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144 results on '"Zambelli, F"'

1. Vortex nucleation and quadrupole deformation of a rotating Bose-Einstein condensate

Author

Kraemer, M., Pitaevskii, L., Stringari, S., and Zambelli, F.

Subjects
Condensed Matter
Abstract

Using a semi-analytic model based on the Thomas-Fermi approximation, we investigate the relevance of the quadrupole deformation of a trapped Bose-Einstein condensate for the nucleation of quantized vortices. For sufficiently high angular velocities $\Omega$ of the trap, the tendency of the system to exhibit spontaneous deformation is shown to lower the barrier which inhibits the nucleation of vortices at smaller $\Omega$. The corresponding value of the critical angular velocity $\Omega_c$ is calculated as a function of the deformation of the trap and of the chemical potential. The theoretical predictions for $\Omega_c$ refer to the case of a sudden switch-on of the deformed rotating trap and they are compared with recent experimental data., Comment: 12 pages, 4 postscript figures

Published
2001

2. Momentum transferred to a trapped Bose-Einstein condensate by stimulated light scattering

Author

Brunello, A., Dalfovo, F., Pitaevskii, L., Stringari, S., and Zambelli, F.

Subjects
Condensed Matter
Abstract

The response of a trapped Bose-Einstein condensed gas to a density perturbation generated by a two-photon Bragg pulse is investigated by solving the time-dependent Gross-Pitaevskii equation. We calculate the total momentum imparted to the condensate as a function of both the time duration of the pulse and the frequency difference of the two laser beams. The role of the dynamic response function in characterizing the time evolution of the system is pointed out, with special emphasis to the phonon regime. Numerical simulations are compared with the predictions of local density approximation. The relevance of our results for the interpretation of current experiments is also discussed., Comment: 7 pages, 3 postscript figures

Published
2001
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3. Overcritical Rotation of a Trapped Bose-Einstein Condensate

Author

Recati, A., Zambelli, F., and Stringari, S.

Subjects
Condensed Matter
Abstract

The rotational motion of an interacting Bose-Einstein condensate confined by a harmonic trap is investigated by solving the hydrodynamic equations of superfluids, with the irrotationality constraint for the velocity field. We point out the occurrence of an overcritical branch where the system can rotate with angular velocity larger than the oscillator frequencies. We show that in the case of isotropic trapping the system exhibits a bifurcation from an axisymmetric to a triaxial configuration, as a consequence of the interatomic forces. The dynamical stability of the rotational motion with respect to the dipole and quadrupole oscillations is explicitly discussed., Comment: 6 pages, 3 postscript figures

Published
2000
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4. Dynamic structure factor and momentum distribution of a trapped Bose gas

Author

Zambelli, F., Pitaevskii, L. P., Stamper-Kurn, D. M., and Stringari, S.

Subjects
Condensed Matter
Abstract

The dynamic structure factor of a trapped Bose-Einstein condensed gas is investigated at zero temperature in the framework of Bogoliubov theory. Different values of momentum transfer are considered, ranging from the phonon to the single-particle regime. Various approximated schemes are discussed, including the local density approximation, where the system is locally described as a uniform gas, and the impulse approximation, where the response is fixed by the momentum distribution of the condensate. A comprehensive approach, based on the eikonal expansion, is presented. The predictions of theory are successfully compared with the results of recent two-photon Bragg scattering experiments, both at low and high momentum transfer. Relevant features of the dynamic structure factor are also discussed using the formalism of sum rules and the concept of scaling. Particular emphasis is given to the regime of high momentum transfer, where the dynamic structure factor is sensitive to the behaviour of the order parameter in momentum space, and some instructive examples showing the consequence of long-range coherence are presented., Comment: 29 pages, 12 figures

Published
1999
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5. Collective oscillations of a classical gas confined in harmonic traps

Author

Guery-Odelin, D., Zambelli, F., Dalibard, J., and Stringari, S.

Subjects
Condensed Matter
Abstract

Starting from the Boltzmann equation we calculate the frequency and the damping of the monopole and quadrupole oscillations of a classical gas confined in an harmonic potential. The collisional term is treated in the relaxation time approximation and a gaussian ansatz is used for its evaluation. Our approach provides an explicit description of the transition between the hydrodynamic and collisionless regimes in both spherical and deformed traps. The predictions are compared with the results of a numerical simulation., Comment: 6 pages, revtex, 2 figures included

Published
1999
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7. INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures

Author

Salomoni, D., Campos, I., Gaido, L., de Lucas, J. Marco, Solagna, P., Gomes, J., Matyska, L., Fuhrman, P., Hardt, M., Donvito, G., Dutka, L., Plociennik, M., Barbera, R., Blanquer, I., Ceccanti, A., Cetinic, E., David, M., Duma, C., López-García, A., Moltó, G., Orviz, P., Sustr, Z., Viljoen, M., Aguilar, F., Alves, L., Antonacci, M., Antonelli, L. A., Bagnasco, S., Bonvin, A. M. J. J., Bruno, R., Chen, Y., Costa, A., Davidovic, D., Ertl, B., Fargetta, M., Fiore, S., Gallozzi, S., Kurkcuoglu, Z., Lloret, L., Martins, J., Nuzzo, A., Nassisi, P., Palazzo, C., Pina, J., Sciacca, E., Spiga, D., Tangaro, M., Urbaniak, M., Vallero, S., Wegh, B., Zaccolo, V., Zambelli, F., and Zok, T.

