Program Annotations: Feedback for Students Learning to Program

This paper presents a novel program annotation mechanism which enables students to obtain feedback from tutors on their programs in a far simpler and more efficient way than is possible with, for example, email. A common scenario with beginning students is to email tutors with copies of their malfunctioning programs. Unfortunately the emailed program often bears little resemblance to the program the student has been trying to make work; often it is incomplete, a different version and corrupted. We propose an annotation mechanism enabling students to simply and easily annotate their programs with comments asking for help. Similarly our mechanism enables tutors to view students’ programs and to reply to their comments in a simple and structured fashion. This means students can get frequent and timely feedback on their programs; tutors can provide such feedback efficiently, and hence students’ learning is greatly improved.

Visual code annotations for cyberphysical programming

User interfaces for source code editing are a crucial component in any software development environment, and in many editors visual annotations (overlaid on the textual source code) are used to provide important contextual information to the programmer. This paper focuses on the real-time programming activity of ‘cyberphysical’ programming, and considers the type of visual annotations which may be helpful in this programming context.

Reconciling folksonomic tagging with taxa for bioacoustic annotations

Acoustic sensors are increasingly used to monitor biodiversity. They can remain deployed in the environment for extended periods to passively and objectively record the sounds of the environment. The collected acoustic data must be analyzed to identify the presence of the sounds made by fauna in order to understand biodiversity. Citizen scientists play an important role in analyzing this data by annotating calls and identifying species. This paper presents our research into bioacoustic annotation techniques. It describes our work in defining a process for managing, creating, and using tags that are applied to our annotations. This paper includes a detailed description of our methodology for correcting and then linking our folksonomic tags to taxonomic data sources. Providing tools and processes for maintaining species naming consistency is critical to the success of a project designed to generate scientific data. We demonstrate that cleaning the folksonomic data and providing links to external taxonomic authorities enhances the scientific utility of the tagging efforts of citizen scientists.

Using annotations to inform an understanding of achievement standards

The implementation of a new national curriculum and standards-referenced assessment in Australia has been an opportunity and a challenge for teacher assessment practices. In this case study of teachers in two Queensland schools, we explore how annotating student or exemplar assessment tasks could support teacher assessment practice. Three learning conversations between the researchers and the teacher teams are interpreted through the lens of Bernstein’s (1999) horizontal and vertical discourses to understand the complexities of coming to know an assessment standard. The study contributes to the literature on the use of annotations by exploring how teachers negotiated the purposes and processes of annotation, how annotating student work or exemplars before teaching commenced supported teachers to experience greater clarity about assessment standards and, finally, some of the tensions experienced by the teachers as they considered this practice within the practicalities of their daily work.

Teachers using annotations to engage students in assessment conversations : recontextualising knowledge

Assessment for Learning practices with students such as feedback, and self- and peer assessment are opportunities for teachers and students to develop a shared understanding of how to create quality learning performances. Quality is often represented through achievement standards. This paper explores how primary school teachers in Australia used the process of annotating work samples to develop shared understanding of achievement standards during their curriculum planning phase, and how this understanding informed their teaching so that their students also developed this understanding. Bernstein's concept of the pedagogic device is used to identify the ways teachers recontextualised their assessment knowledge into their pedagogic practices. Two researchers worked alongside seven primary school teachers in two schools over a year, gathering qualitative data through focus groups and interviews. Three general recontextualising approaches were identified in the case studies; recontextualising standards by reinterpreting the role of rubrics, recontextualising by replicating the annotation process with the students and recontextualising by reinterpreting practices with students. While each approach had strengths and limitations, all of the teachers concluded that annotating conversations in the planning phase enhanced their understanding, and informed their practices in helping students to understand expectations for quality.

Heat maps for aggregating bioacoustic annotations

In our large library of annotated environmental recordings of animal vocalizations, searching annotations by label can return thousands of results. We propose a heat map of aggregated annotation time and frequency bounds, maintaining the shape of the annotations as they appear on the spectrogram. This compactly displays the distribution of annotation bounds for the user's query, and allows them to easily identify unusual annotations. Key to this is allowing zero values on the map to be differentiated from areas where there are single annotations.

