov

05

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.

Oct

26

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.

Oct

19

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.

Oct

14

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.

Oct

07

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.

Sep

27

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.

Sep

24

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.

Sep

18

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 :(

Sep

02

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 :(

Aug

25

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/ .

Jul

31

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.

Jul

17

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.

Jul

09

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 ....

Jul

09

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.

May

27

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

groth@palme$ ls | wc -l
      81
groth@palme$ head -n 4 blastn_seqs.fasta.1.uniq.fasta.txt
intron_7        scaffold_216988 95.83   216     6       1       462     677     34527   34315   1e-94    353
intron_34       GeneScaffold_4662       90.88   274     24      1       607     880     296048  295776  9e-90    337
intron_36       GeneScaffold_2100       94.68   545     28      1       471     1014    185102  184558  0.0      842
intron_60       GeneScaffold_2100       96.97   330     10      0       718     1047    122133  121804  9e-149   533
dgroth@palme$ date; BLASTM8Scanner-Darwin-i386 --infile blastn*.txt | sqlite3 ~/blastn.sqlite3 ; date
Wed May 27 13:51:16 CEST 2009
Wed May 27 13:51:17 CEST 2009
dgroth@palme$ sqlite3 ~/blastn.sqlite3
SQLite version 3.1.3
Enter ".help" for instructions
sqlite> select count(*) from hits where score > 200;
9573
sqlite> select count(*) from hits where score > 2000;
9

Visit the sourceforge facilities to download the first BLASTM8Scanner release: BLASTScannerM8.zip The zip archive contains the source code as well as binaries for Win32, Linux32, Linux64, OSF1-alpha, Solaris-Sparc, and MacOSX (i386, ppc). Filesize around 50kb(!).

DG.

May

26

New website released (dg)

As we had recently problems with the CMS on sourceforge we switched to an external webhoster and during this migration we also chose PmWiki as our new CMS.

Feb

27

Perl lexer development (dg)

Our new project member, elchuxo, is currently working on a Perl lexer, called pplex. The program will allow to write flex like input files for scanner generation. Versions for the programming languages Tcl and Python will be released soon afterwards. The code for the Perl lexer is not yet released but is already in the CVS: http://bioscanners.cvs.sourceforge.net/viewvc/bioscanners/lexer/perl/. In the samples directory is already a wc implementation. Comments and suggestions are welcome.

Jan

08

Re2c sources for the BLASTScanner released

Today the re2c sources for the BLASTScanner application has been released as well. You can use them to modifiy the BLASTScanner source code. The Zip-archiv contains a make file which should build on any computer architecture.

Direct download link src-release: BLASTScanner1.0-src.zip

Direct download link binary-release: BLASTScanner1.0.zip