Published
2018
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8. DOME: recommendations for supervised machine learning validation in biology

Author

Walsh, I., Fishman, D., Garcia-Gasulla, D., Titma, T., Pollastri, G., Capriotti, E., Casadio, R., Capella-Gutierrez, S., Cirillo, D., Del Conte, A., Dimopoulos, A. C., Del Angel, V. D., Dopazo, J., Fariselli, P., Fernandez, J. M., Huber, F., Kreshuk, A., Lenaerts, T., Martelli, P. L., Navarro, A., Broin, P. O., Pinero, J., Piovesan, D., Reczko, M., Ronzano, F., Satagopam, V., Savojardo, C., Spiwok, V., Tangaro, M. A., Tartari, G., Salgado, D., Valencia, A., Zambelli, F., Harrow, J., Psomopoulos, F. E., Tosatto, S. C. E., Barcelona Supercomputing Center, Informatics and Applied Informatics, Artificial Intelligence, Walsh I., Fishman D., Garcia-Gasulla D., Titma T., Pollastri G., Capriotti E., Casadio R., Capella-Gutierrez S., Cirillo D., Del Conte A., Dimopoulos A.C., Del Angel V.D., Dopazo J., Fariselli P., Fernandez J.M., Huber F., Kreshuk A., Lenaerts T., Martelli P.L., Navarro A., Broin P.O., Pinero J., Piovesan D., Reczko M., Ronzano F., Satagopam V., Savojardo C., Spiwok V., Tangaro M.A., Tartari G., Salgado D., Valencia A., Zambelli F., Harrow J., Psomopoulos F.E., and Tosatto S.C.E.

Subjects
FOS: Computer and information sciences, Computer Science - Machine Learning, Standards, Informàtica::Intel·ligència artificial::Aprenentatge automàtic [Àrees temàtiques de la UPC], Center of excellence, European Regional Development Fund, Guidelines as Topic, Algorithms, Computational Biology, Humans, Models, Biological, Research Design, Supervised Machine Learning, Machine learning, computer.software_genre, Biochemistry, Biologia computacional, Machine Learning (cs.LG), 03 medical and health sciences, 0302 clinical medicine, Models, Agency (sociology), media_common.cataloged_instance, Biomedical research, European union, Molecular Biology, 030304 developmental biology, computer.programming_language, media_common, 0303 health sciences, business.industry, Cell Biology, Other Quantitative Biology (q-bio.OT), Biological, Machine Learning, Artificial Intelligence, Machine Learning in Life Science, Focus group, Quantitative Biology - Other Quantitative Biology, Work (electrical), FOS: Biological sciences, Elixir (programming language), Artificial intelligence, business, computer, Software, 030217 neurology & neurosurgery, Biotechnology, Career development
Abstract

Supervised machine learning is widely used in biology and deserves more scrutiny. We present a set of community-wide recommendations (DOME) aiming to help establish standards of supervised machine learning validation in biology. Formulated as questions, the DOME recommendations improve the assessment and reproducibility of papers when included as supplementary material. The work of the Machine Learning Focus Group was funded by ELIXIR, the research infrastructure for life-science data. IW was funded by the A*STAR Career Development Award (project no. C210112057) from the Agency for Science, Technology and Research (A*STAR), Singapore. D.F. was supported by Estonian Research Council grants (PRG1095, PSG59 and ERA-NET TRANSCAN-2 (BioEndoCar)); Project No 2014-2020.4.01.16-0271, ELIXIR and the European Regional Development Fund through EXCITE Center of Excellence. S.C.E.T. has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant agreements No. 778247 and No. 823886, and Italian Ministry of University and Research PRIN 2017 grant 2017483NH8. Peer Reviewed "Article signat per 8 autors més 28 autors/es de l' ELIXIR Machine Learning Focus Group: Emidio Capriotti, Rita Casadio, Salvador Capella-Gutierrez, Davide Cirillo, Alessio Del Conte, Alexandros C. Dimopoulos, Victoria Dominguez Del Angel, Joaquin Dopazo, Piero Fariselli, José Maria Fernández, Florian Huber, Anna Kreshuk, Tom Lenaerts, Pier Luigi Martelli, Arcadi Navarro, Pilib Ó Broin, Janet Piñero, Damiano Piovesan, Martin Reczko, Francesco Ronzano, Venkata Satagopam, Castrense Savojardo, Vojtech Spiwok, Marco Antonio Tangaro, Giacomo Tartari, David Salgado, Alfonso Valencia & Federico Zambelli"

Published
2021

10. O-042 ESHRE good practice recommendations on chromosomal mosaicism

Author

De Rycke, M, primary, Capalbo, A, additional, Coonen, E, additional, Coticchio, G, additional, Fiorentino, F, additional, Goossens, V, additional, MCheik, S, additional, Rubio, C, additional, Sermon, K, additional, Sfontouris, I, additional, Spits, C, additional, Vermeesch, J, additional, Vermeulen, N, additional, Wells, D, additional, Zambelli, F, additional, and Kakourou, G, additional

Published
2022
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13. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Author

