The main result of thr project is the Oncology over Internet portal. You are welcome to access it at the following URL: http://www.o2i.it:8080/o2i/.
You can download the User Manual and the Installation instructions.

A shortlist of requirements includes:
for the client: a browser and a Java Runtime Environment (JRE)
for the server: Apache Tomcat 5.X, MySql 4.X, JDK 1.5 (but please consider using biowep instead)

You may also be interested in knowing about the biowep portal, that is an open source tool derived from the above portal. You can go directly to the portal at http://bioinformatics.istge.it:8080/biowep/ or go through its support site at http://bioinformatics.istge.it/biowep/.

Finally, why not having a look at the review that was recently published in Briefings in Bioinformatics?
P. Romano, Automation of in-silico data analysis processes through workflow management systems, Briefings in Bioinformatics, 2008 9(1):57-68 (doi:10.1093/bib/bbm056) PMID: 18056132 See the published version here, navigate Medline clicking here or view pre-publishing version here.

Publications, communications, posters, manuals, etc...

Papers in peer-reviewed journals
1	F. Corradini, L. Mariani and E. Merelli. An agent-based layered middleware as tool integration, Software Tool Technology Transfer, Springer Journal, January 2004
2	L. Milanesi and I. B. Rogozin, ESTMAP: A System for Expressed Sequence Tags Mapping on Genomic Sequences, IEEE Transaction on Nanobioscience, Vol. 2 NO. 2, 75-78, June 2003.
3	E. A. Nedosekina, E. A. Ananko, L. Milanesi and V. A. Likhoshvai, Mathematical simulation of dynamics of macrophage gene network activated by lipopolysaccharides and/or interferon-gamma. In: Bioinformatics of genome regulation and structure. Ed. by N. Kolchanov and R. Hofestaedt, Kluwer Academic Publishers, Boston / Dordrecht / London, 2004, pp. 283-293.
4	I. B. Rogozin, V. N. Babenko, L. Milanesi and Y. I. Pavlov, Computational analysis of mutation spectra. Brief. Bioinform., 2003, V. 4, N 3
5	P. Romano, M. Kracht, M.A. Manniello, G. Stegehuis and D. Fritze, The role of informatics in the coordinated management of biological resources collections, Applied Bioinformatics. 2005;4(3):175-86
6	P. Romano, O. Aresu, M. A. Manniello and B. Parodi, Interoperability of CABRI services and biochemical pathways databases, Comp Funct Genom 2004; 5:169-172 (doi:10.1002/cfg.376)
7	P. Romano, P. Dawyndt, F. Piersigilli and J. Swings, Improving interoperability between microbial information and sequence databases, BMC Bioinformatics 2005, 6(Suppl 4):S23 (doi:10.1186/1471-2105-6-S4-S23)
8	P. Romano, G. Bertolini, F. De Paoli, M. Fattore, D. Marra, G. Mauri, E. Merelli, I. Porro, S. Scaglione and L. Milanesi, Network integration of data and analysis of oncology interest. Journal of Integrative Bioinformatics, 0021, 2006. Online Journal: http://journal.inbio.de/index.php?paper_id=21
9	P. Romano, D. Marra and L. Milanesi, Web services and workflow management for biological resources, BMC Bioinformatics 2005, 6(Suppl 4):S24 (doi:10.1186/1471-2105-6-S4-S24)
Further publications, oral communications, posters, thesis
1	P. Romano, P. Arrigo, G. Mauri, E. Merelli and L. Milanesi, Oncology over Internet (O2I): information querying, filtering and retrieval by means of standard formats, BIOCOMP 2002, Certosa di Pontignano, Siena, Italy, 15-17 February 2002
2	L. Milanesi, R. Caprera, D. Moraschi, J. Hatton, A. Maniello and P. Romano, Ricerca di informazione oncologica in Internet. @ITIM 2002. Firenze Italy 27-30 Ottobre 2002
