The Computational Thematic Analysis Toolkit

As online communities have grown, Computational Social Science has rapidly developed new techniques to study them. However, these techniques require researchers to become experts in a wide variety of tools in addition to qualitative and computational research methods. Studying online communities also requires researchers to constantly navigate highly contextual ethical and transparency considerations when engaging with data, such as respecting their members' privacy when discussing sensitive or stigmatized topics. To overcome these challenges, we developed the Computational Thematic Analysis Toolkit, a modular software package that supports analysis of online communities by combining aspects of reflexive thematic analysis with computational techniques. Our toolkit demonstrates how common analysis tasks like data collection, cleaning and filtering, modelling and sampling, and coding can be implemented within a single visual interface, and how that interface can encourage researchers to manage ethical and transparency considerations throughout their research process.

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Enhancing the roles of information and communication technologies in doctoral research processes

International Journal of Educational Technology in Higher Education ◽

10.1186/s41239-020-00212-3 ◽

2020 ◽

Vol 17 (1) ◽

Author(s):

Sarah J. Stein ◽

Kwong Nui Sim

Keyword(s):

Information And Communication Technologies ◽

Thematic Analysis ◽

Communication Technologies ◽

Research Process ◽

Formal Learning ◽

Doctoral Study ◽

Ict Skills ◽

Doctoral Research ◽

The People ◽

Information And Communication

Abstract While information and communication technologies (ICT) are prominent in educational practices at most levels of formal learning, there is relatively little known about the skills and understandings that underlie their effective and efficient use in research higher degree settings. This project aimed to identify doctoral supervisors’ and students’ perceptions of their roles in using ICT. Data were gathered through participative drawing and individual discussion sessions. Participants included 11 students and two supervisors from two New Zealand universities. Focus of the thematic analysis was on the views expressed by students about their ideas, practices and beliefs, in relation to their drawings. The major finding was that individuals hold assumptions and expectations about ICT and their use; they make judgements and take action based on those expectations and assumptions. Knowing about ICT and knowing about research processes separately form only part of the work of doctoral study. Just as supervision cannot be considered independently of the research project and the student involved, ICT skills and the use of ICT cannot be considered in the absence of the people and the project. What is more important in terms of facilitating the doctoral research process is students getting their “flow” right. This indicates a need to provide explicit support to enable students to embed ICT within their own research processes.

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TPVTrack v1.0: a watershed segmentation and overlap correspondence method for tracking tropopause polar vortices

Geoscientific Model Development ◽

10.5194/gmd-11-5173-2018 ◽

2018 ◽

Vol 11 (12) ◽

pp. 5173-5187 ◽

Cited By ~ 1

Author(s):

Nicholas Szapiro ◽

Steven Cavallo

Keyword(s):

Software Package ◽

Unstructured Grids ◽

Test Cases ◽

Watershed Segmentation ◽

Spatial Characterization ◽

Modular Software ◽

Mean Structure ◽

Spatial Shape ◽

Physical Features ◽

Effective Representation

Abstract. A new free modular software package is described for tracking tropopause polar vortices (TPVs) natively on structured or unstructured grids. Motivated by limitations in spatial characterization and time tracking within existing approaches, TPVTrack mimics the expected dynamics of TPVs to represent their (1) spatial structure, with variable shapes and intensities, and (2) time evolution, with mergers and splits. TPVs are segmented from the gridded flow field into spatial objects as restricted regional watershed basins on the tropopause, described by geometric metrics, associated over time by overlap similarity into major and minor correspondences, and tracked along major correspondences. Simplified segmentation and correspondence test cases illustrate some of the appeal, sensitivities, and limitations of TPVTrack, including effective representation of spatial shape and reduced false positive associations in time. Tracked TPVs in more realistic historical conditions are consistent in bulk with expectations of life cycle and mean structure. Individual tracks are less reliable when discriminating among multiple overlaps. Modifications to track other physical features are possible, with each application requiring evaluation.

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iSEE: Interactive SummarizedExperiment Explorer

F1000Research ◽

10.12688/f1000research.14966.1 ◽

2018 ◽

Vol 7 ◽

pp. 741 ◽

Cited By ~ 26

Author(s):

Kevin Rue-Albrecht ◽

Federico Marini ◽

Charlotte Soneson ◽

Aaron T.L. Lun

Keyword(s):

High Throughput ◽

Software Package ◽

Biological Data ◽

Data Exploration ◽

Data Sets ◽

Proteomics Data ◽

Code Tracking ◽

Dynamic Linking ◽

Interactive Visualisation ◽

Visual Interface

Data exploration is critical to the comprehension of large biological data sets generated by high-throughput assays such as sequencing. However, most existing tools for interactive visualisation are limited to specific assays or analyses. Here, we present the iSEE (Interactive SummarizedExperiment Explorer) software package, which provides a general visual interface for exploring data in a SummarizedExperiment object. iSEE is directly compatible with many existing R/Bioconductor packages for analysing high-throughput biological data, and provides useful features such as simultaneous examination of (meta)data and analysis results, dynamic linking between plots and code tracking for reproducibility. We demonstrate the utility and flexibility of iSEE by applying it to explore a range of real transcriptomics and proteomics data sets.

