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 ... @@ -44,7 +44,7 @@ Accordingly, the main objective of that study was to relate inter-species differ ... @@ -44,7 +44,7 @@ Accordingly, the main objective of that study was to relate inter-species differ The overall data workflow used in this project is summarized in the chart shown in Fig. \ref{fig:fig2-workflow} (left column). There were three processing episodes: (i) data acquisition, (ii) manual editing and annotation, and (iii) secondary processing. The coloured boxes illustrate the procedure for recording the different types of data and how it was ultimately processed to reconstruct body and leg kinematics as displayed in Fig. 3 in the paper of Theunissen et al. \cite{Theunissen_EtAl_2015}. The colours of the boxes indicate the software used for a given step in the data processing pipeline (yellow: \textit{Vicon Nexus}; green: \textit{PixeLINK Capture}; blue: \textit{MATLAB}). The boxes and connecting arrows are labelled with the data file types produced, the relative file paths to the corresponding subdirectories, and the names of custom-written MATLAB (MathWorks, Natick, MA, USA) scripts. The overall data workflow used in this project is summarized in the chart shown in Fig. \ref{fig:fig2-workflow} (left column). There were three processing episodes: (i) data acquisition, (ii) manual editing and annotation, and (iii) secondary processing. The coloured boxes illustrate the procedure for recording the different types of data and how it was ultimately processed to reconstruct body and leg kinematics as displayed in Fig. 3 in the paper of Theunissen et al. \cite{Theunissen_EtAl_2015}. The colours of the boxes indicate the software used for a given step in the data processing pipeline (yellow: \textit{Vicon Nexus}; green: \textit{PixeLINK Capture}; blue: \textit{MATLAB}). The boxes and connecting arrows are labelled with the data file types produced, the relative file paths to the corresponding subdirectories, and the names of custom-written MATLAB (MathWorks, Natick, MA, USA) scripts. \begin{figure}[ht] \begin{figure}[] \centering \centering \includegraphics[width=11cm,keepaspectratio]{images/fig2-Workflow.png} \includegraphics[width=11cm,keepaspectratio]{images/fig2-Workflow.png} \caption{\textbf{Research data acquisition and processing pipeline.} For raw data acquisition, whole body motions were recorded with a marker-based motion capture system (Vicon) and an additional digital video camera. Furthermore, the anatomy of the animal, along with the marker positions on different body segments were recorded with a microscope camera. In a first step of manual editing and annotation, marker trajectories of selected episodes were labelled and, potentially, connected in case of recording gaps. This step resulted in a \textit{.c3d}-file, a file format described in section \ref{c3dServerIO}. The body pictures were used to generate a body model containing, for example, segment lengths and information about marker position in a body-centred coordinate system. The model is stored in a MATLAB \textit{.mat}-file. Finally, the kinematic reconstruction was achieved in MATLAB by combining marker trajectories with the body documentation. The resulting processed data, i.e., joint angle time courses, gait pattern, and velocity, were saved as another MATLAB file.} \caption{\textbf{Research data acquisition and processing pipeline.} For raw data acquisition, whole body motions were recorded with a marker-based motion capture system (Vicon) and an additional digital video camera. Furthermore, the anatomy of the animal, along with the marker positions on different body segments were recorded with a microscope camera. In a first step of manual editing and annotation, marker trajectories of selected episodes were labelled and, potentially, connected in case of recording gaps. This step resulted in a \textit{.c3d}-file, a file format described in section \ref{c3dServerIO}. The body pictures were used to generate a body model containing, for example, segment lengths and information about marker position in a body-centred coordinate system. The model is stored in a MATLAB \textit{.mat}-file. Finally, the kinematic reconstruction was achieved in MATLAB by combining marker trajectories with the body documentation. The resulting processed data, i.e., joint angle time courses, gait pattern, and velocity, were saved as another MATLAB file.} ... @@ -85,7 +85,7 @@ Accordingly, the main objective of that study was to relate inter-species differ ... @@ -85,7 +85,7 @@ Accordingly, the main objective of that study was to relate inter-species differ \begin{figure}[h] \begin{figure}[] \centering \centering \includegraphics{./images/fig3-MotionCaptureBodyKinematics.jpg} \includegraphics{./images/fig3-MotionCaptureBodyKinematics.jpg} \caption{\textbf{A marker-based motion capture and whole-body kinematics calculations.} \textbf{A:} Insects were labelled with reflective markers. \textbf{B:} For kinematic analysis, the body was modelled by a branched kinematic chain. The main body chain (left) consists of the three thorax segments (Root, T2, T1) and the head. Six side chains (right) model the legs, with the segments coxa, femur and tibia (cox, fem, tib; only right legs are shown, labelled R1 to R3). All rotation axes (DoF) are indicated (3 for the root segment, 2 for thorax/head segments, and 5 per leg). DoF are denoted according to the subsequent segment and the axis of the local coordinate system around which the rotation is executed. Leg DoF are: cox.x, cox.y, cox.z (labelled for R2 in right panel), fem.y and tib.y (labeled for R1 in right panel). [Fig. 1 A, B of \citep{Theunissen_Duerr_2013}]} \caption{\textbf{A marker-based motion capture and whole-body kinematics calculations.