Papers by Chandrasekhar Ramakrishnan
Concurrency and Computation: Practice and Experience, May 13, 2014
We have received feedback from our users and supporters on the functionality and usability of the... more We have received feedback from our users and supporters on the functionality and usability of the Swiss Grid Proteomics Portal during its first year of operation. We have also realized which aspects of the portal could be improved upon through frequent monitoring and interaction with the production system under heavy use. In a second, highly upgraded version of the Swiss Proteomics Portal, called iPortal, we have introduced several new concepts based on this feedback and both user and supporter experience. In this paper we detail the requirements and the improvements we have made, and also give an outlook on future possible improvements.
The Oxford Handbook of Empirical Aesthetics
Integration of methods is an option for interdisciplinary research settings, allowing insights in... more Integration of methods is an option for interdisciplinary research settings, allowing insights into the fleeting moments of aesthetic experience. This chapter aims to exemplify such research settings by introducing two research projects: eMotion: MappingMuseum Experience and ECR—Experimental Concert Research. eMotion concerned aesthetic experiences in the environment of a fine arts museum, and ECR investigates music experience in concerts. Both projects were conducted in ecologically valid environments: the fine art museum and the classical concert hall, respectively. The technical setup of both projects merged different data levels—body movement, heart rate, skin conductance, facial expressions, sociological variables, and emotional and aesthetic evaluations of specific artworks or musical pieces—into an integrated dataset. In both projects, scientists (from musicology, art history, psychology, cultural studies, etc.), technicians, and programmers, as well as practitioners like art...
Just 1000 samples of the normal distribution. Have fun!
The cerebral cortex contains billions of neurons, and their disorganization or misspecification l... more The cerebral cortex contains billions of neurons, and their disorganization or misspecification leads to neurodevelopmental disorders. Understanding how the plethora of projection neuron subtypes are generated by cortical neural stem cells (NSCs) is a major challenge. Here, we focused on elucidating the transcriptional landscape of murine embryonic NSCs, basal progenitors (BPs) and newborn neurons (NBNs) throughout cortical development. We uncover dynamic shifts in transcriptional space over time, and heterogeneity within each progenitor population. We identified signature hallmarks of NSC, BP and NBN clusters, and predict active transcriptional nodes and networks that contribute to neural fate specification. We find that the expression of receptors, ligands and downstream pathway components is highly dynamic over time and throughout the lineage implying differential responsiveness to signals. Thus, we provide an expansive compendium of gene expression during cortical development th...
Auracle is a voice-controlled, networked sound instrument which enables users to control a synthe... more Auracle is a voice-controlled, networked sound instrument which enables users to control a synthesized instrument with their voice and to interact with each other in real time over the Internet. This paper describes the architecture of the system in detail, including the multi-level analysis of vocal input, the communication of that analysis data across the network, and the mapping of that data onto a software synthesizer. 1.
Abstract—We have received feedback from our users and supporters on the functionality and usabili... more Abstract—We have received feedback from our users and supporters on the functionality and usability of the Swiss Grid Proteomics Portal during its first year of operation. We have also realized which aspects of the portal could be improved upon through frequent monitoring and interaction with the production system under heavy use. In a second, highly upgraded version of the Swiss Proteomics Portal, called iPortal, we have introduced several new concepts based on this feedback and both user and supporter experience. In this paper we detail the requirements and the improvements we have made, and also give an outlook on future possible improvements. Keywords—gateway; ease of use; portal; proteomics I.
The initial design of CSL dates back to 1998 (it was then called the CREATE Oscillator, or CO), b... more The initial design of CSL dates back to 1998 (it was then called the CREATE Oscillator, or CO), but the current incarnation was started by students in the MAT 240D Sound Synthesis Techniques course at UCSB in the Spring of 2002. A C++ implementation of a minimal sound synthesis framework (in less than 1000 lines) was developed by the author and introduced at the start of the class, and during the quarter the students added a large number of synthesis classes (refining the basic framework significantly as they went). In the year since that time, CSL has continued to evolve as we used it for several larger applications, and a revised version of the core framework was written (primarily by Chandrasekhar Ramakrishnan) in the Spring of 2003.
The Klangdom is an audio spatialization instrument developed at the Institut fur Musik und Akusti... more The Klangdom is an audio spatialization instrument developed at the Institut fur Musik und Akustik at the ZKM. It is made up of 39 Meyer Sound loudspeakers hung on four sliding tracks, allowing for easy re-configuration of the speaker setup. The audience sits inside the Klangdom, which can be controlled either directly via a mixer, by externally developed software, or by a sequencer for sound movement, Zirkonium, developed at the ZKM. Zirkonium can accept and spatialize audio generated by other applications (even on remote machines) and can simulate the Klangdom over alternate speaker setups to aid composition and dissemination (e.g., in stereo or 5.1).
