Mr Alan Williams

Senior Research Software Engineer

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Publications

  1. 2020
  2. Published

    Landscape Analysis for the Specimen Data Refinery

    Walton, S., Livermore, L., Bánki, O., Cubey, R., Drinkwater, R., Englund, M., Goble, C., Groom, Q., Kermorvant, C., Rey, I., Santos, C., Scott, B., Williams, A. & Wu, Z., 14 Aug 2020, In: Research Ideas and Outcomes. 6, 25 p., e57602.

    Research output: Contribution to journalArticlepeer-review

  3. 2018
  4. Accepted/In press

    FAIR Bioinformatics computation and data management: FAIRDOM and the Norwegian Digital Life initiative

    Stanford, N., Bacall, F., Zamanzad Ghavidel, F., Golebiewski, M., Jonassen, I., Kleppe, R., Krebs, O., Leonov, H., Owen, S., Peterson, K., Rey, M., Soiland-Reyes, S., Tekle, K., Weiderman, A., Williams, A., Wittig, U., Wolstencroft, K., Goksøyr, A., Snoep, J., Vik, J. O. & 2 others, Müller, W. & Goble, C., 4 Sep 2018, (Accepted/In press). 4 p.

    Research output: Contribution to conferenceAbstractpeer-review

  5. 2017
  6. Published

    Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

    McMurry, J. A., Juty, N., Blomberg, N., Burdett, T., Conlin, T., Conte, N., Courtot, M., Deck, J., Dumontier, M., Fellows, D., Gonzalez-Beltran, A., Gormanns, P., Grethe, J., Hastings, J., Hériché, J-K., Hermjakob, H., Ison, J. C., Jimenez, R. C., Jupp, S., Kunze, J. & 24 others, Laibe, C., Le Novère, N., Malone, J., Martin, M. J., McEntyre, J. R., Morris, C., Muilu, J., Müller, W., Rocca-Serra, P., Sansone, S. A., Sariyar, M., Snoep, J. L., Soiland-Reyes, S., Stanford, N. J., Swainston, N., Washington, N., Williams, A. R., Wimalaratne, S. M., Winfree, L. M., Wolstencroft, K., Goble, C., Mungall, C. J., Haendel, M. A. & Parkinson, H., 29 Jun 2017, In: PLoS Biology. 15, 6, 18 p., e2001414.

    Research output: Contribution to journalArticlepeer-review

  7. Published

    biochem4j: integrated and extensible biochemical knowledge through graph databases

    Swainston, N., Batista-Navarro, R. T., Carbonell, P., Dobson, P., Dunstan, M., Jervis, A., Vinaixa, M., Williams, A., Ananiadou, S., Faulon, J-L., Pedrosa Mendes, P., Kell, D., Scrutton, N. & Breitling, R., 2017, In: PLoS ONE. 12, 7, e0179130.

    Research output: Contribution to journalArticlepeer-review

  8. 2016
  9. Published

    BioVeL: A virtual laboratory for data analysis and modelling in biodiversity science and ecology

    Hardisty, A. R., Bacall, F., Beard, N., Balcázar-Vargas, M. P., Balech, B., Barcza, Z., Bourlat, S. J., Giovanni, R., Jong, Y., Leo, F., Dobor, L., Donvito, G., Fellows, D., Guerra, A. F., Ferreira, N., Fetyukova, Y., Fosso, B., Giddy, J., Goble, C., Güntsch, A. & 32 others, Haines, R., Ernst, V. H., Hettling, H., Hidy, D., Horváth, F., Ittzés, D., Ittzés, P., Jones, A., Kottmann, R., Kulawik, R., Leidenberger, S., Lyytikäinen-Saarenmaa, P., Mathew, C., Morrison, N., Nenadic, A., Hidalga, A. N., Obst, M., Oostermeijer, G., Paymal, E., Pesole, G., Pinto, S., Poigné, A., Fernandez, F. Q., Santamaria, M., Saarenmaa, H., Sipos, G., Sylla, K. H., Tähtinen, M., Vicario, S., Vos, R. A., Williams, A. & Yilmaz, P., 20 Oct 2016, In: Ecology. 16, 1, 49.

    Research output: Contribution to journalArticlepeer-review

  10. Published

    SYNBIOCHEM - A SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals.

