The Lish: a data model to support analysis by end user programmers

For end user programmers needing to carry out data analysis, the spreadsheet is an attractive choice, but has little safety net against user errors. Reducing these errors is an active research area, but one aspect rather little investigated is the role played by the underlying data model: the grid of cells. I am working on an alternative model, the “lish”, based on nested lists of cells. Its theoretical advantages include fewer and more concise formulae, and easier updates to the structure. A user study is in preparation to assess its practical utility

The Lish: A Data Model for Grid Free Spreadsheets

Throughout the history of the spreadsheet, and throughout the majority of research into improving it, the grid of cells has remained a constant as the underlying data model. An idea that has received recent interest is to provide users with a spreadsheet-like environment based on something other than a grid. The attraction is that if salient features of the data structure can be made more explicit, the machine will be able to provide certain types of error checking and automation. In this project I consider one such grid replacement, a new data model which I call the “lish”. It is based on nested lists of cells, composed according to rules that allow repeating structures to be described. It allows columns, tables, groups of tables and other structures to be treated as coherent objects. This supports a novel form of cell range selection, and allows the machine to ensure that related structures are kept consistent. The model is also more accommodating than the grid of dynamic space allocation, where the number of cells occupied by a result is not known in advance. Then, I develop a “lish calculus”, an extension to vector arithmetic for hierarchical structures that provides a concise notation for calculations with lishes. This simplifies the usual spreadsheet formula expressions, and enables the machine to interpret them consistently with the context in which they are located. I evaluate the lish in the framework of the cognitive dimensions of notations, with the help of example use cases and a user study based on a prototype lish editor. These verify many of the hypothesised advantages, but also reveal some difficulties for users. I close with an analysis of how the lish might be revised to address these shortcomings, while continuing to capitalise on the essential benefits

Structuring Spreadsheets with the “Lish” Data Model

A spreadsheet is remarkably flexible in representing various forms of structured data, but the individual cells have no knowledge of the larger structures of which they may form a part. This can hamper comprehension and increase formula replication, increasing the risk of error on both scores. We explore a novel data model (called the “lish”) that could form an alternative to the traditional grid in a spreadsheet-like environment. Its aim is to capture some of these higher structures while preserving the simplicity that makes a spreadsheet so attractive. It is based on cells organised into nested lists, in each of which the user may optionally employ a template to prototype repeating structures. These template elements can be likened to the marginal “cells” in the borders of a traditional worksheet, but are proper members of the sheet and may themselves contain internal structure. A small demonstration application shows the “lish” in operation

Wide, long, or nested data? Reconciling the machine and human viewpoints

Data expressed in tables may be re-arranged in various forms, while conveying the same information. This can create a tension when one form is easier to comprehend by a human reader, but another form is more convenient for processing by machine. This problem has received considerable attention for data scientists writing code, but rather less for end user analysts using spreadsheets. We propose a new data model, the “lish”, which supports a spreadsheet-like flexibility of layout, while capturing sufficient structure to facilitate processing. Using a typical example in a prototype editor, we demonstrate how it might help users resolve the tension between the two forms. A user study is in preparation

Kepler-16: A Transiting Circumbinary Planet

We report the detection of a planet whose orbit surrounds a pair of low-mass stars. Data from the Kepler spacecraft reveal transits of the planet across both stars, in addition to the mutual eclipses of the stars, giving precise constraints on the absolute dimensions of all three bodies. The planet is comparable to Saturn in mass and size, and is on a nearly circular 229-day orbit around its two parent stars. The eclipsing stars are 20% and 69% as massive as the sun, and have an eccentric 41-day orbit. The motions of all three bodies are confined to within 0.5 degree of a single plane, suggesting that the planet formed within a circumbinary disk.Comment: Science, in press; for supplemental material see http://www.sciencemag.org/content/suppl/2011/09/14/333.6049.1602.DC1/1210923.Doyle.SOM.pd

Planetary Candidates Observed by Kepler, III: Analysis of the First 16 Months of Data