Ostrovsky, AE, Mahmoud, A, Lonie, AJ, Syme, A, Fouilloux, A, Bretaudeau, A, Nekrutenko, A, Kumar, A, Eschenlauer, AC, DeSanto, AD, Guerler, A, Serrano-Solano, B, Batut, B, Gruening, BA, Langhorst, BW, Carr, B, Raubenolt, BA, Hyde, CJ, Bromhead, CJ, Barnett, CB, Royaux, C, Gallardo, C, Blankenberg, D, Fornika, DJ, Baker, D, Bouvier, D, Clements, D, Morais, DADL, Tabernero, DL, Lariviere, D, Nasr, E, Afgan, E, Zambelli, F, Heyl, F, Psomopoulos, F, Coppens, F, Price, GR, Cuccuru, G, Le Corguille, G, Von Kuster, G, Akbulut, GG, Rasche, H, Hans-Rudolf, H, Eguinoa, I, Makunin, I, Ranawaka, IJ, Taylor, JP, Joshi, J, Hillman-Jackson, J, Goecks, J, Chilton, JM, Kamali, K, Suderman, K, Poterlowicz, K, Yvan, LB, Lopez-Delisle, L, Sargent, L, Bassetti, ME, Tangaro, MA, van den Beek, M, Cech, M, Bernt, M, Fahrner, M, Tekman, M, Foell, MC, Schatz, MC, Crusoe, MR, Roncoroni, M, Kucher, N, Coraor, N, Stoler, N, Rhodes, N, Soranzo, N, Pinter, N, Goonasekera, NA, Moreno, PA, Videm, P, Melanie, P, Mandreoli, P, Jagtap, PD, Gu, Q, Weber, RJM, Lazarus, R, Vorderman, RHP, Hiltemann, S, Golitsynskiy, S, Garg, S, Bray, SA, Gladman, SL, Leo, S, Mehta, SP, Griffin, TJ, Jalili, V, Yves, V, Wen, V, Nagampalli, VK, Bacon, WA, de Koning, W, Maier, W, Briggs, PJ, Ostrovsky, AE, Mahmoud, A, Lonie, AJ, Syme, A, Fouilloux, A, Bretaudeau, A, Nekrutenko, A, Kumar, A, Eschenlauer, AC, DeSanto, AD, Guerler, A, Serrano-Solano, B, Batut, B, Gruening, BA, Langhorst, BW, Carr, B, Raubenolt, BA, Hyde, CJ, Bromhead, CJ, Barnett, CB, Royaux, C, Gallardo, C, Blankenberg, D, Fornika, DJ, Baker, D, Bouvier, D, Clements, D, Morais, DADL, Tabernero, DL, Lariviere, D, Nasr, E, Afgan, E, Zambelli, F, Heyl, F, Psomopoulos, F, Coppens, F, Price, GR, Cuccuru, G, Le Corguille, G, Von Kuster, G, Akbulut, GG, Rasche, H, Hans-Rudolf, H, Eguinoa, I, Makunin, I, Ranawaka, IJ, Taylor, JP, Joshi, J, Hillman-Jackson, J, Goecks, J, Chilton, JM, Kamali, K, Suderman, K, Poterlowicz, K, Yvan, LB, Lopez-Delisle, L, Sargent, L, Bassetti, ME, Tangaro, MA, van den Beek, M, Cech, M, Bernt, M, Fahrner, M, Tekman, M, Foell, MC, Schatz, MC, Crusoe, MR, Roncoroni, M, Kucher, N, Coraor, N, Stoler, N, Rhodes, N, Soranzo, N, Pinter, N, Goonasekera, NA, Moreno, PA, Videm, P, Melanie, P, Mandreoli, P, Jagtap, PD, Gu, Q, Weber, RJM, Lazarus, R, Vorderman, RHP, Hiltemann, S, Golitsynskiy, S, Garg, S, Bray, SA, Gladman, SL, Leo, S, Mehta, SP, Griffin, TJ, Jalili, V, Yves, V, Wen, V, Nagampalli, VK, Bacon, WA, de Koning, W, Maier, W, and Briggs, PJ

Abstract

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.

Published
2022

14. Maternally inherited differences in mitochondrial DNA genotype between ART and spontaneously conceived individuals associate with low birthweight

Author

Mertens, J., Belva, F., Van Montfoort, A., Zambelli, F., Seneca, S., de Deckersberg, E. Couvreu, Bonduelle, M., Tournaye, H., Stouffs, K., Barbe, K., Smeets, H., Van De Velde, H., Sermon, K., Blockeel, C., Spits, C., Basic (bio-) Medical Sciences, Faculty of Medicine and Pharmacy, Clinical sciences, Medical Genetics, Reproduction and Genetics, Vriendenkring VUB, Surgical clinical sciences, Biology of the Testis, Centre for Reproductive Medicine - Gynaecology, Radiation Therapy, Artificial Intelligence supported Modelling in clinical Sciences, Biostatistics and medical informatics, Digital Mathematics, Public Health Sciences, and Applied Physics and Photonics

Published
2021

16. O-184 Maternally inherited differences in mitochondrial DNA genotype between ART and spontaneously conceived individuals associate with low birthweight

Author

Mertens, J, primary, Belva, F, additional, Van Montfoort, A, additional, Zambelli, F, additional, Seneca, S, additional, Couvreu de Deckersberg, E, additional, Bonduelle, M, additional, Tournaye, H, additional, Stouffs, K, additional, Barbé, K, additional, Smeets, H, additional, Van de Velde, H, additional, Sermon, K, additional, Blockeel, C, additional, and Spits, C, additional

Published
2021
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17. Human oocyte meiotic maturation is associated with a specific profile of alternatively spliced transcript isoforms

Author

Cornet-Bartolomé D, Barragán M, Zambelli F, Ferrer-Vaquer A, Tiscornia G, Balcells S, Rodriguez A, Grinberg-Vaisman DR, and Vassena R

Subjects
alternative splicing, antral follicular count, human oocyte, developmental competence
Abstract