Exploiting inference from semantic annotations for information retrieval

The increasing amount of information that is annotated against standardised semantic resources offers opportunities to incorporate sophisticated levels of reasoning, or inference, into the retrieval process. In this position paper, we reflect on the need to incorporate semantic inference into retrieval (in particular for medical information retrieval) as well as previous attempts that have been made so far with mixed success. Medical information retrieval is a fertile ground for testing inference mechanisms to augment retrieval. The medical domain offers a plethora of carefully curated, structured, semantic resources, along with well established entity extraction and linking tools, and search topics that intuitively require a number of different inferential processes (e.g., conceptual similarity, conceptual implication, etc.). We argue that integrating semantic inference in information retrieval has the potential to uncover a large amount of information that otherwise would be inaccessible; but inference is also risky and, if not used cautiously, can harm retrieval.

BioPatML : pattern sharing for the genomic sciences

Computational biology increasingly demands the sharing of sophisticated data and annotations between research groups. Web 2.0 style sharing and publication requires that biological systems be described in well-defined, yet flexible and extensible formats which enhance exchange and re-use. In contrast to many of the standards for exchange in the genomic sciences, descriptions of biological sequences show a great diversity in format and function, impeding the definition and exchange of sequence patterns. In this presentation, we introduce BioPatML, an XML-based pattern description language that supports a wide range of patterns and allows the construction of complex, hierarchically structured patterns and pattern libraries. BioPatML unifies the diversity of current pattern description languages and fills a gap in the set of XML-based description languages for biological systems. We discuss the structure and elements of the language, and demonstrate its advantages on a series of applications, showing lightweight integration between the BioPatML parser and search engine, and the SilverGene genome browser. We conclude by describing our site to enable large scale pattern sharing, and our efforts to seed this repository.

Conceptual Modelling in 3D Virtual Worlds for Process Communication

Traditionally, conceptual modelling of business processes involves the use of visual grammars for the representation of, amongst other things, activities, choices and events. These grammars, while very useful for experts, are difficult to understand by naive stakeholders. Annotations of such process models have been developed to assist in understanding aspects of these grammars via map-based approaches, and further work has looked at forms of 3D conceptual models. However, no one has sought to embed the conceptual models into a fully featured 3D world, using the spatial annotations to explicate the underlying model clearly. In this paper, we present an approach to conceptual process model visualisation that enhances a 3D virtual world with annotations representing process constructs, facilitating insight into the developed model. We then present a prototype implementation of a 3D Virtual BPMN Editor that embeds BPMN process models into a 3D world. We show how this gives extra support for tasks performed by the conceptual modeller, providing better process model communication to stakeholders..

Unsupervised alignment of thousands of images

The task addressed in this thesis is the automatic alignment of an ensemble of misaligned images in an unsupervised manner. This application is especially useful in computer vision applications where annotations of the shape of an object of interest present in a collection of images is required. Performing this task manually is a slow, tedious, expensive and error prone process which hinders the progress of research laboratories and businesses. Most recently, the unsupervised removal of geometric variation present in a collection of images has been referred to as congealing based on the seminal work of Learned-Miller [21]. The only assumption made in congealing is that the parametric nature of the misalignment is known a priori (e.g. translation, similarity, a�ne, etc) and that the object of interest is guaranteed to be present in each image. The capability to congeal an ensemble of misaligned images stemming from the same object class has numerous applications in object recognition, detection and tracking. This thesis concerns itself with the construction of a congealing algorithm titled, least-squares congealing, which is inspired by the well known image to image alignment algorithm developed by Lucas and Kanade [24]. The algorithm is shown to have superior performance characteristics when compared to previously established methods: canonical congealing by Learned-Miller [21] and stochastic congealing by Z�ollei [39].