3	R. Rizzi, L. Milanesi and L. Mussio, L'integrazione di banche dati genomiche e proteiche. 6° Conferenza Nazionale dell.ASITA, vol. 2. Perugia, p.1803-1808. 2003
4	E. Bartocci, S. Moeller, L. Toldo and E. Merelli. Integration of EnsEMBL with BioAgent, BIOCOMP 2003, Frascati, Rome, Italy, 28-29 March 2003
5	A. Mucci, A. Cusmano, M. De Francisci, A. Manniello, D. Marra, P. Romano and G. Mauri, Integration of data from different sources: a prototype devoted to p53 mutations, BIOCOMP 2003, Frascati, Rome, Italy, 28-29 March 2003
6	Specchio, R., Caprera, A., Hatton, J., Milanesi, L., GeneGrid: a workflow system for sequences analysis. BIOCOMP 2003, Frascati, Rome, Italy 28-29 March 2003
7	E. Bartocci, L. Mariani and E. Merelli. An XML view of the world. Proceedings of the 5th International Conference on Enterprise Information Systems ICEIS 2003, Angers, April 23-26, 2003
8	L. Milanesi, F. Basilico, L. Benazzi, J. Hatton, S. Sedini and P.L. Mauri. Bioinformatics tools for hemoglobin variants characterization, ESF Programme in Functional Genomics: 1st European Conference. Prague, Czech Republic, May 14-17, 2003
9	D. Bonura, L. Mariani and E. Merelli. Designing Modular Agent Systems, Net.ObjectDays 2003 Conference, Erfurt, September 22-25, 2003
10	L. Milanesi and R. Rizzi, Microarray image data analysis SPOTVIEW, NETTAB 2003, Bologna 27-28 November 2003
11	F. Corradini, A. Pierantonio and E. Merelli, Workflow as composition of Domain-Specific Languages, Technical Report TR04, Dipartimento di Informatica, Università di L'Aquila, (2003).
12	F. Corradini, L. Mariani and E. Merelli. A Programming Environment for Global Activity-based Application. Workshop WOA 2003 - Dagli Oggetti agli Agenti, Villasimius (CA), Italy, 10-11 Settembre 2003.
13	L. Leoni, BioOntology Service, Progettazione di una ontologia nel dominio della BioInformatica, Tesi di Laurea in Informatica, Università di Camerino, a.a. 2002-2003
14	P. D.Ursi, E. Rovida, G. Merati, E. Biguzzi, A. Caprera, L. Milanesi and E. Faioni, Computational analysis of naturally occurring protein C mutants: electrostatic properties implications. BITS2004 Bioinformatics Italian Society Meeting, Padova, 26-27 March 2004.
15	B. Lazzari L. Milanesi, A. Stella, A. Caprera, F. Bianchi, A. Vecchietti and C. Pozzi, ESTree DB: a Tool for Peach Functional Genomici. BITS2004 Bioinformatics Italian Society Meeting, Padova, 26-27 March 2004.
16	E. Merelli, P. Romano and L. Scortichini. A workflow service for BioMedical Applications, BITS2004 Bioinformatics Italian Society Meeting, Padova, 26-27 March 2004
17	M. Passamano, N. D.Agostino, A. Caprera and L. Milanesi, Comprehensive tools for the management of Protein Kinase Domains. BITS2004 Bioinformatics Italian Society Meeting. Padova 26-27 March 2004.
18	P. Romano, E. Merelli, D. Marra and A. Manniello, Workflows management for data and analysis integration in bioinformatics, Proc. of the 1st Convention of the National Cancer Research Institute, Genova, 15/6/2004.
19	R. Amici, F. Corradini and E. Merelli, A Process Algebra View of Coordination Models with a Case Study in Computational System Biology, 1st Intl Workshop on Coordination and Petri Nets - PNC04, Bologna, June 22, 2004.
20	F. Corradini, E. Merelli and A. Pierantonio. Workflow as Composition of Domain-Specific Languages, 1st Intl Workshop on Coordination and Petri Nets - PNC04, Bologna, June 22, 2004.
21	L. Milanesi and E. Merelli, Modelling of protein surface to identify and analyze functional determinants using GRID technologies. AgentLink III, Technical Forum I, Rome, June 30th - July 2nd 2004