    Carbonell, P., Currin, A., Dunstan, M., Fellows, D., Jervis, A., Rattray, N. J. W., Robinson, C. J., Swainston, N., Vinaixa, M., Williams, A., Yan, C., Barran, P., Breitling, R., Chen, G. G-Q., Faulon, J-L., Goble, C., Goodacre, R., Kell, D. B., Feuvre, R. L., Micklefield, J. & 4 others, Scrutton, N. S., Shapira, P., Takano, E. & Turner, N. J., 15 Jun 2016, In: Biochemical Society Transactions. 44, 3, p. 675-7

    Research output: Contribution to journalArticlepeer-review

  11. Accepted/In press

    FAIRDOM: Reproducible Systems Biology through FAIR Asset Management

    Stanford, N., Bacall, F., Golebiewski, M., Krebs, O., Kuzyakiv, R., Nguyen, Q., Owen, S., Soiland-Reyes, S., Straszewski, J., van Niekerk, D., Williams, A., Wolstencroft, K., Malmström, L., Rinn, B., Snoep, J., Müller, W. & Goble, C., 2016, (Accepted/In press). 5 p.

    Research output: Contribution to conferencePaperpeer-review

  12. Published

    SYNBIOCHEM Synthetic Biology Research Centre, Manchester - A UK foundry for fine and speciality chemicals production

    Feuvre, R. L., Carbonell, P., Currin, A., Dunstan, M., Fellows, D., Jervis, A., Rattray, N. J. W., Robinson, C. J., Swainston, N., Vinaixa, M., Williams, A., Yan, C., Barran, P., Breitling, R., Chen, G. G-Q., Faulon, J-L., Goble, C., Goodacre, R., Kell, D. B., Micklefield, J. & 4 others, Scrutton, N. S., Shapira, P., Takano, E. & Turner, N. J., 2016, In: Synthetic and Systems Biotechnology.

    Research output: Contribution to journalArticlepeer-review

  13. 2015
  14. Published

    Towards a Data Science Collaboratory

    Vanschoren, J., Bischl, B., Hutter, F., Sebag, M., Kegl, B., Schmid, M., Napolitano, G., Wolstencroft, K., Williams, A. & Lawrence, N., 1 Oct 2015, In: LNCS. 9385 , p. XIX-XXI 3 p.

    Research output: Contribution to journalArticlepeer-review

  15. Published

    ENM Components: a new set of web service-based workflow components for ecological niche modelling

    De Giovanni, R., Williams, A., Hernandez Ernst, V., Kulawik, R., Quevedo Fernandez, F. & Hardisty, A., 1 Jul 2015, In: Ecography. 39, 4, p. 376-383 8 p.

    Research output: Contribution to journalArticlepeer-review

  16. Published

    Mapping present and future potential distribution patterns for a meso-grazer guild in the Baltic Sea

    Leidenberger, S., De Giovanni, R., Kulawik, R., Williams, A. & Bourlat, S. J., 1 Feb 2015, In: Journal of Biogeography. 42, 2, p. 241-254 14 p.

    Research output: Contribution to journalArticlepeer-review

  17. 2014
  18. Published

    Taverna Tutorials 2014-09-01 (Bonn): Training material

    Wolstencroft, K., Pawlik, A., Williams, A. R., Li, P., Morrison, N., Soiland-Reyes, S. & Brenninkmeijer, C., 1 Sep 2014

    Research output: Other contribution

  19. Published

    A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control

    Mathew, C., Güntsch, A., Obst, M., Vicario, S., Haines, R., Williams, A., de Jong, Y. & Goble, C., 2014, In: Biodiversity data journal. 2, p. e4221

    Research output: Contribution to journalArticlepeer-review

  20. Published

    DistillFlow: removing redundancy in scientific workflows

    Chen, J., Boulakia, S. C., Froidevaux, C., Goble, C. A., Missier, P. & Williams, A., 2014, Conference on Scientific and Statistical Database Management, SSDBM '14, Aalborg, Denmark, June 30 - July 02, 2014.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  21. Published

    Distilling structure in Taverna scientific workflows: a refactoring approach.