} \textbf{A:} Insects were labelled with reflective markers. \textbf{B:} For kinematic analysis, the body was modelled by a branched kinematic chain. The main body chain (left) consists of the three thorax segments (Root, T2, T1) and the head. Six side chains (right) model the legs, with the segments coxa, femur and tibia (cox, fem, tib; only right legs are shown, labelled R1 to R3). All rotation axes (DoF) are indicated (3 for the root segment, 2 for thorax/head segments, and 5 per leg). DoF are denoted according to the subsequent segment and the axis of the local coordinate system around which the rotation is executed. Leg DoF are: cox.x, cox.y, cox.z (labelled for R2 in right panel), fem.y and tib.y (labeled for R1 in right panel). [Fig. 1 A, B of \citep{Theunissen_Duerr_2013}]} ... @@ -165,7 +165,7 @@ As a result of our reproduction experiment we could reproduce the walking and cl ... @@ -165,7 +165,7 @@ As a result of our reproduction experiment we could reproduce the walking and cl Figure \ref{fig:compare_duerr} shows on the left the original panel from the paper published by Theunissen et al. \cite{Theunissen_EtAl_2015} for \textit{C. morosus}. On the right, our reproduction of the same trial is depicted. As the figure shows, asides from the rendering of the obstacle and the colouring, we could successfully reproduce the plots from the original paper. Figure \ref{fig:compare_duerr} shows on the left the original panel from the paper published by Theunissen et al. \cite{Theunissen_EtAl_2015} for \textit{C. morosus}. On the right, our reproduction of the same trial is depicted. As the figure shows, asides from the rendering of the obstacle and the colouring, we could successfully reproduce the plots from the original paper. \begin{figure}[ht] \begin{figure}[] \centering \centering \includegraphics[width=12cm]{../ch2-BiologyDuerr/images/fig5-compare.png} \includegraphics[width=12cm]{../ch2-BiologyDuerr/images/fig5-compare.png} \caption{\textbf{Representative trial of unrestrained walking and climbing behaviour of \textit{C. morosus} as one of the three species investigated in the original paper published by Theunissen et al. \cite{Theunissen_EtAl_2015} (Figure 3).} \caption{\textbf{Representative trial of unrestrained walking and climbing behaviour of \textit{C. morosus} as one of the three species investigated in the original paper published by Theunissen et al. \cite{Theunissen_EtAl_2015} (Figure 3).} ... @@ -185,12 +185,14 @@ Figure \ref{fig:compare_duerr} shows on the left the original panel from the pa ... @@ -185,12 +185,14 @@ Figure \ref{fig:compare_duerr} shows on the left the original panel from the pa We have described a reproducibility case study in the field of biology. We have in particular attempted to represent the main results of a study in whole-body movement analysis of three species of stick insects. The main objective of the study was to relate inter-species differences in kinematics to differences in overall morphology, including features such as leg-to-body-length ratio, that were not an obvious result of phylogenetic or ecological divergence. We have shown that we could successfully reproduce a main figure of the paper \emph{Comparative whole-body kinematics of closely related insect species with different body morphology''} by Theunissen et al. \cite{Theunissen_EtAl_2015}. We classify this case as one of \emph{limited analytical reproducibility}. While we could reproduce the whole-body movements for a number of experimental runs that the authors provided in a GIT repository, this has only been possible by direct guidance of the authors. Further, the reproduction relies on use of commercial software, in particular MATLAB as well as the C3Dserver running on Windows only. We have described a reproducibility case study in the field of biology. We have in particular attempted to represent the main results of a study in whole-body movement analysis of three species of stick insects. The main objective of the study was to relate inter-species differences in kinematics to differences in overall morphology, including features such as leg-to-body-length ratio, that were not an obvious result of phylogenetic or ecological divergence. We have shown that we could successfully reproduce a main figure of the paper \emph{Comparative whole-body kinematics of closely related insect species with different body morphology''} by Theunissen et al. \cite{Theunissen_EtAl_2015}. We classify this case as one of \emph{limited analytical reproducibility}. While we could reproduce the whole-body movements for a number of experimental runs that the authors provided in a GIT repository, this has only been possible by direct guidance of the authors. Further, the reproduction relies on use of commercial software, in particular MATLAB as well as the C3Dserver running on Windows only. \FloatBarrier \section*{Acknowledgements} \section*{Acknowledgements} We would like to thank Florian Paul Schmidt for uploading the files to the \textit{biological-cybernetics} repo in the Gitlab \textit{Conquaire} group. We would like to thank Lukas Biermann and Fabian Herrmann (Student Assistants in Conquaire) for helping with the reproduction of the analyses in MATLAB. We would like to thank Florian Paul Schmidt for uploading the files to the \textit{biological-cybernetics} repo in the Gitlab \textit{Conquaire} group. We would like to thank Lukas Biermann and Fabian Herrmann (Student Assistants in Conquaire) for helping with the reproduction of the analyses in MATLAB. \bibliographystyle{plain} \bibliographystyle{unsrt} {\raggedright % group bib left align {\raggedright % group bib left align \bibliography{ch2-BiologyDuerr} \bibliography{ch2-BiologyDuerr} } } ... ...