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Computational approaches for the prediction of protein function in the mitochondrion

AJP Cell Physiology ◽

10.1152/ajpcell.00225.2006 ◽

2006 ◽

Vol 291 (6) ◽

pp. C1121-C1128 ◽

Cited By ~ 14

Author(s):

Toni Gabaldón

Keyword(s):

Biological System ◽

Protein Function ◽

Research Field ◽

Computational Techniques ◽

Complex Biological System ◽

Computational Approaches ◽

Functional Interactions ◽

Physical Interactions ◽

Computational Research

Understanding a complex biological system, such as the mitochondrion, requires the identification of the complete repertoire of proteins targeted to the organelle, the characterization of these, and finally, the elucidation of the functional and physical interactions that occur within the mitochondrion. In the last decade, significant developments have contributed to increase our understanding of the mitochondrion, and among these, computational research has played a significant role. Not only general bioinformatics tools have been applied in the context of the mitochondrion, but also some computational techniques have been specifically developed to address problems that arose from within the mitochondrial research field. In this review the contribution of bioinformatics to mitochondrial biology is addressed through a survey of current computational methods that can be applied to predict which proteins will be localized to the mitochondrion and to unravel their functional interactions.

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C hem S hell—a modular software package for QM / MM simulations

Wiley Interdisciplinary Reviews Computational Molecular Science ◽

10.1002/wcms.1163 ◽

2013 ◽

Vol 4 (2) ◽

pp. 101-110 ◽

Cited By ~ 167

Author(s):

Sebastian Metz ◽

Johannes Kästner ◽

Alexey A. Sokol ◽

Thomas W. Keal ◽

Paul Sherwood

Keyword(s):

Software Package ◽

Modular Software

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Is Digital Scholarship Meaningful?: A Campus Study Tracking Multidisciplinary Perceptions

KULA knowledge creation dissemination and preservation studies ◽

10.18357/kula.130 ◽

2021 ◽

Vol 5 (2) ◽

Author(s):

Nickoal Eichmann-Kalwara ◽

Frederick Carey ◽

Melissa Hart Cantrell ◽

Stacy Gilbert ◽

Philip B. White ◽

...

Keyword(s):

Graduate Students ◽

Social Science ◽

Research Process ◽

Computational Social Science ◽

Local Context ◽

Research Strategies ◽

Digital History ◽

Domain Specific ◽

University Of Colorado ◽

Digital Scholarship

Increased computational and multimodal approaches to research over the past decades have enabled scholars and learners to forge creative avenues of inquiry, adopt new methodological approaches, and interrogate information in innovative ways. As such, academic libraries have begun to offer a suite of services to support these digitally inflected and data-intense research strategies. These supports, dubbed digital scholarship services in the library profession, break traditional disciplinary boundaries and highlight the methodological significance of research inquiry. Externally, however, these practices appear as domain-specific niches, e.g., digital history or digital humanities in humanities disciplines, e-science and e-research in STEM, and e-social science or computational social science in social science disciplines. The authors conducted a study examining the meaningfulness of the term digital scholarship within the local context at University of Colorado Boulder by investigating how the interpretation of digital scholarship varies according to graduate students, faculty, and other researchers. Nearly half of the definitions (46 percent) mentioned research process or methods as part of digital scholarship. Faculty and staff declined or were unable to define digital scholarship more often than graduate students or post-doctoral researchers. Therefore, digital scholarship as a term is not meaningful to all researchers. We recommend that librarians inflect their practices with the understanding that researchers and library users’ perceptions of digital scholarship vary greatly across contexts.