22	M. Fattore and P. Arrigo, Topical clustering of biomedical abstract by self organizing maps, Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2004), July 25-30, 2004, Akademgorodok, Novosibirsk, Russia.
23	D. Marra and P. Romano, Mutation data interoperability: SRS implementation of the TP53 IARC mutation database providing XML output, Workshop NETTAB 2004 on "Models and metaphors from biology to bioinformatics tools", Camerino, September 5-7, 2004, pp. 209-11.
24	Perin F., XML INSERTION TOOL: Software di aggiornamento per la base di conoscenza relativa al progetto O2I, Tesi di Laurea in Informatica, Università di Milano Bicocca, 2004
25	Rafani S., Progetto O2I - Oncology Over Internet: Progettazione e implementazione di una meta-data bank di supporto all.attività di web agents nell.ambito della ricerca oncologica, Tesi di Laurea in Informatica, Università di Milano Bicocca, 2004
26	L. Scortichini, Sviluppo di un sistema basato su agenti per la gestione di Bio-workflow, Tesi di Laurea in Informatica, Università di Camerino, a.a. 2002-2003
27	R. Specchio, A. Caprera, J. Hatton and L. Milanesi, GeneGrid: a workflow system for sequences analysis. BIOCOMP 2003, Frascati, Rome, Italy 28-29 march 2003.
28	Sturaro F., Descrizione dei Web Services e trasformazione di un'applicazione stand-alone in Servizio Web, Tesi di Laurea in Informatica, Università di Milano Bicocca, 2004
29	Succi Cimentino L., Sviluppo di un HTML Wrapper, Tesi di Laurea in Informatica, Università di Milano Bicocca, 2004
30	Zonca M., Protocolli di comunicazione dei Web Services e Sviluppo di Servizi Web in Ambiente Java, Tesi di Laurea in Informatica, Università di Milano Bicocca, 2004
31	Marra, D., Romano, P., Improving accessibility of TP53 IARC database, 2nd Meeting of the Bioinformatics Italian Society (BITS2005), Milano, March 18-19, 2005, P53
32	D. Marra and P. Romano, Mutation data interoperability: SRS implementation of the TP53 IARC mutation database providing XML output, Workshop NETTAB 2004 on "Models and metaphors from biology to bioinformatics tools", Camerino, September 5-7, 2004, pp. 209-11.
33	Romano P., Bertolini G., De Paoli F., Fattore M., Marra D, Mauri G., Merelli E., Porro I., Scaglione S. and Milanesi L., Oncology over Internet: integrating data and analysis of oncology interest on the net by means of workflows, Symposium Integrative Bioinformatics, Bielefeld, July 4-5, 2005
34	Marra, D., Parodi, B., Manniello, M. A., and Romano, P., Annotation of cell lines by using workflows: a first experience, 5th International Workshop NETTAB 2005 on "Workflows management: new abilities for the biological information overflow", Napoli, October 5-7, 2005, P2.
35	Marra, D. and Romano, P., A set of simple workflows simplifying access to TP53 mutation database, 5th International Workshop NETTAB 2005 on "Workflows management: new abilities for the biological information overflow., Napoli, October 5-7, 2005, P3.
36	Romano P., Bertolini G., De Paoli F., Fattore M., Marra D, Mauri G., Merelli E., Porro I., Scaglione S. and Milanesi L., Oncology over Internet: integrating data and analysis of oncology interest on the net by means of workflows, 5th International Workshop NETTAB 2005 on "Workflows management: new abilities for the biological information overflow., Napoli, 5-7 Ottobre 2005.
37	Vigano D., Progetto O2I - Oncology Over Internet: Progetto e sviluppo di un portale oncologico per l'utilizzo dei workflows, Tesi di Laurea in Informatica, Università di Milano Bicocca, 2005
38	Tatani K., Progetto O2I - Oncology Over Internet: Un portale che consente l.esecuzione di workflow, Tesi di Laurea in Informatica, Università di Milano Bicocca, 2005