New transiting planet candidates are identified in sixteen months (May 2009 - September 2010) of data from the Kepler spacecraft. Nearly five thousand periodic transit-like signals are vetted against astrophysical and instrumental false positives yielding 1,091 viable new planet candidates, bringing the total count up to over 2,300. Improved vetting metrics are employed, contributing to higher catalog reliability. Most notable is the noise-weighted robust averaging of multi-quarter photo-center offsets derived from difference image analysis which identifies likely background eclipsing binaries. Twenty-two months of photometry are used for the purpose of characterizing each of the new candidates. Ephemerides (transit epoch, T_0, and orbital period, P) are tabulated as well as the products of light curve modeling: reduced radius (Rp/R*), reduced semi-major axis (d/R*), and impact parameter (b). The largest fractional increases are seen for the smallest planet candidates (197% for candidates smaller than 2Re compared to 52% for candidates larger than 2Re) and those at longer orbital periods (123% for candidates outside of 50-day orbits versus 85% for candidates inside of 50-day orbits). The gains are larger than expected from increasing the observing window from thirteen months (Quarter 1-- Quarter 5) to sixteen months (Quarter 1 -- Quarter 6). This demonstrates the benefit of continued development of pipeline analysis software. The fraction of all host stars with multiple candidates has grown from 17% to 20%, and the paucity of short-period giant planets in multiple systems is still evident. The progression toward smaller planets at longer orbital periods with each new catalog release suggests that Earth-size planets in the Habitable Zone are forthcoming if, indeed, such planets are abundant.Comment: Submitted to ApJS. Machine-readable tables are available at http://kepler.nasa.gov, http://archive.stsci.edu/kepler/results.html, and the NASA Exoplanet Archiv

Airships: A New Horizon for Science

The "Airships: A New Horizon for Science" study at the Keck Institute for Space Studies investigated the potential of a variety of airships currently operable or under development to serve as observatories and science instrumentation platforms for a range of space, atmospheric, and Earth science. The participants represent a diverse cross-section of the aerospace sector, NASA, and academia. Over the last two decades, there has been wide interest in developing a high altitude, stratospheric lighter-than-air (LTA) airship that could maneuver and remain in a desired geographic position (i.e., "station-keeping") for weeks, months or even years. Our study found considerable scientific value in both low altitude (< 40 kft) and high altitude (> 60 kft) airships across a wide spectrum of space, atmospheric, and Earth science programs. Over the course of the study period, we identified stratospheric tethered aerostats as a viable alternative to airships where station-keeping was valued over maneuverability. By opening up the sky and Earth's stratospheric horizon in affordable ways with long-term flexibility, airships allow us to push technology and science forward in a project-rich environment that complements existing space observatories as well as aircraft and high-altitude balloon missions.Comment: This low resolution version of the report is 8.6 MB. For the high resolution version see: http://kiss.caltech.edu/study/airship

Genome sequence of the tsetse fly (Glossina morsitans):Vector of African trypanosomiasis

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.IS

Human Tumour Immune Evasion via TGF-β Blocks NK Cell Activation but Not Survival Allowing Therapeutic Restoration of Anti-Tumour Activity

Immune evasion is now recognized as a key feature of cancer progression. In animal models, the activity of cytotoxic lymphocytes is suppressed in the tumour microenvironment by the immunosuppressive cytokine, Transforming Growth Factor (TGF)-β. Release from TGF-β-mediated inhibition restores anti-tumour immunity, suggesting a therapeutic strategy for human cancer. We demonstrate that human natural killer (NK) cells are inhibited in a TGF-β dependent manner following chronic contact-dependent interactions with tumour cells in vitro. In vivo, NK cell inhibition was localised to the human tumour microenvironment and primary ovarian tumours conferred TGF-β dependent inhibition upon autologous NK cells ex vivo. TGF-β antagonized the interleukin (IL)-15 induced proliferation and gene expression associated with NK cell activation, inhibiting the expression of both NK cell activation receptor molecules and components of the cytotoxic apparatus. Interleukin-15 also promotes NK cell survival and IL-15 excluded the pro-apoptotic transcription factor FOXO3 from the nucleus. However, this IL-15 mediated pathway was unaffected by TGF-β treatment, allowing NK cell survival. This suggested that NK cells in the tumour microenvironment might have their activity restored by TGF-β blockade and both anti-TGF-β antibodies and a small molecule inhibitor of TGF-β signalling restored the effector function of NK cells inhibited by autologous tumour cells. Thus, TGF-β blunts NK cell activation within the human tumour microenvironment but this evasion mechanism can be therapeutically targeted, boosting anti-tumour immunity