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How New and Expecting Fathers Engage With an App-Based Online Forum: Qualitative Analysis (Preprint)

10.2196/preprints.9999 ◽

2018 ◽

Author(s):

Becky K White ◽

Roslyn C Giglia ◽

Jane A Scott ◽

Sharyn K Burns

Keyword(s):

Social Support ◽

Qualitative Analysis ◽

Thematic Analysis ◽

Software Package ◽

Perinatal Period ◽

Mobile App ◽

Informational Support ◽

Online Forum ◽

Support Provision ◽

Paternal Support

BACKGROUND Breastfeeding is important for infants, and fathers are influential in supporting their partner in their decision to breastfeed and how long they breastfeed for. Fathers can feel excluded from traditional antenatal education and support opportunities but highly value social support from peers. Online health forums can be a useful source of social support, yet little is known about how fathers would use a conversation forum embedded in a breastfeeding-focused app. Milk Man is a mobile app that aimed to increase paternal support for breastfeeding using a range of strategies, including a conversation forum. OBJECTIVE The aim of this study was to examine how fathers used a breastfeeding-focused conversation forum contained within a mobile app throughout the perinatal period. METHODS A qualitative analysis of comments posted by users in the online forum contained within the Milk Man app was conducted. The app contained a library of information for fathers, as well as a conversation forum. Thematic analysis was used to organize and understand the data. The NVivo 11 software package was used to code comments into common nodes, which were then organized into key themes. RESULTS In all, 208 contributors (35.5% [208/586] of those who had access to the app) posted at least once within the forum. In total, 1497 comments were included for analysis. These comments were coded to 3799 individual nodes and then summarized to 54 tree nodes from which four themes emerged to describe how fathers used the app. Themes included seek and offer support, social connection, informational support provision, and sharing experiences. Posting in the forum was concentrated in the antenatal period and up to approximately 6 weeks postpartum. CONCLUSIONS These data show that fathers are prepared to use a breastfeeding-focused online forum in a variety of ways to facilitate social support. Fathers can be difficult to reach in the perinatal period, yet engaging them and increasing social support is important. This research demonstrates the acceptability of an innovative way of engaging new and expecting fathers.

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When Bots and Users Meet: Automated Manipulation and the New Culture of Online Suspicion

Global Perspectives ◽

10.1525/gp.2021.24955 ◽

2021 ◽

Vol 2 (1) ◽

Author(s):

Yoav Halperin

Keyword(s):

Social Media ◽

Public Opinion ◽

Thematic Analysis ◽

Public Awareness ◽

National Elections ◽

New Techniques ◽

Discussion Threads ◽

Online Exchanges ◽

Media Environments ◽

Facebook Pages

This article examines the growing public awareness of deceptive online campaigns where automated networks of social media bots are deployed to manipulate public opinion, disrupt debates, and stoke intercommunal strife. Drawing on a grounded thematic analysis of discussion threads that appeared on Israeli politicians’ Facebook pages during the lead-up to Israel’s national elections in April 2019, I argue that users’ frequent allusions and reactions to the presence of suspected manipulative agents allow these users to negotiate, challenge, and raise competing claims regarding whether certain prominent voices on social media are reflective of actual public opinion. As such, this article contributes to the emerging body of literature about online manipulation, which in recent years has focused mostly on examining the nature and scope of deceptive bot campaigns around the globe and on devising new techniques for detecting and countering the activities of fake social media accounts. The present investigation, in contrast, seeks to shift attention away from bots themselves and toward their intended targets: ordinary users and their discourse. In so doing, it aims to contribute to and expand the study of how automated manipulation is shaping contemporary social media environments by asking: What do ordinary users have to say about the deployment of political bots? How does users’ growing awareness of deceptive bot campaigns inform their interpretations of their own online experiences? And how do users leverage claims about bot activity in online exchanges with others to advance their political agendas?

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A systematized approach to AVHRR image navigation

Annals of Glaciology ◽

10.3189/s0260305500013185 ◽

1993 ◽

Vol 17 ◽

pp. 414-420 ◽

Cited By ~ 1

Author(s):

D.G. Baldwin ◽

W.J. Emery

Keyword(s):

Software Package ◽

Systematic Approach ◽

Control Point ◽

Registration Accuracy ◽

Registration Errors ◽

Modular Software ◽

Image Navigation ◽

Current Systems ◽

Different Sources ◽

Very High

Accurate co-location and geo-registration of AVHRR (Advanced Very High Resolution Radiometer) is necessary for most applications involving these data. To obtain the necessary accuracy, most of the current systems available for AVHRR image rectification require corrections to errors arising from several different sources. This paper presents a software package which is able to correct registration errors from all sources using effective roll, pitch, and yaw values determined from ground control point offsets. These effective values are used to establish a baseline registration against which other models are compared. Spacecraft and sampling geometry are revisited in order to systemize and better define the procedure of AVHRR geo-registration. This systematic approach has resulted in a modular software package which has a registration accuracy of 1 satellite pixel, and is easily modified and improved.

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