The transition from a transcriptionally active state (GV) to a transcriptionally inactive state (mature MII oocytes) is required for the acquisition of oocyte developmental competence. We hypothesize that the expression of specific genes at the in vivo matured (MII) stage could be modulated by posttranscriptional mechanisms, particularly regulation of alternative splicing (AS). In this study, we examined the transcriptional activity of GV oocytes after ovarian stimulation followed by oocyte pick-up and the landscape of alternatively spliced isoforms in human MII oocytes. Individual oocytes were processed and analyzed for transcriptional activity (GV), gene expression (GV and MII), and AS signatures (GV and MII) on HTA 2.0 microarrays. Samples were grouped according to maturation stage, and then subgrouped according to women's age and antral follicular count (AFC); array results were validated by quantitative polymerase chain reaction. Differentially expressed genes between GV and MII oocytes clustered mainly in biological processes related to mitochondrial metabolism. Interestingly, 16 genes that were related to the regulation of transcription and mitochondrial translation showed differences in alternatively spliced isoform profiles despite not being differentially expressed between groups. Altogether, our results contribute to our understanding of the role of AS in oocyte developmental competence acquisition.

Published
2021

19. The bio.tools registry of software tools and data resources for the life sciences

Author

Ison, J., Ienasescu, H., Chmura, P., Rydza, E., Menager, H., Kalas, M., Schwammle, V., Gruning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Varekova, R.S., Racek, T., Vondrasek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R., Nyronen, T., Valencia, A., Capella, S., Gelpi, J., Zambelli, F., Savakis, B., Leskosek, B., Rapacki, K., Blanchet, C, Jimenez, R., Oliveira, A., Vriend, G., Collin, O., Helden, Jacques van, Longreen, P., Brunak, S., Ison, J., Ienasescu, H., Chmura, P., Rydza, E., Menager, H., Kalas, M., Schwammle, V., Gruning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Varekova, R.S., Racek, T., Vondrasek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R., Nyronen, T., Valencia, A., Capella, S., Gelpi, J., Zambelli, F., Savakis, B., Leskosek, B., Rapacki, K., Blanchet, C, Jimenez, R., Oliveira, A., Vriend, G., Collin, O., Helden, Jacques van, Longreen, P., and Brunak, S.

Abstract

Contains fulltext : 208582.pdf (publisher's version ) (Open Access), Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.

Published
2019

20. Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance

Author

Bertolini, J, Favaro, R, Zhu, Y, Pagin, M, Ngan, C, Wong, C, Tjong, H, Vermunt, M, Martynoga, B, Barone, C, Mariani, J, Cardozo, M, Tabanera, N, Zambelli, F, Mercurio, S, Ottolenghi, S, Robson, P, Creyghton, M, Bovolenta, P, Pavesi, G, Guillemot, F, Nicolis, S, Wei, C, Bertolini, Jessica A., Favaro, Rebecca, Zhu, Yanfen, Pagin, Miriam, Ngan, Chew Yee, Wong, Chee Hong, Tjong, Harianto, Vermunt, Marit W., Martynoga, Ben, Barone, Cristiana, Mariani, Jessica, Cardozo, Marcos Julián, Tabanera, Noemi, Zambelli, Federico, Mercurio, Sara, Ottolenghi, Sergio, Robson, Paul, Creyghton, Menno P., Bovolenta, Paola, Pavesi, Giulio, Guillemot, Francois, Nicolis, Silvia K., Wei, Chia-Lin, Bertolini, J, Favaro, R, Zhu, Y, Pagin, M, Ngan, C, Wong, C, Tjong, H, Vermunt, M, Martynoga, B, Barone, C, Mariani, J, Cardozo, M, Tabanera, N, Zambelli, F, Mercurio, S, Ottolenghi, S, Robson, P, Creyghton, M, Bovolenta, P, Pavesi, G, Guillemot, F, Nicolis, S, Wei, C, Bertolini, Jessica A., Favaro, Rebecca, Zhu, Yanfen, Pagin, Miriam, Ngan, Chew Yee, Wong, Chee Hong, Tjong, Harianto, Vermunt, Marit W., Martynoga, Ben, Barone, Cristiana, Mariani, Jessica, Cardozo, Marcos Julián, Tabanera, Noemi, Zambelli, Federico, Mercurio, Sara, Ottolenghi, Sergio, Robson, Paul, Creyghton, Menno P., Bovolenta, Paola, Pavesi, Giulio, Guillemot, Francois, Nicolis, Silvia K., and Wei, Chia-Lin

Abstract

The SOX2 transcription factor is critical for neural stem cell (NSC) maintenance and brain development. Through chromatin immunoprecipitation (ChIP) and chromatin interaction analysis (ChIA-PET), we determined genome-wide SOX2-bound regions and Pol II-mediated long-range chromatin interactions in brain-derived NSCs. SOX2-bound DNA was highly enriched in distal chromatin regions interacting with promoters and carrying epigenetic enhancer marks. Sox2 deletion caused widespread reduction of Pol II-mediated long-range interactions and decreased gene expression. Genes showing reduced expression in Sox2-deleted cells were significantly enriched in interactions between promoters and SOX2-bound distal enhancers. Expression of one such gene, Suppressor of Cytokine Signaling 3 (Socs3), rescued the self-renewal defect of Sox2-ablated NSCs. Our work identifies SOX2 as a major regulator of gene expression through connections to the enhancer network in NSCs. Through the definition of such a connectivity network, our study shows the way to the identification of genes and enhancers involved in NSC maintenance and neurodevelopmental disorders

