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. [email protected].) 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 <[email protected]> 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 ([email protected]) > > 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 <[email protected]> > 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 <[email protected]> >> 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 >>> >>