<p>Good scientific practice requires good documentation and traceability of every research ... more <p>Good scientific practice requires good documentation and traceability of every research step in order to ensure reproducibility and repeatability of our research. However, with increasing data availability and ability to record big data, experiments and data analysis become more complex. This complexity often requires many pre- and post-processing steps that all need to be documented for reproducibility of final results. This poses very different challenges for numerical experiments, laboratory work and field-data analysis. The platform Renku (https://renkulab.io/), developed by the Swiss Data Science Center, aims at facilitating reproducibility and repeatability of all these scientific workflows. Renku stores all data, code and scripts in an online repository, and records in their history how these files are generated, interlinked and modified. The linkages between files (inputs, code and outputs) lead to the so-called <span>knowledge graph, used to record the provenance of results and connecting those with all other relevant entities in the project.</span></p><p>We will discuss here several use examples, including mathematical analysis, laboratory experiments, data analysis and numerical experiments, all related to scientific projects presented separately. Reproducibility of mathematical analysis is facilitated by clear variable definitions and a computer algebra package that enables reproducible symbolic derivations. We will present the use of the Python package ESSM (https://essm.readthedocs.io) for this purpose, and how it can be integrated into a Renku workflow. Reproducibility of laboratory results is facilitated by tracking of experimental conditions for each data record and instrument re-calibration activities, mainly through Jupyter notebooks. Data analysis based on different data sources requires the preservation of links to external datasets and snapshots of the dataset versions imported into the project, that is facilitated by Renku. Renku also takes care of clear links between input, code and output of large numerical experiments, our last use example, and enables systematic updating if any of the input or code files are changed.</p><p>These different examples demonstrate how Renku can assist in documenting the scientific process from input to output and the final paper. All code and data are directly available online, and the recording of the workflows ensures reproducibility and repeatability.</p>
This paper describes recent advances in platformindependent object-oriented software for music an... more This paper describes recent advances in platformindependent object-oriented software for music and sound processing. The Siren system is the result of almost 20 years of continuous development in the Smalltalk programming language; it incorporates an abstract music representation language, interfaces for real-time I/O in several media, a user interface framework, and connections to object databases. To support ambitious compositional and performance applications, the system is integrated with a scalable realtime distributed processing framework. Rather than presenting a system overview (Siren is exhaustively documented elsewhere), we discuss the new features of the system here, including its integration with new DSP frameworks, new I/O interfaces, and its use in several recent compositions.
Auracle is a "group instrument," controlled by the voice, for real-time, interactive, d... more Auracle is a "group instrument," controlled by the voice, for real-time, interactive, distributed music making over the Internet. It is implemented in the Java™ programming language using a combination of publicly available libraries (JSyn and TransJam) and custom-built components. This paper describes how the various pieces --- the voice analysis, network communication, and sound synthesis --- are individually built and how they are combined to form Auracle.
We have implemented a high-level vocal gesture classifier which uses Adaptive Principal Component... more We have implemented a high-level vocal gesture classifier which uses Adaptive Principal Component EXtraction (APEX), a neural network implementation of Principal Components Analysis (PCA), to reduce a multi-dimensional space of statistical features into a three-dimensional highlevel feature space. The classifier is used within Auracle, a real-time, collaborative, Internet-based instrument: highlevel features, along with envelope data extracted from lowlevel voice analysis, are used to drive sound synthesis. The APEX neural network is initially trained with a sample database of vocal gestures, and it continues to adapt (both within single user sessions and over longer time periods) in response to user interaction. Both training and evolution are accomplished without supervision, so that the nature of the classifications is determined more by how users interact with the system than by the preconceptions of its designers.
The CREATE Signal Library (CSL) is a portable general-purpose software framework for sound synthe... more The CREATE Signal Library (CSL) is a portable general-purpose software framework for sound synthesis and digital audio signal processing. It is implemented as a C++ class library to be used as a standalone synthesis server, or embedded as a library into other programs. This first section of this paper describes the overall design of CSL version 3 and gives a series of progressive code examples. We also present CSL's facilities for network I/O of control and sample streams, and the development and deployment of distributed CSL systems. What is more interesting is the discussion that follows of the design issues we faced in implementing CSL, and the presentation of a few of the applications in which we've used CSL over the last year.
Organised Sound, 2009
Zirkonium is a flexible, non-invasive, open-source program for sound spatialisation over spherica... more Zirkonium is a flexible, non-invasive, open-source program for sound spatialisation over spherical (dome-shaped) loudspeaker setups. By non-invasive, we mean that Zirkonium offers the artist spatialisation capabilities without forcing her to change her usual way of working. This is achieved by supporting a variety of means of designing and controlling spatialisations. Zikonium accommodates user-defined speaker distributions and offers HRTF-based headphone simulation for situations when the actual speaker setup is not available. It can acquire sound sources from files, live input, or via the so-called device mode, which allows Zirkonium to appear to other programs as an audio interface. Control data may be predefined and stored in a file or generated elsewhere and sent over OSC. This paper details Zirkonium, its design philosophy and implementation, and how we have been using it since 2005.