Published
2019

22. Gain of 20q11.21 in Human Pluripotent Stem Cells Impairs TGF-β-Dependent Neuroectodermal Commitment

Author

Markouli, C., primary, Couvreu De Deckersberg, E., additional, Regin, M., additional, Nguyen, H.T., additional, Zambelli, F., additional, Keller, A., additional, Dziedzicka, D., additional, De Kock, J., additional, Tilleman, L., additional, Van Nieuwerburgh, F., additional, Franceschini, L., additional, Sermon, K., additional, Geens, M., additional, and Spits, C., additional

Published
2019
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23. INDIGO-DataCloud: a platform to facilitate seamless access to e-infrastructures

Author

European Commission, Salomoni, Davide, Campos, Isabel, Gaido, Luciano, Marco, Jesús, Solagna, P., Gomes, Jorge, Matyska, Ludek, Fuhrmann, Patrick, Hardt, Marcus, Donvito, Giacinto, Dutka, L., Plociennik, Marcin, Barbera, R., Blanquer, Ignacio, Ceccanti, Andrea, Cetinic, E., David, Mario, Duma, Doina Cristina, López García, Álvaro, Moltó, Germán, Orviz, Pablo, Šustr, Zdenêk, Viljoen, M., Aguilar, Fernando, Alves, Lincoln M., Antonacci, Marica, Antonelli, L., Bagnasco, Stefano, Bonvin, A. M. J. J., Bruno, R., Chen, Y., Costa, A., Davidovic, D., Ertl, B., Fargetta, M., Fiore, S., Gallozzi, S., Kurkcuoglu, Z., Lloret Iglesias, Lara, Martins Careto, João António, Nuzzo, A., Nassisi, P., Palazzo, C., Pina, Joâo, Sciacca, E., Spiga, Daniele, Tangaro, M., Urbaniak, Michał, Vallero, Sara, Wegh, B., Zaccolo, Valentina, Zambelli, F., Zok, T., European Commission, Salomoni, Davide, Campos, Isabel, Gaido, Luciano, Marco, Jesús, Solagna, P., Gomes, Jorge, Matyska, Ludek, Fuhrmann, Patrick, Hardt, Marcus, Donvito, Giacinto, Dutka, L., Plociennik, Marcin, Barbera, R., Blanquer, Ignacio, Ceccanti, Andrea, Cetinic, E., David, Mario, Duma, Doina Cristina, López García, Álvaro, Moltó, Germán, Orviz, Pablo, Šustr, Zdenêk, Viljoen, M., Aguilar, Fernando, Alves, Lincoln M., Antonacci, Marica, Antonelli, L., Bagnasco, Stefano, Bonvin, A. M. J. J., Bruno, R., Chen, Y., Costa, A., Davidovic, D., Ertl, B., Fargetta, M., Fiore, S., Gallozzi, S., Kurkcuoglu, Z., Lloret Iglesias, Lara, Martins Careto, João António, Nuzzo, A., Nassisi, P., Palazzo, C., Pina, Joâo, Sciacca, E., Spiga, Daniele, Tangaro, M., Urbaniak, Michał, Vallero, Sara, Wegh, B., Zaccolo, Valentina, Zambelli, F., and Zok, T.

Abstract

This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud framework enhancements to manage the demanding requirements of scientific communities, either locally or through enhanced interfaces. The middleware developed allows to federate hybrid resources, to easily write, port and run scientific applications to the cloud. In particular, we have extended existing PaaS (Platform as a Service) solutions, allowing public and private e-infrastructures, including those provided by EGI, EUDAT, and Helix Nebula, to integrate their existing services and make them available through AAI services compliant with GEANT interfederation policies, thus guaranteeing transparency and trust in the provisioning of such services. Our middleware facilitates the execution of applications using containers on Cloud and Grid based infrastructures, as well as on HPC clusters. Our developments are freely downloadable as open source components, and are already being integrated into many scientific applications.

Published
2018

25. Tools and data services registry: a community effort to document bioinformatics resources

Author

Ison, J., Rapacki, K., Menager, H., Kalas, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G.D., Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Gruning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M.C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J.W., Licata, L., Mareuil, F., Micetic, I., Friborg, R.M., Moretti, S., Morris, C., Moller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwammle, V., Smith, C., Sperotto, M.M., Stockinger, H., Varekova, R.S., Tosatto, S.C., Torre, V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Longreen, P., Brunak, S., Ison, J., Rapacki, K., Menager, H., Kalas, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G.D., Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Gruning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M.C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J.W., Licata, L., Mareuil, F., Micetic, I., Friborg, R.M., Moretti, S., Morris, C., Moller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwammle, V., Smith, C., Sperotto, M.M., Stockinger, H., Varekova, R.S., Tosatto, S.C., Torre, V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Longreen, P., and Brunak, S.

Abstract

Contains fulltext : 171819.pdf (publisher's version ) (Open Access), Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