 ... @@ -256,13 +256,14 @@ The data has been uploaded to the DFG FOR1525 project website (https://www.ice-n ... @@ -256,13 +256,14 @@ The data has been uploaded to the DFG FOR1525 project website (https://www.ice-n %aimed at reproducing the analytical workflow that lead to the results published in the paper \emph{BINARY: an optical freezing array for assessing temperature and time dependence of heterogeneous ice nucleation'} by Budke and Koop \cite{Budke2015}. The central diagram of this work showing the relation between the number of active sites of ice nucleation in dependence of temperature could be successfully reproduced by reimplementing the original analytical workflow in OriginPro via a Python script. As we did not exactly reproduce the original workflow, we have thus a case of limited analytical reproducibility. As a result of the project, both the derived data and the Python script described in this chapter are available for further re-use and validation of the original results. %aimed at reproducing the analytical workflow that lead to the results published in the paper \emph{BINARY: an optical freezing array for assessing temperature and time dependence of heterogeneous ice nucleation'} by Budke and Koop \cite{Budke2015}. The central diagram of this work showing the relation between the number of active sites of ice nucleation in dependence of temperature could be successfully reproduced by reimplementing the original analytical workflow in OriginPro via a Python script. As we did not exactly reproduce the original workflow, we have thus a case of limited analytical reproducibility. As a result of the project, both the derived data and the Python script described in this chapter are available for further re-use and validation of the original results. % % %S-7 \FloatBarrier \section*{Acknowledgments} \label{Ack} \section*{Acknowledgments} \label{Ack} %S-7 %S-7 We thank Carsten Budke for providing the data and technical discussions during the computational reproducibility process. We thank Carsten Budke for providing the data and technical discussions during the computational reproducibility process. \bibliographystyle{plain} \bibliographystyle{unsrt} {\raggedright % group bib left align {\raggedright % group bib left align \bibliography{ch4-ChemistryKoop} \bibliography{ch4-ChemistryKoop} } } ... ...
 ... @@ -316,7 +316,8 @@ Inspite of all data being available and the results being in principle reproduci ... @@ -316,7 +316,8 @@ Inspite of all data being available and the results being in principle reproduci %S-6 %S-6 This chapter has described a Analytical Reproducibility case study in the area of neuro-cognitive psychology. In particular, we have described our effort to reproduce the main results of the article by Foerster and Schneider: \emph{Expectation violations in sensorimotor sequences: Shifting from LTM-based attentional selection to visual search'} \cite{foerster_schneider_2015b}. The main result of the article mentioned above was the finding that expectation violations in a well-learned sensorimotor sequence in humans caused a regression from LTM-based attentional selection to visual search. The authors of the original publication (also co-authors of this article) provided the Conquaire project with all primary data and all scripts and spreadsheets used to reproduce the results. While we were successful in reproducing the results, we classify this use case as one of \emph{limited analytical reproducibility}. The reason for this is that some parts of the analytical pipeline rely on proprietary and commercial tools such as Matlab or SPSS that can not easily be replaced by open and free tools. Further, the lack of documentation of the pipeline requires interaction with the original authors to reproduce the pipeline faithfully. Both limitations could be easily overcome if further efforts are invested. This chapter has described a Analytical Reproducibility case study in the area of neuro-cognitive psychology. In particular, we have described our effort to reproduce the main results of the article by Foerster and Schneider: \emph{Expectation violations in sensorimotor sequences: Shifting from LTM-based attentional selection to visual search'} \cite{foerster_schneider_2015b}. The main result of the article mentioned above was the finding that expectation violations in a well-learned sensorimotor sequence in humans caused a regression from LTM-based attentional selection to visual search. The authors of the original publication (also co-authors of this article) provided the Conquaire project with all primary data and all scripts and spreadsheets used to reproduce the results. While we were successful in reproducing the results, we classify this use case as one of \emph{limited analytical reproducibility}. The reason for this is that some parts of the analytical pipeline rely on proprietary and commercial tools such as Matlab or SPSS that can not easily be replaced by open and free tools. Further, the lack of documentation of the pipeline requires interaction with the original authors to reproduce the pipeline faithfully. Both limitations could be easily overcome if further efforts are invested. %S-*7 \FloatBarrier \section*{Acknowledgements} \section*{Acknowledgements} %S-*7 %S-*7 We thank Lukas Biermann and Cord Wiljes for assistance with the reproduction of the analyses. We thank Lukas Biermann and Cord Wiljes for assistance with the reproduction of the analyses. ... @@ -328,7 +329,8 @@ We thank Lukas Biermann and Cord Wiljes for assistance with the reproduction of ... @@ -328,7 +329,8 @@ We thank Lukas Biermann and Cord Wiljes for assistance with the reproduction of %\end{verbatim} %\end{verbatim} \bibliographystyle{plain} \bibliographystyle{unsrt} {\raggedright % group bib left align {\raggedright % group bib left align \bibliography{ch8-PsychologySchneider} \bibliography{ch8-PsychologySchneider} } } ... ...