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Add downloader script for projects & update projects w/ current data
Downloaded 2018-05-04 16:59 CDT
1 parent f151b10 commit ea9ed39

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-2
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‎converters/download_projects.py

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#!/usr/bin/env python3
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from subprocess import Popen, PIPE
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import os
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import sys
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import urllib.parse
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import urllib.request
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params = {
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"count_active": "on",
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"count_enabled": "on",
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}
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query = urllib.parse.urlencode(params)
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url = "https://myosg.grid.iu.edu/miscproject/xml?count_sg_1&%s" % query
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with urllib.request.urlopen(url) as req:
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data = req.read().decode("utf-8")
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newenv = os.environ.copy()
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newenv["XMLLINT_INDENT"] = "\t"
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proc = Popen("xmllint --format -", stdin=PIPE, stdout=sys.stdout, shell=True, encoding="utf-8", env=newenv)
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proc.communicate(data)

‎projects/DiffCorr.yaml

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Department: Department of Physics and Astronomy
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Description: Dynamics of electrons with different degree of correlations
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FieldOfScience: Computational Condensed Matter Physics
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ID: '506'
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Name: DiffCorr
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Organization: University of Tennessee
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PIName: Jacek Herbrych
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Sponsor:
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CampusGrid:
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ID: '14'
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Name: OSG Connect

‎projects/FDDRCS.yaml

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Department: Economics
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Description: The Project entails the estimation of a general equilibrium heterogenous
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firms dynamic model with default. The Project is related to the paper "Financial
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Development, Default Rates, and Credit Spreads" (abstract below), at the moment
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R&R at the Economic Journal.
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FieldOfScience: Economics
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ID: '509'
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Name: FDDRCS
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Organization: CU Boulder
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PIName: Alessandro Peri
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Sponsor:
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CampusGrid:
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ID: '14'
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Name: OSG Connect

‎projects/GLUEX.yaml

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@@ -4,7 +4,7 @@ FieldOfScience: Nuclear Physics
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ID: '405'
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Name: GLUEX
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Organization: JLAB
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PIName: Kurt Johann Strosahl
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PIName: Kurt Strosahl
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Sponsor:
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VirtualOrganization:
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ID: '99'

‎projects/GlobalDH.yaml

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Department: INSTAAR
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Description: Test a tool to deal with global data sets.
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FieldOfScience: Earth Sciences
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ID: '508'
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Name: GlobalDH
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Organization: UNIVERSITY of COLORADO at BOULDER
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PIName: Kang Wang
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Sponsor:
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CampusGrid:
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ID: '14'
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Name: OSG Connect

‎projects/cellpainting.yaml

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Department: Imaging Platform
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Description: "We aim to pioneer a new era where images of cells become\npowerful,\
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\ rich, unbiased data sources for comparing cell state. We predict that\ndoing so\
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\ will allow rapid and inexpensive interrogation of the impact of genetic\nor chemical\
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\ perturbations on a cell - useful for a variety of important\napplications in biology.\n\
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\nIn morphological profiling, we construct signatures of genes, chemicals, or\n\
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other treatments by measuring the structural changes in treated cells, as\nobserved\
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\ under a microscope. Cells are stained with fluorescent dyes that mark\nseveral\
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\ constituents, producing images from which hundreds of distinct\nmeasurements can\
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\ be extracted at the single cell level. We will carry out\nproof-of-principle computational\
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\ experiments using morphological profiling in\ndiverse and significant applications,\
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\ such as connecting unannotated genes to\nknown pathways, identifying signatures\
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\ of disease, predicting a small molecule\u2019s\nmechanism of action, enriching\
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\ chemical libraries for diverse bioactivity, and\nidentifying new compounds or\
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\ materials with desired phenotypic effects. Despite\nour successes in this field\
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\ so far, the methods development for morphological\nprofiling is a wild frontier:\
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\ novel methods are used but not compared,\nintegration with other data types (such\
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\ as transcriptomics) has not !\nbeen explored, and deep learning is not yet leveraged\
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\ to its potential. We will\ncontinue to push forward the technology development\
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\ needed in our driving\nbiological projects. We will make data and code publicly\
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\ available to catalyze\nthe field. Ultimately, we aim to develop best practices\
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\ for the field and create\nthe foundation for user-friendly, open-source tools\
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\ to discover and quantify\nrelationships among genetic or chemical perturbations\
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\ and disease state, across\na diverse array of biological areas of study and disease\
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\ areas."
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FieldOfScience: Molecular and Structural Biosciences
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ID: '510'
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Name: cellpainting
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Organization: Broad Institute
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PIName: Shantanu Singh
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Sponsor:
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CampusGrid:
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ID: '14'
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Name: OSG Connect

‎projects/polymer.yaml

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Department: Mechanical Engineering
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Description: 'Investigate the thermal conductivity of polymer and polymer
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composites using MD simulation'
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FieldOfScience: Materials Science
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ID: '507'
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Name: polymer
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Organization: University of Oklahoma
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PIName: rajmohan muthaiah
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Sponsor:
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CampusGrid:
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ID: '14'
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Name: OSG Connect

