![](bg4.png)
delimited file is also stored and can be downloaded
by a user for usage with external software or further
analysis.
In Fig. 2 we show the web page of an experiment.
In the left side of the page a menu allows the user
to access to suitable pages either to insert new infor-
mation (i.e. Insert organism, Insert design, etc.), or to
require the visualization of stored data (i.e., Organism
List, Experiment list, etc.).
3 CONCLUSIONS AND FUTURE
WORK
The Microarray System copes with the problem of
managing the large amount of data collected from ex-
periments made with the DNA-microarray technol-
ogy by the FGC of the University of Verona. The
proposed system is able to manage MIAME com-
patible information, achieving the needs of sharing
data with the scientific community working on DNA-
microarrays.
As future work, we plan to extend the database
for considering other types of microarray, and in or-
der to avoid the use of external applications, we plan
to upgrade the Microarray System by implementing
modules for data normalization and data analysis.
REFERENCES
Altschul, S., Gish, W., Miller, W., Myers, W., and Lipman,
D. (1990). Basic Local Alignment Search Tool. J.
Mol. Biol., 215:403–410.
Bergsten, H. (2003). JavaServer Pages, 3rd Edition.
O’Reilly & Associates, Inc., Sebastopol, CA, USA.
Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G.,
and Spellman, P. (2001). Minimum Information about
a Microarray Experiment (MIAME) - toward stan-
dards for microarray data. Nature Genetics, 29:365
– 371.
Consortium, T. U. (2008). The Universal Protein Reasource
(UniProt). Nucleic Acids Res., 36:D190–D195.
Demeter, J., Beauheim, C., Gollub, J., Hernandez-
Boussard, T., Jin, H., Maier, D., Matese, J., Nitzberg,
M., Wymore, F., Zachariah, Z., Brown, P., Sherlock,
G., and Ball, C. (2007). The stanford microarray
database: implementation of new analysis tools and
open source release of software. Nucl Acids Res,
35:D766–770.
Edgar, R., Domrachev, M., and Lash, A. (2002). Gene
Expression Omnibus (GEO): NCBI gene expressione
and hybridation array data repository. Nucleic Acids
Research, 30:207–210.
Fang, H., Harris, S., Su, Z., Chen, M., Qian, F., Shi, L.,
Perkins, R., and Tong, W. (2009). Arraytrack: An fda
and public genomic tool. Methods Mol Biol, 563:379–
98.
Gattiker, A., Hermida, L., Liechti, R., Xenarios, I., Collin,
O., Rougemont, J., and Primig, M. (2009). Mimas 3.0
is a multiomics information management and annota-
tion system. BMC Bioinformatics, 10:151.
Leff, A. and Rayfield, J. (2001). Web-Application Devel-
opment Using the Model/View/Controller Design Pat-
tern. Enterprise Distributed Object Computing Con-
ference, IEEE International, 0:0118.
Marzolf, B., Deutsch, E., Moss, P., Campbell, D., John-
son, M., and Galitski, T. (2006). Sbeams-microarray:
database software supporting genomic expression
analyses for systems biology. BMC Bioinformatics,
7:286.
Maurer, K., Cooper, J., Caraballo, M., Crye, J., Suciu, D.,
Ghindilis, A., Leonetti, J., Wang, W., Rossi, F., St
¨
over,
A., Larson, C., Gao, H., Dill, K., and McShea, A.
(2006). Electrochemically generated acid and its con-
tainment to 100 micron reaction areas for the produc-
tion of dna microarrays. PLoS ONE, 1(1):e34.
Parkinson, H., Sarkans, U., Shojatalab, M., Abeygunawar-
dena, N., Contrino, S., Coulson, R., Farne, A., Lara,
G. G., Holloway, E., Kapushesky, M., Lilja, P.,
Mukherjee, G., Oezcimen, A., Rayner, T., Rocca-
serra, P., Sharma, A., Sansone, S., and Brazma, A.
(2005). ArrayExpress – a public repository for mi-
croarray gene expression data at the EBI. Nucleic
Acids Research, 33:553–555.
Rayner, T., Rocca-Serra, P., Spellman, P., Causton, H.,
Farne, A., Halloway, E., Irizarry, R., Liu, J., Maier, D.,
Miller, M., Petersen, K., Quackenbush, J., Sherlock,
G., Stoeckert, C., White, J., Whetzel, P., Wymore,
F., Parkinson, H., Sarkans, U., Ball, C., and Brazma,
A. (2006). A simple spreadsheet-based, MIAME-
supportive format for microarray data: MAGE-TAB.
BioMed Central, 7:18.
Spellman, P., Miller, M., Stewart, J., Troup, C., Sarkans,
U., Chervitz, S., Bernhart, D., Sherlock, G., Ball,
C., Lepage, M., Swiatek, M., Marks, W., Goncalves,
J., Markel, S., Iordan, D., Shojatalab, M., Pizarro,
A., White, J., Hubley, R., Deutsch, E., Senger, M.,
Aronow, B., Robinson, A., Bassett, D., Stoeckert, C.,
and Brazma, A. (2002). Design and implementa-
tion of microarray gene expression markup language
(MAGE-ML). Genome Biology, 3(9):research0046.1–
research0046.9.
Vallon-Christersson, J., Nordborg, N., Svensson, M., and
Hakkinen, J. (2009). Base - 2nd generation software
for microarray data management and analysis. BMC
Bioinformatics, 10(1):330.
Widenius, M. and Axmark, D. (2002). Mysql Reference
Manual. O’Reilly & Associates, Inc., Sebastopol, CA,
USA.
Zhai, J. (2001). Making GenePix Array List (GAL) Files.
robinsonlab.stanford.edu/microarrays/gal/docs/
Making GAL Files.pdf.
Zhu, Y., Zhu, Y., and Xu, W. (2008). Ezarray: a web-
based highly automated affymetrix expression array
data management and analysis system. BMC Bioin-
formatics, 9:46.
BIOINFORMATICS 2011 - International Conference on Bioinformatics Models, Methods and Algorithms
296