26. Tools and data services registry: A community effort to document bioinformatics resources

Author

Ison, J, Rapacki, K, Ménager, H, Kalaš, M, Rydza, E, Chmura, P, Anthon, C, Beard, N, Berka, K, Bolser, D, Booth, T, Bretaudeau, A, Brezovsky, J, Casadio, R, Cesareni, G, Coppens, F, Cornell, M, Cuccuru, G, Davidsen, K, DELLA VEDOVA, G, Dogan, T, Doppelt Azeroual, O, Emery, L, Gasteiger, E, Gatter, T, Goldberg, T, Grosjean, M, Grüning, B, Helmer Citterich, M, Ienasescu, H, Ioannidis, V, Jespersen, M, Jimenez, R, Juty, N, Juvan, P, Koch, M, Laibe, C, Li, J, Licata, L, Mareuil, F, Mičetić, I, Friborg, R, Moretti, S, Morris, C, Möller, S, Nenadic, A, Peterson, H, Profiti, G, Rice, P, Romano, P, Roncaglia, P, Saidi, R, Schafferhans, A, Schwämmle, V, Smith, C, Sperotto, M, Stockinger, H, Vařeková, R, Tosatto, S, de la Torre, V, Uva, P, Via, A, Yachdav, G, Zambelli, F, Vriend, G, Rost, B, Parkinson, H, Løngreen, P, Brunak, S, DELLA VEDOVA, GIANLUCA, Brunak, S., Ison, J, Rapacki, K, Ménager, H, Kalaš, M, Rydza, E, Chmura, P, Anthon, C, Beard, N, Berka, K, Bolser, D, Booth, T, Bretaudeau, A, Brezovsky, J, Casadio, R, Cesareni, G, Coppens, F, Cornell, M, Cuccuru, G, Davidsen, K, DELLA VEDOVA, G, Dogan, T, Doppelt Azeroual, O, Emery, L, Gasteiger, E, Gatter, T, Goldberg, T, Grosjean, M, Grüning, B, Helmer Citterich, M, Ienasescu, H, Ioannidis, V, Jespersen, M, Jimenez, R, Juty, N, Juvan, P, Koch, M, Laibe, C, Li, J, Licata, L, Mareuil, F, Mičetić, I, Friborg, R, Moretti, S, Morris, C, Möller, S, Nenadic, A, Peterson, H, Profiti, G, Rice, P, Romano, P, Roncaglia, P, Saidi, R, Schafferhans, A, Schwämmle, V, Smith, C, Sperotto, M, Stockinger, H, Vařeková, R, Tosatto, S, de la Torre, V, Uva, P, Via, A, Yachdav, G, Zambelli, F, Vriend, G, Rost, B, Parkinson, H, Løngreen, P, Brunak, S, DELLA VEDOVA, GIANLUCA, and Brunak, S.

Abstract

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

27. The LIBI Grid Platform for Bioinformatics

Author

The LIBI Grid Platform Developers, Italy, Mirto M, Fiore S, Negro A, Tartarini D, Lezzi D, Marra O, Turi A, Donvito G, Carota L, Cuscela G, Maggi GP, La Rocca G, Mazzucato M, My S, Selvaggi G, Scioscia G, Leo P, Di Pace L, Pappadà G, Quinto V, Berardi M, Falciano F, Emerson A, Rossi E, Lavorgna G, Vanni A, Bartoli L, Di Lena P, Fariselli P, Fronza R, Margara L, Montanucci L, Martelli PL, Rossi I, Vassura M, Casadio R, Castrignanò T, D’Elia D, Grillo G, Licciulli F, Liuni S, Gisel A, Santamaria M, Vicario S, Saccone C, Anselmo A, Horner D, Mignone F, Pavesi G, Picardi E, Piccolo V, Re M, Zambelli F, Pesole G., EPICOCO, Italo, CAFARO, Massimo, FERRAMOSCA, Alessandra, ZARA, Vincenzo, ALOISIO, Giovanni, The LIBI Grid Platform Developers, Italy, Mirto, M, Epicoco, Italo, Fiore, S, Cafaro, Massimo, Negro, A, Tartarini, D, Lezzi, D, Marra, O, Turi, A, Ferramosca, Alessandra, Zara, Vincenzo, Aloisio, Giovanni, Donvito, G, Carota, L, Cuscela, G, Maggi, Gp, La Rocca, G, Mazzucato, M, My, S, Selvaggi, G, Scioscia, G, Leo, P, Di Pace, L, Pappadà, G, Quinto, V, Berardi, M, Falciano, F, Emerson, A, Rossi, E, Lavorgna, G, Vanni, A, Bartoli, L, Di Lena, P, Fariselli, P, Fronza, R, Margara, L, Montanucci, L, Martelli, Pl, Rossi, I, Vassura, M, Casadio, R, Castrignanò, T, D’Elia, D, Grillo, G, Licciulli, F, Liuni, S, Gisel, A, Santamaria, M, Vicario, S, Saccone, C, Anselmo, A, Horner, D, Mignone, F, Pavesi, G, Picardi, E, Piccolo, V, Re, M, Zambelli, F, and Pesole, G.

Subjects
Bioinformatics, Grid Computing
Abstract

The LIBI project (International Laboratory of BioInformatics), which started in 2005 and will end in 2009, was initiated with the aim of setting up an advanced bioinformatics and computational biology laboratory, focusing on basic and applied research in modern biology and biotechnologies. One of the goals of this project has been the development of a Grid Problem Solving Environment, built on top of EGEE, DEISA and SPACI infrastructures, to allow the submission and monitoring of jobs mapped to complex experiments in bioinformatics. In this work we describe the architecture of this environment and describe several case studies and related results which have been obtained using it.

