Develop proposal for special issue - Revision history

Bakinam at 20:18, 25 June 2015

2015-06-25T20:18:42Z

Yolanda: Set PropertyValue: Progress = 100

2015-06-05T23:16:06Z

Set PropertyValue: Progress = 100

Yolanda: Added PropertyValue: Participants = Jon Goodall

2015-04-26T18:32:50Z

Added PropertyValue: Participants = Jon Goodall

Xuan: /* Yu: [Yu, Bhatt, Rousseau, Pardo-Alvarez, and Duffy 2015] */

2015-04-19T01:16:54Z

‎Yu: [Yu, Bhatt, Rousseau, Pardo-Alvarez, and Duffy 2015]

Mimi: /* Tzeng: [Tzeng and Park 2015] */ added Brian Dz to author line

2015-04-17T21:01:48Z

‎Tzeng: [Tzeng and Park 2015]: added Brian Dz to author line

Xuan: /* Yu: [Yu, Bhatt, Rousseau, Pardo-Alvarez, and Duffy 2015] */

2015-04-17T18:34:45Z

‎Yu: [Yu, Bhatt, Rousseau, Pardo-Alvarez, and Duffy 2015]

Sandra: /* [Villamizar, Pai, and Harmon 2015] */

2015-04-17T18:14:52Z

‎[Villamizar, Pai, and Harmon 2015]

Sandra: /* [Villamizar, Pai, and Harmon 2015] */

2015-04-17T17:37:55Z

‎[Villamizar, Pai, and Harmon 2015]

Sandra: /* [Villamizar, Pai, and Harmon 2015] */

2015-04-17T17:37:10Z

‎[Villamizar, Pai, and Harmon 2015]

Sandra: /* [Villamizar, Pai, and Harmon 2015] */

2015-04-17T17:20:17Z

‎[Villamizar, Pai, and Harmon 2015]

@@ Line 73: / Line 73: @@
 * '''Authors and affiliations:''' Bakinam T. Essawy, [[Jon Goodall | Jonathan L. Goodall]], Mirza Billah, and Hao Xu, Department of Civil and Environmental Engineering, University of Virginia.
 * '''Keywords of research area:''' Hydrology, Automating workflows, Reproducibility, sharing
-* '''Tentative title:''' Post-processing Workflows Using Data Grids to Support Hydrologic Modeling
+* '''Tentative title:''' Using iRODS Workflow Structured Objects to Support Hydrologic Modeling of Regional-Scale Systems
 * '''Short abstract:''' Data grids are architectures that allow scientists to access and share large data sets that are geographically distributed on the Internet, but appear to the scientist as a single file management system. Data grids are useful for scientific communities, like hydrology, that rely on multiple resource providers and data resources that are distributed across the Internet. One data grid technology is the Integrated Rule-Oriented System (iRODS). This paper leverages iRODS and demonstrates how it can be used to access distributed data, encapsulate hydrological modeling knowledge as workflows, and interoperate with other community-driven cyberinfrastructures. Included within iRODS is the concept of Workflow Structured Objects (WSO) that can be used to automate data processing using data collections stored within iRODS. A use case is presented that demonstrates creating WSOs that automate the creation of data visualizations from large model output collections. By co-locating the workflow used to create the visualization with the data collection, the use case demonstrates how data grid technology aids in reuse, reproducibility, and sharing of workflows within scientific communities.  The use case leverages output from a hydrologic model (the Variable Infiltration Capacity model) for the Carolinas region of the US, and is part of a larger effort under the DataNet Federation Consortium (DFC) project that aims to demonstrate data and computational interoperability across scientific communities.
 * '''Challenge:''' This paper discusses how to automate workflows to make it reproducible and sharable by other disciplines.

@@ Line 225: / Line 225: @@
 {{#set:
 	Owner=Chris_Duffy|
 	Participants=Scott_Peckham|
 	Participants=Cedric_David|
@@ Line 240: / Line 239: @@
 	Participants=Xuan_Yu|
 	Participants=Yolanda_Gil|
-	Progress=80|
+	Participants=Jon_Goodall|
 	StartDate=2015-03-10|
 	TargetDate=2015-03-16|
 	Type=Low}}

@@ Line 225: / Line 225: @@
 {{#set:
 	Owner=Chris_Duffy|
 	Participants=Scott_Peckham|
 	Participants=Cedric_David|

@@ Line 183: / Line 183: @@
 Chris Duffy, Department of Civil & Environmental Engineering, Pennsylvania State University.
 * '''Keywords of research area:''' coupled processes, integrated hydrologic modeling, PIHM, surface flow, subsurface flow, open science
-* '''Tentative title:''' Learning integrated modeling of coupled surface and subsurface hydrology from scratch
+* '''Tentative title:''' Learn integrated modeling of coupled surface and subsurface hydrology from scratch
 * '''Short abstract:''' Integrated modeling of coupled surface and subsurface flow for diverse earth system processes is of current interest to researchers not only to establish the interconnectedness of hydrological, and atmospheric processes, but also to understand the local- scale features of land-surface energy balances, biogeochemical and ecological processes, geochemical weathering and landscape evolution dynamics. A growing number of complex hydrologic models have been used for resolving environmental processes, hypothesis testing, hydrologic predictions for effective watershed management, though very few of these resources been made accessible to the potentially large group of model users. The users have to invest an extraordinary amount of time and effort to reproduce, and understand the workflow of hydrologic simulation in a modeling paper. To provide a challenging and stimulating use case focusing on integrated modeling of coupled surface and subsurface flow, we describe the use case for a new user of an integrated process model PIHM (Penn State Integrated Hydrologic Model). The user is guided through the data and model development process by reproducing a numerical benchmarking example, and a real watershed application. Specifically, we document PIHM and its modeling workflow to enable basic understanding of simulating coupled surface and subsurface flow processes. We detail the strategy of a new user attempting to implement a community model and national geospatial and data services. In addition, we describe the user experience as an important dimension in the modeling workflow, and enable clear strategy for provenance and deeper communications between model developers and users. The workflow has important implications for smoothing, accelerating and automating open scientific collaborations in geosciences research.
 * '''Challenge:''' Reproducibility; Reproduce published simulations by a existing model with the latest version. Benchmarking modeling application for numerical experiment and field data.