    Cohen-Boulakia, S., Chen, J., Missier, P., Goble, C., Williams, A. & Froidevaux, C., 2014, In: BMC Bioinformatics. 15, p. S12

    Research output: Contribution to journalArticlepeer-review

  22. Published

    Enriched biodiversity data as a resource and service

    Vos, R. A., Biserkov, J. V., Balech, B., Beard, N., Blissett, M., Brenninkmeijer, C., van Dooren, T., Eades, D., Gosline, G., Groom, Q. J., Hamann, T. D., Hettling, H., Hoehndorf, R., Holleman, A., Hovenkamp, P., Kelbert, P., King, D., Kirkup, D., Lammers, Y., DeMeulemeester, T. & 15 others, Mietchen, D., Miller, J. A., Mounce, R., Nicolson, N., Page, R., Pawlik, A., Pereira, S., Penev, L., Richards, K., Sautter, G., Shorthouse, D. P., Tähtinen, M., Weiland, C., Williams, A. & Sierra, S., 2014, In: Biodiversity data journal. 2, p. e1125

    Research output: Contribution to journalArticlepeer-review

  23. 2013
  24. Published

    The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud.

    Wolstencroft, K., Haines, R., Fellows, D., Williams, A., Withers, D., Owen, S., Soiland-Reyes, S., Dunlop, I., Nenadic, A., Fisher, P., Bhagat, J., Belhajjame, K., Bacall, F., Hardisty, A., Nieva de la Hidalga, A., Balcazar Vargas, M. P., Sufi, S. & Goble, C., Jul 2013, In: Nucleic acids research.. 41, p. W557-561

    Research output: Contribution to journalArticlepeer-review

  25. 2012
  26. Published

    Distilling structure in scientific workflows

    Chen, J., Froidevaux, C., Goble, C., Williams, A. & Cohen-Boulakia, S., 2012, In: EMBnet.journal. 18, B

    Research output: Contribution to journalArticlepeer-review

  27. Published

    Opening new gateways to workflows for life scientists

    Karasavvas, K., Wolstencroft, K., Mina, E., Cruickshank, D., Williams, A., De Roure, D., Goble, C. & Roos, M., 2012, In: Studies in Health Technology and Informatics. 175, p. 131-141 10 p.

    Research output: Contribution to journalArticlepeer-review

  28. 2011
  29. Published

    Scufl2 – because a workflow is more than its definition

    Soiland-Reyes, S., Williams, A., Owen, S., Withers, D. & Goble, C., 15 Jun 2011, p. 37-37. 1 p.

    Research output: Contribution to conferenceAbstractpeer-review

  30. Published

    An experimental workflow development platform for historical document digitisation and analysis

    Neudecker, C., Schlarb, S., Dogan, Z. M., Missier, P., Sufi, S., Williams, A. & Wolstencroft, K., 2011, ACM International Conference Proceeding Series|ACM Int. Conf. Proc. Ser.. Association for Computing Machinery, p. 161-168 7 p. (HIP '11).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  31. Published

    Combining RapidMiner Operators with Bioinformatics Services - A Powerful Combination

    Jupp, S., Eales, J., Fischer, S., Land, S., Ramgolam, R., Williams, A. & Stevens, R., 2011, Proceedings of the 2nd RapidMiner Community Meeting and Conference. Fischer, S. & Mierswa, I. (eds.). p. 75-86 12 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  32. Published

    The RapidMiner Plugin for Taverna: Bringing Data Mining Tools to Bioinformatics Workflows

    Jupp, S., Eales, J., Fischer, S., Land, S., Ramgolam, R., Williams, A. & Stevens, R., 2011, Bioinformatics Open Source Conference 2011, a SIG held in conjuction with ISMB 2011.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  33. 2010
  34. Published

    Community-driven computational biology with Debian Linux

    Möller, S., Krabbenhöft, H. N., Tille, A., Paleino, D., Williams, A., Wolstencroft, K., Goble, C., Holland, R., Belhachemi, D. & Plessy, C., 21 Dec 2010, In: BMC Bioinformatics. 11, 12, S5.

    Research output: Contribution to journalArticlepeer-review

  35. Published

    Community-driven computational biology with Debian and Taverna

    Moeller, S., Krabbenhoeft, H., Tille, A., Paleino, D., Williams, A., Wolstencroft, K., Goble, C. & Plessy, C., Jul 2010, BOSC 2010.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  36. Published

    Taverna, reloaded

    Missier, P., Soiland-Reyes, S., Owen, S., Tan, W., Nenadic, A., Dunlop, I., Williams, A., Oinn, T. & Goble, C., 2010, In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6187, p. 471-481 10 p.