Further papers, published after the conclusion of the project, but linked to its results
1	G. Armano, V. Breton, L. Milanesi, P. Romano, Special Section on GRID, Web Services, Software Agents, and Ontology Applications for Life Sciences (Guest Editorial), IEEE Transactions on NanoBioscience (IEEE-TNB), 2007, 6(2):101-103.
2	E. Bartocci, D. Cacciagrano, N. Cannata, F. Corradini, Merelli, L. Milanesi, and P. Romano, An Agent-based Multilayer Architecture for Bioinformatics Grids, IEEE Transactions on NanoBioscience (IEEE-TNB), 2007, 6(2):142-148.
3	Beltrame F, Papadimitropoulos A, Porro I, Scaglione S, Schenone A, Torterolo L, Viti F, A Grid Environment for Microarray Management and Analysis in Bone Marrow Stem Cells Experiments, Future Generation Computer Systems 23 (2007) 382-390
4	Marra, D. and Romano, P., Integrating mutation data of the TP53 human gene in the bioinformatics network environment, Proc. First International Conference on Bioinformatics Research and Development BIRD '07, March 12-14, 2007, Berlin, Springer Lecture Notes in Bioinformatics LNBI 4414, pp. 453-463, 2007, Springer Verlag Berlin Heidelberg 2007
5	Romano P, Bartocci E, Bertolini G, De Paoli F, Marra D, Mauri G, Merelli E, Milanesi L, Biowep: a workflow enactment portal for bioinformatics applications, BMC Bioinformatics 2007, 8 (Suppl 1):S19
6	Romano P., Automation of in-silico data analysis processes through workflow management systems, Briefings in Bioinformatics Advance Access published online on December 2, 2007, doi:10.1093/bib/bbm056
7	Romano P., Marra D., SWS: accessing SRS sites contents through Web Services, BMC Bioinformatics 2008 (in press)
8	Cannata N., Schroeder M., Marangoni R., Romano P., A Semantic Web for Bioinformatics: goals, tools, systems, applications, BMC Bioinformatics 2008 (in press)
Further publications, published after the conclusion of the project, but linked to its results
1	Bartocci E., Cannata N., Corradini F., Merelli E., Milanesi L., Romano P., A multilayer architecture to support bioinformatics of today and tomorrow, 3rd Meeting of the Bioinformatics Italian Society BITS 2006, Bologna, Italy, April 28-29, 2006, P99.
2	Marra D. and Romano P., Web services for biological resources: the CABRI experience, XXV Annual Meeting of European Culture Collections. Organization ECCO XXV, Budapest, Hungary, June 8-10, 2006
3	Bartocci E., Cacciagrano D., Cannata N., Corradini F., Merelli E., Milanesi L., and Romano P., A Grid-based multilayer architecture for bioinformatics, 6th International Workshop NETTAB 2006 on "Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics", Santa Margherita di Pula (CA), July 10-12, 2006.
4	Bartocci E. and Romano P., Towards a comparison of Workflow Management Systems in Bioinformatics, 6th International Workshop NETTAB 2006 on .Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics., Santa Margherita di Pula (CA), July 10-12, 2006.
5	Falzone A, Melato M, Porro I, Ratto S, Schenone A, Torterolo L, A Grid infrastructure for managing workflows in bioinformatics applications, NETTAB workshop on "Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics", Santa Margherita di Pula (CA), Italy, July 10-12, 2006
6	Marra D., Romano P., A workflow enactment portal for bioinformatics, 3rd International Workshop on Data Integration in Life Sciences 2006 (DILS.06), Hinxton, UK, July 20-22, 2006
7	Romano P., Rasi C., Marra D., The automation of bioinformatics processes through workflow management systems, 7th Annual Spanish Bioinformatics Conference (JdB'06), Zaragoza, Spain, November 20.22, 2006
8	Marra D., Romano P., Integrating mutations data of the TP53 human gene in the bioinformatics network environment, 1st International Conference on Bioinformatics Research and Development (BIRD `07), March 12-14, 2007, Berlin, Germany.
9	Romano P., Marra D. and Rasi C., Semi-automatic and efficient annotation of bioinformatics processors in the biowep workflow enactment portal, 4th Meeting of the Bioinformatics Italian Society BITS 2007, Napoli, Italy, April 26-28, 2007
10	Romano P. and Marra D., SWS: accessing SRS sites contents through Web Services, 4th Meeting of the Bioinformatics Italian Society BITS 2007, Napoli, Italy, April 26-28, 2007
11	Romano P., Bioinformatics Web Services at the National Cancer Research Institute of Genoa, 7th International Workshop NETTAB 2007 on "A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications", Pisa, June 12-15, 2007, P17, pp. 395-401
12	Rasi C. and Romano P., XScufl definitions extended: bringing semantic data to workflow processors, 7th International Workshop NETTAB 2007 on "A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications", Pisa, June 12-15, 2007, P18, pp. 403-407
13	Rasi C., Marra D., and Romano P., A Web-based tool for Bioinformatics workflows enactment, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), Vienna, July 21-25, 2007
14	Romano P., Rasi C., and Marra D., Enhanced access to biomedical databases through Web Services, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), Vienna, July 21-25, 2007