Published
2009

32. The LIBI Grid Platform an International Laboratory for Bioinformatics

Author

Mirto, M., Epicoco, I., Fiore, S., Cafaro, M., Ferramosca, A., Zara, V., Scioscia, ALOISIO G SCIOSCIA G. ALOISIO G., Leo, P., Donvito, G., Cuscela, G., Maggi, G., Pierro, A., Falciano, F., Rossi, E., Castrignano', T., Fariselli, P., Fronza, R., Margara, L., Montanucci, L., Martelli, P. L., Rossi, I., Vassura, M., DI LENA, P., Casadio, R., Anselmo, A., Grillo, G., Horner, D., Licciulli, F., Liuni, S., Gisel, A., Mignone, F., Pavesi, G., Pesole, G., Picardi, E., Piccolo, V., Re, M., Saccone, C., Santamaria, M., Vicario, S., Zambelli, F., M. Mirto, I. Epicoco, S. Fiore, M. Cafaro, A. Ferramosca, V. Zara, G. Aloisio G. Scioscia, P. Leo, G. Donvito, G. Cuscela, G. Maggi, A. Pierro, F. Falciano, E. Rossi, T. Castrignanò, P. Fariselli, R. Fronza, L. Margara, L. Montanucci, P. L. Martelli, I. Rossi, M. Vassura, P. Di Lena, R. Casadio, A. Anselmo, G. Grillo, D. Horner, F. Licciulli, S. Liuni, A. Gisel, F. Mignone, G. Pavesi, G. Pesole, E. Picardi, V. Piccolo, M. Re, C. Saccone, M. Santamaria, S. Vicario, and F. Zambelli

Abstract

The International Laboratory of BioInformatics (LIBI - www.libi.it) aims at setting up of an advanced Bioinformatics and Computational Biology Laboratory, focusing on the central activities of basic and applied research in modern Biology and Biotechnologies. The main activities include the construction and the maintenance of general genomic, proteomic and transcriptomic databases (e.g. ENSEMBL) as well as specialized databases developed by LIBI partners (e.g. MitoRes, UTRdb, UTRSite, ASPicDB, CSTdb, etc.); the design and implementation of new algorithms and software for the analysis of genomes and their expression products and for the prediction of the structure of proteins; the development of a Grid Problem Solving Environment in order to exploit the distributed computational infrastructure.

Published
2008

33. Formazione degli insegnanti e ricerca didattica universitaria

Author

Messina, Laura and Zambelli, F.

Subjects
ricerca didattica universitaria, ricerca didattica universitaria, centri di ateneo per l'insegnamento e l'apprendimento,formazione degli insegnanti, centri di ateneo per l'insegnamento e l'apprendimento, formazione degli insegnanti
Published
2008

35. Finite size effects on the collective oscillations of a trapped Bose gas

Author

Zambelli, F. and Sandro Stringari

Subjects
Condensed Matter::Quantum Gases, High Energy Physics::Lattice, Condensed Matter (cond-mat), FOS: Physical sciences, Condensed Matter
Abstract

Sum rules are used to calculate the corrections to the hydrodynamic collective frequencies of a harmonically trapped Bose gas at T=0, due to finite size effects. We show that, with logarithmic accuracy, the relative corrections behave like $(a_{ho}/R)^4\log(R/a_{ho})$, where $R$ is the Thomas-Fermi radius of the condensate and $a_{ho}$ is the oscillator length. Results are given for both spherical and axi-symmetric trapping., 10 pages

Published
2001

36. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

Author

Martelli, P, D'Antonio, M, Bonizzoni, P, Castrignanò, T, D'Erchia, A, D'Onorio De Meo, P, Fariselli, P, Finelli, M, Licciulli, F, Mangiulli, M, Mignone, F, Pavesi, G, Picardi, E, Rizzi, R, Rossi, I, Valletti, A, Zauli, A, Zambelli, F, Casadio, R, Pesole, G, Martelli, PL, D'Erchia, AM, Pesole, G., BONIZZONI, PAOLA, RIZZI, RAFFAELLA, Martelli, P, D'Antonio, M, Bonizzoni, P, Castrignanò, T, D'Erchia, A, D'Onorio De Meo, P, Fariselli, P, Finelli, M, Licciulli, F, Mangiulli, M, Mignone, F, Pavesi, G, Picardi, E, Rizzi, R, Rossi, I, Valletti, A, Zauli, A, Zambelli, F, Casadio, R, Pesole, G, Martelli, PL, D'Erchia, AM, Pesole, G., BONIZZONI, PAOLA, and RIZZI, RAFFAELLA

Abstract

Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256939 protein variants from 17191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www.caspur.it/ASPicDB/.

Published
2011

37. MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes

Author

Pavesi, G, Mereghetti, P, Zambelli, F, Stefani, M, Mauri, G, Pesole, G, Pesole, G., MAURI, GIANCARLO, Pavesi, G, Mereghetti, P, Zambelli, F, Stefani, M, Mauri, G, Pesole, G, Pesole, G., and MAURI, GIANCARLO

Abstract

Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif Discovery) Tools web server comprises a set of tools for the discovery of novel conserved sequence and structure motifs in nucleotide sequences, motifs that in turn are good candidates for regulatory activity. The server includes the following programs: Weeder, for the discovery of conserved transcription factor binding sites (TFBSs) in nucleotide sequences from co-regulated genes; WeederH, for the discovery of conserved TFBSs and distal regulatory modules in sequences from homologous genes; RNAProfile, for the discovery of conserved secondary structure motifs in unaligned RNA sequences whose secondary structure is not known. In this way, a given gene can be compared with other co-regulated genes or with its homologs, or its mRNA can be analyzed for conserved motifs regulating its post-transcriptional fate. The web server thus provides researchers with different strategies and methods to investigate the regulation of gene expression, at both the transcriptional and post-transcriptional levels. Available at http://www.pesolelab.it/modtools/ and http://www.beacon.unimi. it/modtools/.

