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1.  Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry 
PLoS ONE  2015;10(4):e0125108.
In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size.
Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data.
Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at
PMCID: PMC4416046  PMID: 25927999
2.  eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows 
Bioinformatics  2013;29(7):963-964.
Summary: The Python-based, open-source eMZed framework was developed for mass spectrometry (MS) users to create tailored workflows for liquid chromatography (LC)/MS data analysis. The goal was to establish a unique framework with comprehensive basic functionalities that are easy to apply and allow for the extension and modification of the framework in a straightforward manner. eMZed supports the iterative development and prototyping of individual evaluation strategies by providing a computing environment and tools for inspecting and modifying underlying LC/MS data. The framework specifically addresses non-expert programmers, as it requires only basic knowledge of Python and relies largely on existing successful open-source software, e.g. OpenMS.
Availability: The framework eMZed and its documentation are freely available at eMZed is published under the GPL 3.0 license, and an online discussion group is available at
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3605603  PMID: 23418185
3.  Effect of Local Heating and Cooling on Cambial Activity and Cell Differentiation in the Stem of Norway Spruce (Picea abies) 
Annals of Botany  2006;97(6):943-951.
• Background and Aims The effect of heating and cooling on cambial activity and cell differentiation in part of the stem of Norway spruce (Picea abies) was investigated.
• Methods A heating experiment (23–25 °C) was carried out in spring, before normal reactivation of the cambium, and cooling (9–11 °C) at the height of cambial activity in summer. The cambium, xylem and phloem were investigated by means of light- and transmission electron microscopy and UV-microspectrophotometry in tissues sampled from living trees.
• Key Results Localized heating for 10 d initiated cambial divisions on the phloem side and after 20 d also on the xylem side. In a control tree, regular cambial activity started after 30 d. In the heat-treated sample, up to 15 earlywood cells undergoing differentiation were found to be present. The response of the cambium to stem cooling was less pronounced, and no anatomical differences were detected between the control and cool-treated samples after 10 or 20 d. After 30 d, latewood started to form in the sample exposed to cooling. In addition, almost no radially expanding tracheids were observed and the cambium consisted of only five layers of cells. Low temperatures reduced cambial activity, as indicated by the decreased proportion of latewood. On the phloem side, no alterations were observed among cool-treated and non-treated samples.
• Conclusions Heating and cooling can influence cambial activity and cell differentiation in Norway spruce. However, at the ultrastructural and topochemical levels, no changes were observed in the pattern of secondary cell-wall formation and lignification or in lignin structure, respectively.
PMCID: PMC2803384  PMID: 16613904
Norway spruce; Picea abies; cambium; xylem; phloem; cell differentiation; heating; cooling; light microscopy; transmission electron microscopy; UV-microspectrophotometry
4.  Differentiation of Terminal Latewood Tracheids in Silver Fir Trees During Autumn 
Annals of Botany  2005;95(6):959-965.
• Background and Aims The differentiation of terminal latewood tracheids of silver fir (Abies alba) trees grown in Slovenia was investigated in autumn/winter 2001/2002.
• Methods The experimental trees were divided into three groups: one with narrow annual rings, width less than 1 mm; one with annual ring widths between 1 and 4 mm; and one group with broad rings larger than 4 mm. The differentiation of terminal latewood tracheids was investigated by light-, electron- and UV-microscopy in tissues sampled in October and November 2001 and March 2002.
• Key Results In the middle of October, cambial divisions did not occur any more in any of the trees. In trees with narrow annual rings, cell wall deposition as well as lignification were completed in terminal latewood tracheids at this date, whereas in trees with annual ring widths of more than 1 mm these processes still continued. Electron microscopy as well as UV microscopy revealed an unlignified inner S2 layer and the absence of S3 and warty layers. With increasing distance from the cambium, wall formation and lignification gradually appeared to be completed. Samples of all trees taken in the middle of November only contained differentiated terminal latewood tracheids. At the structural and lignin topochemical level, November and March samples showed completed differentiation of walls of terminal latewood tracheids.
• Conclusions In trees with broader annual rings, the final steps of differentiation of the youngest latewood tracheids near the cambium still continued during autumn, but were finished prior to winter. It was concluded from structural observations that duration of cambial activity is longer in trees with broad annual rings than in trees with narrow rings.
PMCID: PMC4246759  PMID: 15760912
Silver fir (Abies alba); latewood tracheids; cell wall structure; autumn differentiation; lignification; light microscopy; transmission electron microscopy; UV-microspectrophotometry

Results 1-5 (5)