BLAST Atlas : a function based multiple genome browser

BLAST Atlas is a visual analysis system for comparative genomics that supports genome-wide gene characterisation, functional assignment and function-based browsing of one or more chromosomes. Inspired by applications such as the WorldWide Telescope, Bing Maps 3D and Google Earth, BLAST Atlas uses novel three-dimensional gene and function views that provide a highly interactive and intuitive way for scientists to navigate, query and compare gene annotations. The system can be used for gene identification and functional assignment or as a function-based multiple genome comparison tool which complements existing position based comparison and alignment viewers.

Automatic generation of assertions to detect potential security vulnerabilities in C programs that use union and pointer types

Type unions, pointer variables and function pointers are a long standing source of subtle security bugs in C program code. Their use can lead to hard-to-diagnose crashes or exploitable vulnerabilities that allow an attacker to attain privileged access over classified data. This paper describes an automatable framework for detecting such weaknesses in C programs statically, where possible, and for generating assertions that will detect them dynamically, in other cases. Exclusively based on analysis of the source code, it identifies required assertions using a type inference system supported by a custom made symbol table. In our preliminary findings, our type system was able to infer the correct type of unions in different scopes, without manual code annotations or rewriting. Whenever an evaluation is not possible or is difficult to resolve, appropriate runtime assertions are formed and inserted into the source code. The approach is demonstrated via a prototype C analysis tool.

Using the semantic grid to build bridges between museums and indigenous communities

In this paper we describe a Semantic Grid application designed to enable museums and indigenous communities in distributed locations, to collaboratively discuss, describe and annotate digital objects and documents in museums that originally belonged to or are of cultural or historical significance to indigenous groups. By extending and refining an existing application, Vannotea, we enable users on access grid nodes to collaboratively attach descriptive, rights and tribal care metadata and annotations to digital images, video or 3D representations. The aim is to deploy the software within museums to enable the traditional owners to describe and contextualize museum content in their own words and from their own perspectives. This sharing and exchange of knowledge will hopefully revitalize cultures eroded through colonization and globalization and repair and strengthen relationships between museums and indigenous communities.

An annotated bibliography of phenomenographic research : Selected publications to 1997

This resource has been compiled from "Phenomenographic Research: An annotated Bibliogrphy (Third Edition)" and "1997 Supplement". This listing, containing more than one hundred citations, does not claim by any means to be comprehensive and it includes only material written in English. However, it has been attempted to cover material of significance in the development of phenomenographic research and pedagogy. The annotations in this publication are intended to offer prospective qualitative researchers and/or post-graduate research students a helping hand to enter the sometimes challenging research conversation that is centred around phenomenography. Please use this volume as diversely as your needs are to maximise its contents and to improve your experience of this distinctive approach to research.

Overview of the INEX 2009 Ad Hoc Track

This paper gives an overview of the INEX 2009 Ad Hoc Track. The main goals of the Ad Hoc Track were three-fold. The first goal was to investigate the impact of the collection scale and markup, by using a new collection that is again based on a the Wikipedia but is over 4 times larger, with longer articles and additional semantic annotations. For this reason the Ad Hoc track tasks stayed unchanged, and the Thorough Task of INEX 2002–2006 returns. The second goal was to study the impact of more verbose queries on retrieval effectiveness, by using the available markup as structural constraints—now using both the Wikipedia’s layout-based markup, as well as the enriched semantic markup—and by the use of phrases. The third goal was to compare different result granularities by allowing systems to retrieve XML elements, ranges of XML elements, or arbitrary passages of text. This investigates the value of the internal document structure (as provided by the XML mark-up) for retrieving relevant information. The INEX 2009 Ad Hoc Track featured four tasks: For the Thorough Task a ranked-list of results (elements or passages) by estimated relevance was needed. For the Focused Task a ranked-list of non-overlapping results (elements or passages) was needed. For the Relevant in Context Task non-overlapping results (elements or passages) were returned grouped by the article from which they came. For the Best in Context Task a single starting point (element start tag or passage start) for each article was needed. We discuss the setup of the track, and the results for the four tasks.