Published
2006

39. POSTER VIEWING SESSION - STEM CELLS

Author

O'Leary, T., primary, Heindryckx, B., additional, Lierman, S., additional, De Sutter, P., additional, Shlush, K., additional, Fainaru, O., additional, Grosman, G., additional, Faraji, G., additional, Michaeli, M., additional, Hallak, M., additional, Ellenbogen, A., additional, Zambelli, F., additional, Magli, M. C., additional, Stanghellini, I., additional, Ferraretti, A. P., additional, Ventura, C., additional, Gianaroli, L., additional, Mas, A., additional, Cervello, I., additional, Gil-Sanchis, C., additional, Peris-Pardo, L., additional, Faus, A., additional, Ferro, J., additional, Pellicer, A., additional, Simon, C., additional, Kobayashi, M., additional, Kurotaki, Y., additional, Takeuchi, T., additional, Yoshida, A., additional, Behjati, R., additional, Kawai, K., additional, Kano, J., additional, Akhondi, M. A., additional, Akaza, H., additional, Noguchi, M., additional, Desai, N., additional, Tsulaia, T., additional, Xu, J., additional, Anand, R., additional, Goldberg, J., additional, Falcone, T., additional, Eguizabal, C., additional, Montserrat, N., additional, Vassena, R., additional, Barragan, M., additional, Garreta, E., additional, Garcia-Quevedo, L., additional, Vidal, F., additional, Giorgetti, A., additional, Veiga, A., additional, Ispizua-Belmonte, J. C., additional, Carrasco, B., additional, Boada, M., additional, Coroleu, B., additional, Izpisua, J. C., additional, Chikhovskaya, J. V., additional, Repping, S., additional, van Pelt, A. M. M., additional, Namm, A., additional, Arend, A., additional, Aunapuu, M., additional, Duggal, G., additional, O'Leary, T., additional, Deforce, D., additional, Chuva de Sousa Lopes, S., additional, Koruji, M., additional, Janan, A., additional, Azizi, H., additional, Mirzapour, T., additional, Shahverdi, A., additional, Baharvand, H., additional, Medrano, J. V., additional, Nguyen, H. N., additional, Ramathal, C., additional, Reijo Pera, R. A., additional, Salit, M., additional, Sabry, D., additional, Azmy, O., additional, Al-Inany, H., additional, Montico, F., additional, Hetzl, A. C., additional, Billis, A., additional, Favaro, W. J., additional, Cagnon, V. H. A., additional, Ben - Yosef, D., additional, Amit, A., additional, Malcov, M., additional, Frumkin, T., additional, Eldar, I., additional, Mei Raz, N., additional, Shwartz, T., additional, Azem, F., additional, Altarescu, G., additional, Beeri, B., additional, Varshaver, I., additional, Eldar-Geva, T., additional, Epsztejn-Litman, S., additional, Levy-Lahad, E., additional, Eiges, R., additional, Sergeev, S. A., additional, Khramova, Y. V., additional, Kosheleva, N. V., additional, Saburina, I. N., additional, and Semenova, M. L., additional

Published
2011
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40. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

Author

Martelli, P. L., primary, D'Antonio, M., additional, Bonizzoni, P., additional, Castrignano, T., additional, D'Erchia, A. M., additional, D'Onorio De Meo, P., additional, Fariselli, P., additional, Finelli, M., additional, Licciulli, F., additional, Mangiulli, M., additional, Mignone, F., additional, Pavesi, G., additional, Picardi, E., additional, Rizzi, R., additional, Rossi, I., additional, Valletti, A., additional, Zauli, A., additional, Zambelli, F., additional, Casadio, R., additional, and Pesole, G., additional

Published
2010
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41. Momentum Distribution Of A Bose Condensed Trapped Gas

Author

Martellucci, Sergio, Chester, Arthur N., Aspect, Alain, Inguscio, Massimo, Stringari, S., Pitaevskii, L., Stamper-Kurn, D. M., Zambelli, F., Martellucci, Sergio, Chester, Arthur N., Aspect, Alain, Inguscio, Massimo, Stringari, S., Pitaevskii, L., Stamper-Kurn, D. M., and Zambelli, F.

Abstract

A peculiarity of trapped atomic gases is that Bose-Einstein condensation (BEC) shows up not only in momentum space, where it is usually discussed in traditional textbooks, but also in coordinate space. This is the consequence of the inhomogeneity of these systems, which makes it possible to separate the condensate from the thermal component also in coordinate space. Actually, most of measurements in trapped gases have been so far limited to the study of density profiles and of the effects of BEC in coordinate space. The possibility of a direct measurement of the momentum distribution, as emerged from recent experiments based on two-photon Bragg scattering, is highly appealing. In fact, despite the inhomogeneity of the gas, BEC shows up more deeply in momentum than in coordinate space. In current experiments on harmonically-confined Bose gases, the sizes of the condensate R and of the thermal cloud R_T are in fact typically comparable.

Published
2002

50. Vortex nucleation and quadrupole deformation of a rotating Bose-Einstein condensate

Author

Krämer, M., Pitaevskii, L., Sandro Stringari, and Zambelli, F.

Subjects
Condensed Matter::Quantum Gases, Condensed Matter (cond-mat), FOS: Physical sciences, Condensed Matter
Abstract

Using a semi-analytic model based on the Thomas-Fermi approximation, we investigate the relevance of the quadrupole deformation of a trapped Bose-Einstein condensate for the nucleation of quantized vortices. For sufficiently high angular velocities $\Omega$ of the trap, the tendency of the system to exhibit spontaneous deformation is shown to lower the barrier which inhibits the nucleation of vortices at smaller $\Omega$. The corresponding value of the critical angular velocity $\Omega_c$ is calculated as a function of the deformation of the trap and of the chemical potential. The theoretical predictions for $\Omega_c$ refer to the case of a sudden switch-on of the deformed rotating trap and they are compared with recent experimental data., Comment: 12 pages, 4 postscript figures

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