    Research output: Contribution to journalArticlepeer-review

  37. 2008
  38. Published

    Metadata management in the taverna workflow system

    Belhajjame, K., Wolstencroft, K., Corcho, O., Oinn, T., Tanoh, F., William, A., Goble, C. & Williams, A., 2008, Proceedings CCGRID 2008 - 8th IEEE International Symposium on Cluster Computing and the Grid|Proc. CCGRID - IEEE Int. Symp. Cluster Comput. Grid. IEEE Computer Society , p. 651-656 5 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  39. 2007
  40. Published

    Data integration in eHealth: A domain/disease specific roadmap

    Ure, J., Procter, R., Martone, M., Porteous, D., Lloyd, S., Lawrie, S., Job, D., Baldock, R., Philp, A., Liewald, D., Rakebrandt, F., Blaikie, A., McKay, C., Anderson, S., Ainsworth, J., Van Hemert, J., Blanquer, I., Sinnott, R., Barillot, C., Gibaud, F. B. & 17 others, Williams, A., Hartswood, M., Watson, P., Smith, L., Burger, A., Kennedy, J., Gonzalez-Velez, H., Stevens, R., Corcho, O., Morton, R., Linksted, P., Deschenes, M., McGilchrist, M., Johnson, P., Voss, A., Gertz, R. & Wardlaw, J., 2007, In: Studies in Health Technology and Informatics. 126, p. 144-153 9 p.

    Research output: Contribution to journalArticlepeer-review

  41. 2006
  42. Published

    Web Services for Digital Mammography Research

    Rose, CJ., Turi, D., Williams, AR., Wolstencroft, KJ. & Taylor, CJ., 2006, In: Proceedings of Medical Image Understanding and Analysis. 2

    Research output: Contribution to journalArticlepeer-review

  43. Published

    Web services for the DDSM and digital mammography research

    Rose, C., Turi, D., Williams, A., Wolstencroft, K. & Taylor, C., 2006, In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4046, p. 376-383 7 p.

    Research output: Contribution to journalArticlepeer-review

  44. 2001
  45. Published

    A generic framework for transforming EXPRESS information models

    Kahn, H., Filer, N., Williams, A. & Whitaker, N., Jun 2001, In: CAD Computer Aided Design. 33, 7, p. 501-510 9 p.

    Research output: Contribution to journalArticlepeer-review

  46. 2000
  47. Published

    Geotechnical site investigation: A model based study

    Kahn, H. J., Williams, A. R. & Filer, N. R., 2000, Product and process modelling in building and construction : proceedings of the third European Conference on Product and Process Modelling in the Building and Related Industries, Lisbon, Portugal, 25-27, September 2000 /. Gonçalves, R. (ed.). A. A. Balkema, p. 275-284

    Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

  48. Published

    Knowledge management in the designer/constructor interface

    McCarthy, TJ., Kahn, HJ., Elhag, TMS., Williams, AR., Milburn, R. & Patel, MB., 2000, Computing in civil and building engineering: proceedings of the eighth international conference : August 14-16, 2000, Stanford University, Stanford, California . Fruchter, R. (ed.). Reston, Va.: American Society of Civil Engineers, p. 836-843 8 p.

    Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

  49. Published

    Transforming information models to support the generation of efficient implementations

    Kahn, H. J., Filer, N. P., Williams, A. R., Whitaker, N. A. & Reilly, D. J., 2000, Proceedings of the Hawaii International Conference on System Sciences|Proc Hawaii Int Conf Syst Sci. Los Alamitos, CA, United States: IEEE, p. 244

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  50. 1996
  51. Published

    EDIF Version 4 0 0

    Williams, A. & Association, E. I., 1996, In: ANSI/EIA 682-1996 Standard.

    Research output: Contribution to journalArticlepeer-review

  52. 1995
  53. Published

    EDIF technical centre

    Clark, J., Kahn, H., Roth, G., Whitaker, N. & Williams, A., Oct 1995, In: Circuit Design. 12, 10, p. 17-19 2 p.

    Research output: Contribution to journalArticlepeer-review

  54. 1992
  55. Published

    IMG information model of EDIF version 2 0 0. Version 1.0

    Henderson, R., Lau, R., Scholz, G., Ungerer, M., Williams, A. & Wilkes, W., 1992, In: Unknown Journal.

    Research output: Contribution to journalArticlepeer-review

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Research output: Contribution to conferenceAbstractpeer-review

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Research output: Contribution to journalArticlepeer-review

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Research output: Contribution to conferencePaperpeer-review

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Research output: Contribution to conferenceAbstractpeer-review