‎tests/projects.xml

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@@ -1364,6 +1364,46 @@ These proteins, like any machine, need to change shape and visit many conformati
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</VirtualOrganization>
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</Sponsor>
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</Project>
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<Project>
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<ID>510</ID>
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<Name>cellpainting</Name>
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<Description>We aim to pioneer a new era where images of cells become
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powerful, rich, unbiased data sources for comparing cell state. We predict that
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doing so will allow rapid and inexpensive interrogation of the impact of genetic
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or chemical perturbations on a cell - useful for a variety of important
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applications in biology.
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In morphological profiling, we construct signatures of genes, chemicals, or
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other treatments by measuring the structural changes in treated cells, as
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observed under a microscope. Cells are stained with fluorescent dyes that mark
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several constituents, producing images from which hundreds of distinct
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measurements can be extracted at the single cell level. We will carry out
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proof-of-principle computational experiments using morphological profiling in
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diverse and significant applications, such as connecting unannotated genes to
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known pathways, identifying signatures of disease, predicting a small molecule’s
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mechanism of action, enriching chemical libraries for diverse bioactivity, and
1385+
identifying new compounds or materials with desired phenotypic effects. Despite
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our successes in this field so far, the methods development for morphological
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profiling is a wild frontier: novel methods are used but not compared,
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integration with other data types (such as transcriptomics) has not !
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been explored, and deep learning is not yet leveraged to its potential. We will
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continue to push forward the technology development needed in our driving
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biological projects. We will make data and code publicly available to catalyze
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the field. Ultimately, we aim to develop best practices for the field and create
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the foundation for user-friendly, open-source tools to discover and quantify
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relationships among genetic or chemical perturbations and disease state, across
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a diverse array of biological areas of study and disease areas.</Description>
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<PIName>Shantanu Singh</PIName>
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<Organization>Broad Institute</Organization>
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<Department>Imaging Platform</Department>
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<FieldOfScience>Molecular and Structural Biosciences</FieldOfScience>
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<Sponsor>
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<CampusGrid>
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<ID>14</ID>
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<Name>OSG Connect</Name>
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</CampusGrid>
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</Sponsor>
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</Project>
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<Project>
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<ID>112</ID>
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<Name>CentaurSim</Name>
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</VirtualOrganization>
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</Sponsor>
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</Project>
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<Project>
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<ID>506</ID>
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<Name>DiffCorr</Name>
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<Description>Dynamics of electrons with different degree of correlations</Description>
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<PIName>Jacek Herbrych</PIName>
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<Organization>University of Tennessee</Organization>
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<Department>Department of Physics and Astronomy</Department>
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<FieldOfScience>Computational Condensed Matter Physics</FieldOfScience>
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<Sponsor>
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<CampusGrid>
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<ID>14</ID>
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<Name>OSG Connect</Name>
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</CampusGrid>
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</Sponsor>
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</Project>
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<Project>
26342689
<ID>457</ID>
26352690
<Name>Diffpred</Name>
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</CampusGrid>
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</Sponsor>
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</Project>
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<Project>
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<ID>509</ID>
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<Name>FDDRCS</Name>
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<Description>The Project entails the estimation of a general equilibrium heterogenous firms dynamic model with default. The Project is related to the paper "Financial Development, Default Rates, and Credit Spreads" (abstract below), at the moment R&amp;R at the Economic Journal.</Description>
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<PIName>Alessandro Peri</PIName>
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<Organization>CU Boulder</Organization>
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<Department>Economics</Department>
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<FieldOfScience>Economics</FieldOfScience>
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<Sponsor>
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<CampusGrid>
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<ID>14</ID>
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<Name>OSG Connect</Name>
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</CampusGrid>
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</Sponsor>
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</Project>
32023272
<Project>
32033273
<ID>486</ID>
32043274
<Name>Fermilab</Name>
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</CampusGrid>
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</Sponsor>
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</Project>
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<Project>
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<ID>508</ID>
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<Name>GlobalDH</Name>
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<Description>Test a tool to deal with global data sets.</Description>
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<PIName>Kang Wang</PIName>
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<Organization>UNIVERSITY of COLORADO at BOULDER</Organization>
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<Department>INSTAAR</Department>
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<FieldOfScience>Earth Sciences</FieldOfScience>
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<Sponsor>
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<CampusGrid>
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<ID>14</ID>
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<Name>OSG Connect</Name>
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</CampusGrid>
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</Sponsor>
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</Project>
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<Project>
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<ID>405</ID>
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<Name>GLUEX</Name>
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<Description>GlueX project</Description>
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<PIName>Kurt Johann Strosahl</PIName>
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<PIName>Kurt Strosahl</PIName>
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<Organization>JLAB</Organization>
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<Department>Physics</Department>
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<FieldOfScience>Nuclear Physics</FieldOfScience>
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</CampusGrid>
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</Sponsor>
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</Project>
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<Project>
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<ID>507</ID>
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<Name>polymer</Name>
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<Description>Investigate the thermal conductivity of polymer and polymer
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composites using MD simulation</Description>
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<PIName>rajmohan muthaiah</PIName>
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<Organization>University of Oklahoma</Organization>
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<Department>Mechanical Engineering</Department>
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<FieldOfScience>Materials Science</FieldOfScience>
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<Sponsor>
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<CampusGrid>
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<ID>14</ID>
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<Name>OSG Connect</Name>
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</CampusGrid>
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</Sponsor>
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</Project>
51095210
<Project>
51105211
<ID>469</ID>
51115212
<Name>popage</Name>

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