&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;... more &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;Numerical experiments become more and more complex, resulting in workflows that are hard to repeat or reproduce. Even though many journals and funding agencies now require open access to data and model code, the linkages between these elements are often still poorly documented or even completely missing. The software platform Renku (https://renkulab.io/), developed by the Swiss Data Science Center, aims at improving reproducibility and repeatability of the entire scientific workflow. Data, scripts and code are stored in an online repository, and Renku records explicitly all the steps from data import to the generation of final plots, in the form of a knowledge graph. In this way, all output files have a history attached, including linkages to scripts and input files used generate them. Renku can visualize the knowledge graph, to show all scientific links between inputs, outputs, scripts and models. It enables easy re-use and reproduction of the entire workflow or parts thereof.&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;In the test case presented here, the Vegetation Optimality Model (VOM, Schymanski et al., 2009) is applied along six study sites of the North-Australian Tropical Transect to simulate observed canopy-atmosphere exchange of water and carbon dioxide. The VOM optimizes vegetation properties, such as rooting depths and canopy properties, in order to maximize the Net Carbon Profit, i.e. the total carbon taken up by photosynthesis minus all the carbon costs of the plant organs involved. The vegetation is schematized as one big leaf for trees and one leaf for seasonal grasses, and is combined with a water balance model. Flux tower measurements of evaporation and CO2-assimilation, and remotely sensed vegetation cover are used for model evaluation, in addition to meteorological data as input for the model. A numerical optimization, the Shuffled Complex Evolution, is used to optimize the vegetation properties for each individual site by repeatedly running the model with different parametrizations and computing the net carbon profit over 20 years. The optimization was repeated several times for each site to analyze the sensitivity of the results to a range of different input parameters.&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;This case demonstrates an example of a complex numerical experiment with all its associated challenges concerning documenting model choices, large datasets and a variety of pre- and post- processing steps. Renku assured the repeatability and reproducibility of this experiment, by documenting this in a proper and systematic way. We demonstrate how Renku helped us to repeat analyses and update results, and we will present the knowledge graph of this experiment.&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;div&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;strong&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;References&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;br&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/strong&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;Schymanski, S.J., Sivapalan, M., Roderick, M.L., Hutley, L.B., Beringer, J., 2009. An optimality&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#8208;based model of the dynamic feedbacks between natural vegetation and the water balance. Water Resources Research 45. https://doi.org/10.1029/2008WR006841&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/div&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;
Abstract The CREATE Signal Library (CSL) is a generalpurpose software framework,for sound synthes... more Abstract The CREATE Signal Library (CSL) is a generalpurpose software framework,for sound synthesis and digital audio signal processing. It is implemented,as a C++ class library to be used to build stand-alone synthesis servers, or embedded into other programs. This paper describes the overall design and implementation of CSL version 3. We also present CSL's facilities for network I/O of control and sample streams, and the development,and deployment,of distributed systems. What is more interesting is the discussion that follows of the design issues we faced in CSL, and the presentation of several of the applications in which we've used CSL over the last year.
Bioinformatics, 2015
The open-source platform openBIS (open Biology Information System) offers an Electronic Laborator... more The open-source platform openBIS (open Biology Information System) offers an Electronic Laboratory Notebook and a Laboratory Information Management System (ELN-LIMS) solution suitable for the academic life science laboratories. openBIS ELN-LIMS allows researchers to efficiently document their work, to describe materials and methods and to collect raw and analyzed data. The system comes with a user-friendly web interface where data can be added, edited, browsed and searched. Availability and implementation: The openBIS software, a user guide and a demo instance are available at https://openbis-eln-lims.ethz.ch. The demo instance contains some data from our laboratory as an example to demonstrate the possibilities of the ELN-LIMS (Ottoz et al., 2014). For rapid local testing, a VirtualBox image of the ELN-LIMS is also available.
Abstract The CREATE Signal Library (CSL) is a generalpurpose software framework,for sound synthes... more Abstract The CREATE Signal Library (CSL) is a generalpurpose software framework,for sound synthesis and digital audio signal processing. It is implemented,as a C++ class library to be used to build stand-alone synthesis servers, or embedded into other programs. This paper describes the overall design and implementation of CSL version 3. We also present CSL's facilities for network I/O of control and sample streams, and the development,and deployment,of distributed systems. What is more interesting is the discussion that follows of the design issues we faced in CSL, and the presentation of several of the applications in which we've used CSL over the last year.
This paper describes recent advances in platform- independent object-oriented software for music ... more This paper describes recent advances in platform- independent object-oriented software for music and sound processing. The Siren system is the result of almost 20 years of continuous development in the Smalltalk programming language; it incorporates an abstract music representation language, interfaces for real-time I/O in several media, a user interface frame- work, and connections to object databases. To sup- port ambitious compositional and performance appli- cations, the system is integrated with a scalable real- time distributed processing framework. Rather than presenting a system overview (Siren is exhaustively documented elsewhere), we discuss the new features of the system here, including its integra- tion with new DSP frameworks, new I/O interfaces, and its use in several recent compositions.
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Papers by Chandrasekhar Ramakrishnan