I mocked up a Publications page on my blog. https://galenaylor.wordpress.com/2016/01/11/references-and-publications/ (Wordpress did not like the 4th level headers (e.g., ####2015), so I would fix that, of course.)
It seems like this should be two pages: one for how to reference Taverna and the website, and one to list relevant publications. Also, I wasn't sure what to do about the reference to the latest canonical citations. Does this seem like a good start, or what should be changed? (Sorry for the long emails with abstracts. I just now found the direct links to the papers.) Gale On Mon, Jan 11, 2016 at 1:48 PM Gale Naylor <ga...@noventussolutions.com> wrote: > What about this paper from October 2014? Would you want to include this on > a publications page? > > Title: BIFI: a Taverna plugin for a simplified and user-friendly workflow > platform. > > Authors: Yildiz A; Dilaveroglu E; Visne I; Günay B; Sefer E; Weinhausel > A; Rattay F; Goble CA; Pandey RV; Kriegner A (Health & Environment > Department, AIT Austrian Institute of Technology GmbH, Vienna, Austria. > albert.krieg...@ait.ac.at.) > > Source: BMC Research Notes [BMC Res Notes] 2014 Oct 20; Vol. 7, pp. 740. > Date of Electronic Publication: 2014 Oct 20. > > Journal Info: Publisher: Biomed Central Country of Publication: England > NLM ID: 101462768 Publication Model: Electronic Cited Medium: Internet > ISSN: 1756-0500 (Electronic) Linking ISSN: 17560500 NLM ISO Abbreviation: > BMC Res Notes Subsets: MEDLINE > > Abstract: Background: Heterogeneity in the features, input-output > behaviour and user interface for available bioinformatics tools and > services is still a bottleneck for both expert and non-expert users. > Advancement in providing common interfaces over such tools and services are > gaining interest among researchers. However, the lack of (meta-) > information about input-output data and parameter prevents to provide > automated and standardized solutions, which can assist users in setting the > appropriate parameters. These limitations must be resolved especially in > the workflow-based solution in order to ease the integration of software. > > Findings: We report a Taverna Workbench plugin: the XworX BIFI (Beautiful > Interfaces for Inputs) implemented as a solution for the aforementioned > issues. BIFI provides a Graphical User Interface (GUI) definition language > used to layout the user interface and to define parameter options for > Taverna workflows. BIFI is also able to submit GUI Definition Files (GDF) > directly or discover appropriate instances from a configured repository. In > the absence of a GDF, BIFI generates a default interface. > > Conclusion: The Taverna Workbench is an open source software providing the > ability to combine various services within a workflow. Nevertheless, users > can supply input data to the workflow via a simple user interface providing > only a text area to enter the input in text form. The workflow may contain > meta-information in human readable form such as description text for the > port and an example value. However, not all workflow ports are documented > so well or have all the required information.BIFI uses custom user > interface components for ports which give users feedback on the parameter > data type or structure to be used for service execution and enables > client-side data validations. Moreover, BIFI offers user interfaces that > allow users to interactively construct workflow views and share them with > the community, thus significantly increasing usability of heterogeneous, > distributed service consumption. > > DOI: 10.1186/1756-0500-7-740 > > > On Mon, Jan 11, 2016 at 1:01 PM Gale Naylor <ga...@noventussolutions.com> > wrote: > >> On the other hand, I found this September 2015 paper on EBSCOHost, and it >> looks promising: >> >> Title: Scientific workflow optimization for improved peptide and protein >> identification. >> Authors: Holl, Sonja; Mohammed, Yassene; Zimmermann, Olav; Palmblad, >> Magnus (n.m.palmb...@lumc.nl) >> >> Source: BMC Bioinformatics. 9/3/2015, Vol. 16 Issue 1, p1-13. 13p. 1 >> Color Photograph, 1 Diagram, 3 Charts, 4 Graphs. >> >> Author-Supplied Keywords: Optimization, Scientific workflow, Tandem mass >> spectrometry, Taverna workbench, X!Tandem >> >> Abstract: Background: Peptide-spectrum matching is a common step in most >> data processing workflows for mass spectrometry-based proteomics. Many >> algorithms and software packages, both free and commercial, have been >> developed to address this task. However, these algorithms typically require >> the user to select instrument- and sample-dependent parameters, such as >> mass measurement error tolerances and number of missed enzymatic cleavages. >> In order to select the best algorithm and parameter set for a particular >> dataset, in-depth knowledge about the data as well as the algorithms >> themselves is needed. Most researchers therefore tend to use default >> parameters, which are not necessarily optimal. Results: *We have applied >> a new optimization framework for the Taverna scientific workflow management >> system* (http://ms-utils.org/Taverna_Optimization.pdf) to find the best >> combination of parameters for a given scientific workflow to perform >> peptide-spectrum matching. The optimizations themselves are non-trivial, as >> demonstrated by several phenomena that can be observed when allowing for >> larger mass measurement errors in sequence database searches. On-the-fly >> parameter optimization embedded in scientific workflow management systems >> enables experts and non-experts alike to extract the maximum amount of >> information from the data. The same workflows could be used for exploring >> the parameter space and compare algorithms, not only for peptide-spectrum >> matching, but also for other tasks, such as retention time prediction. >> Conclusion: Using the optimization framework, we were able to learn about >> how the data was acquired as well as the explored algorithms. We observed a >> phenomenon identifying many ammonia-loss b-ion spectra as peptides with >> N-terminal pyroglutamate and a large precursor mass measurement error. >> These insights could only be gained with the extension of the common range >> for the mass measurement error tolerance parameters explored by the >> optimization framework. [ABSTRACT FROM AUTHOR] >> >> Copyright of BMC Bioinformatics is the property of BioMed Central and its >> content may not be copied or emailed to multiple sites or posted to a >> listserv without the copyright holder's express written permission. >> However, users may print, download, or email articles for individual use. >> This abstract may be abridged. No warranty is given about the accuracy of >> the copy. Users should refer to the original published version of the >> material for the full abstract. (Copyright applies to all Abstracts.) >> >> DOI: 10.1186/s12859-015-0714-x >> >> >> On Mon, Jan 11, 2016 at 12:42 PM Gale Naylor <ga...@noventussolutions.com> >> wrote: >> >>> I looked at the links to the Google scholar searches above and mostly >>> found oblique references to Apache Taverna, along the lines of what Alan >>> mentioned. The only one that looked promising to me was this one: >>> >>> Local Graph Patterns for Scientific Workflow Similarity Search >>> >>> >>> https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/teaching/studienDiplomArbeiten/running/expose_wiegandt_151116.pdf >>> >>> >>> But, it looked more like a detailed abstract and not a compete paper. >>> >>> >>> The other searches seemed only to return older references to Taverna >>> (2013 and earlier). >>> >>> >>> I can make an Apache Taverna page for citations, but I will need help >>> with what publications you think are good to include. >>> >>> >>> Gale >>> >>> >>> >>> On Mon, Jan 11, 2016 at 8:21 AM alaninmcr <alanin...@googlemail.com> >>> wrote: >>> >>>> Just a warning that you need to be careful when doing a search. A lot of >>>> the citations will be unhelpful like "Popular workflow systems include >>>> X, Y, Taverna and Z" or "Our system is better than X, Y, Taverna and Z >>>> because ...". >>>> >>>> Alan >>>> >>>