@@ Line 152: / Line 152: @@
 * '''Expected submission date:''' Late June 2015
-=== Tzeng: [Tzeng and Park 2015] ===
+=== Tzeng: [Tzeng, Park, and Dzwonkowski 2015] ===
 * '''Authors and affiliations:''' [[Mimi Tzeng]], Brian Dzwonkowski (DISL); Kyeong Park (TAMU Galveston)

@@ Line 168: / Line 168: @@
 * '''Keywords of research area:''' River Ecohydrology
 * '''Tentative title:''' Producing long-term series of whole-stream metabolism using readily available data.
-* '''Short abstract:''' Continuous water quality and river discharge data that are readily available through government websites may be used to produce valuable information about key processes within a river ecosystem. In this paper I describe in detail the steps for acquisition and processing of river flow, dissolved oxygen, temperature, and specific conductance data that, combined with atmospheric data and physical properties of the river reach of interest, allow for the production of a long-term series of whole stream metabolism. This information is key in understanding the structure and function of an ecosystem such as the San Joaquin River in the Central Valley of California which has been increasingly degraded during the last 60 years due to intensive human intervention but now, since 2010, has been going through a restoration effort. The key advantage of this tool is that it uses readily available information to produce knowledge about a river ecosystem. This set of scripts, written in the R code, can be used immediately for any other river for which the key parameters (river flow, dissolved oxygen, temperature, and specific conductivity) are available. The scripts can also be modified by users to fit their particular site conditions.
+* '''Short abstract:''' Continuous water quality and river discharge data that are readily available through government websites may be used to produce valuable information about key processes within a river ecosystem. In this technical note, I describe in detail the steps for acquisition and processing of river flow, dissolved oxygen, temperature, and specific conductance data that, combined with atmospheric data and physical properties of the river reach of interest, allow for the production of a long-term series of whole stream metabolism, an important piece of information for the purposes of understanding the structure and function of river ecosystems. The restoration reach of the San Joaquin River in California (USA) has been intensively instrumented since 2010 and serves as an ideal case for testing this tool. The set of scripts, written in the R code, can be used immediately for any other river for which the key parameters (river flow, dissolved oxygen, temperature, and specific conductivity) are available and can be modified by the new users to fit their particular site conditions.
 * '''Challenge:''' Reproducibility; Dark Code; Document new software/applications. This set of scripts was written after the necessity of generating daily estimates of metabolic rates for long periods of time and at various sites within the San Joaquin River.

@@ Line 171: / Line 171: @@
 * '''Challenge:''' Reproducibility; Dark Code; Document new software/applications. This set of scripts was written after the necessity of generating daily estimates of metabolic rates for long periods of time and at various sites within the San Joaquin River.
-* '''Relationship to other publications:''' This will be a new publication
+* '''Relationship to other publications:''' This will be a new publication - Potentially a Technical Note
 * '''Pointer to the wiki page that documents the article:''' [[Document_GPF_activities_by_Sandra_Villamizar | Page]]
 * '''Expected submission date:''' June 2015

@@ Line 165: / Line 165: @@
 === [Villamizar, Pai, and Harmon 2015] ===
-* '''Authors and affiliations:''' [[Sandra Villamizar]],[[Henry Pai]] and [[Thomas Harmon]], University of California, Merced
+* '''Authors and affiliations:''' [[Sandra Villamizar]], Henry Pai and Thomas Harmon, University of California, Merced
-* '''Keywords of research area:''' river ecohydrology
+* '''Keywords of research area:''' River Ecohydrology
 * '''Tentative title:''' Producing long-term series of whole-stream metabolism using readily available data.
 * '''Short abstract:''' Continuous water quality and river discharge data that are readily available through government websites may be used to produce valuable information about key processes within a river ecosystem. In this paper I describe in detail the steps for acquisition and processing of river flow, dissolved oxygen, temperature, and specific conductance data that, combined with atmospheric data and physical properties of the river reach of interest, allow for the production of a long-term series of whole stream metabolism. This information is key in understanding the structure and function of an ecosystem such as the San Joaquin River in the Central Valley of California which has been increasingly degraded during the last 60 years due to intensive human intervention but now, since 2010, has been going through a restoration effort. The key advantage of this tool is that it uses readily available information to produce knowledge about a river ecosystem. This set of scripts, written in the R code, can be used immediately for any other river for which the key parameters (river flow, dissolved oxygen, temperature, and specific conductivity) are available. The scripts can also be modified by users to fit their particular site conditions.