Beside the portal prototype software, some tools have been developed and can be usefully accessed by end users.
Here is a short list of the most meaningful ones.

• Bio-WorkFlow service agent of the BioAgent platform:
  In this site you will find some demos of the BioAgent multi-agent platform. BioAgent is a project born from the collaboration of the information systems and intelligent systems group of the university of Camerino with Luca Toldo. The project aims to develop an intelligent agent platform to support biological data analyses and to define a declarative language to define and manipulate "Biological Agents".
  The Bio-WorkFlow service agent is a prototype implementation of a workflow manager allowing for the creation and execution of workflows involving access to literature, mutation and cell lines databases.
  


• SRS implementation of the IARC database of TP53 gene mutations:
  This site includes the implementation of the complete suite of databases related to the mutated TP53 human gene. These databases are maintained at the IARC (International Agency for Research on Cancer, Lyon, France). The SRS implementation adds new search features and is a valuable add-on to the scientific reasearch in this field, but its main aim is the evaluation of XML output features available with SRS 7. This implementation allows for the retrieval of results of end users' searches in four different XML outputs, all based on the same DTD.
  


• PubClust Text Mining tool developed at the ISMAC BioCOMP group:
  One of the major challenges in the post-genomic era is the speeding up of the process of identification of molecules involved in a specific disease (molecular targets). Even if the experimental procedure have greatly enhanced the analytical capability, the textual data analysis still play a central role in the experimental activity design or in the data collection.
  The extraction of useful information from published papers is still strongly dependent on the human expertise in the selection and retrieval of relevant papers. The search of abstract in MEDLINE or PubMed databases, is a common activity for researchers. Often the navigation in textual databases is not simple and in many cases the user can retrieve only list of abstracts without any kind of additional information about the relatedness of the abstract contents with the submitted query.
  In the last decade, the application of Natural Language Processing (NLP) tools has acquired some relevance in bioinformatic field.
  The possibility of retrieving and organizing the textual information, according specific topics, allows the user to select and analyse only a reduced set of papers. In our work we present an application of a document clustering system, founded on Self-Organizing Maps, to reorganize in a hierarchical way the cluster of abstracts retrieved by PubMed query.
  


• Kinweb - Kinase database at the Institute of Biomedical Technology of the National Research Council CNR server:
  Kinweb is a collection of protein kinases encoded in the human genome. This site provides a comprehensive analysis of functional domains of each gene product. For each kinase, GenBank RefSeq and the SwissProt entry name are available along with information about kinase classification (Hanks and Hunter classification).
  


• Alzheimer database at the Institute of Biomedical Technology of the National Research Council CNR server:
  
  


• EmoVarDB at the Institute of Biomedical Technology of the National Research Council CNR server:
  pepDB: a peptidomic tool for Hb mutations identification.
  


• DifferentialMass at the Institute of Biomedical Technology of the National Research Council CNR server:
  a tool for the indication of possible point mutations or aminoacidic post-translational modification.