{"action":"created","comment":{"url":"https://api.github.com/repos/scipy-conference/scipy_proceedings/pulls/comments/194243426","pull_request_review_id":127383229,"id":194243426,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDE5NDI0MzQyNg==","diff_hunk":"@@ -0,0 +1,485 @@\n+:author: Matthew J. Shannon\n+:email: Matthew.J.Shannon@nasa.gov\n+:institution: Universities Space Research Association, Columbia, MD\n+:institution: NASA Ames Research Center, MS245-6, Moffett Field, CA 94035-1000\n+\n+:author: Christiaan Boersma\n+:email: Christiaan.Boersma@nasa.gov\n+:institution: San José State University Research Foundation, 210 N 4th St Fl 4, San Jose, CA 95112\n+:institution: NASA Ames Research Center, MS245-6, Moffett Field, CA 94035-1000\n+\n+:bibliography: bib\n+\n+-----------------------------------------------------------------------------------------------------------------------\n+Organic Molecules in Space: Insights from the NASA Ames Molecular Database in the era of the James Webb Space Telescope\n+-----------------------------------------------------------------------------------------------------------------------\n+\n+.. class:: abstract\n+\n+   We present the software tool pypahdb to the scientific astronomical\n+   community, which is used to characterize emission from one of the\n+   most prevalent types of organic molecules in space, namely\n+   polycyclic aromatic hydrocarbons (PAHs). It leverages the detailed\n+   studies of organic molecules done at the NASA Ames Research\n+   Center. pypahdb is a streamlined Python version of the NASA Ames\n+   PAH IR Spectroscopic Database (PAHdb; `www.astrochemistry.org\n+   <http://www.astrochemistry.org/pahdb>`_) suite of IDL tools. PAHdb\n+   has been extensively used to analyze and interpret the PAH\n+   signature from a plethora of emission sources, ranging from\n+   solar-system objects to entire galaxies. pypahdb decomposes\n+   astronomical PAH emission spectra into contributing PAH sub-classes\n+   in terms of charge and size using a database-fitting technique. The\n+   inputs for the fit are spectra constructed using the spectroscopic\n+   libraries of PAHdb and take into account the detailed photo-physics\n+   of the PAH excitation/emission process.\n+\n+.. class:: keywords\n+\n+   astronomy, databases, fitting, data analysis\n+\n+Science background\n+==================\n+\n+Polycyclic aromatic hydrocarbons\n+--------------------------------\n+\n+Polycyclic aromatic hydrocarbons (PAHs) are important interstellar\n+molecules that are found throughout the Universe. They dominate the\n+mid-infrared (IR) emission of many astronomical objects, as they\n+absorb ultraviolet (UV) photons and re-emit that energy through a\n+series of IR emission features between 3-20 µm. They are seen in\n+reflection nebulae, protoplanetary disks, the diffuse interstellar\n+medium (ISM), planetary nebulae, and entire galaxies (e.g., Figure\n+:ref:`fig:M82`), among other environments. Interstellar PAHs are\n+extraordinarily large, typically containing 50-100 carbon atoms. In\n+contrast, the largest non-PAH carbon-rich interstellar molecule known,\n+HC\\ :sub:`11`\\ N, contains 11 carbon atoms. PAHs are composed of an\n+interlocking hexagonal carbon lattice with hydrogen atoms attached to\n+its periphery (see Figure :ref:`fig:PAHdb`). PAHs are exceptionally\n+stable, allowing them to survive the harsh conditions amongst a\n+remarkably wide variety of astronomical objects.\n+\n+.. figure:: fig_M82.png\n+   :align: center\n+   :scale: 55%\n+\n+   A combined visible light-IR image from the *Spitzer Space\n+   Telescope* of the galaxy Messier-82 (M82), also known as the Cigar\n+   galaxy because of its cigar-like shape in visible light. The red\n+   region streaming away from the galaxy into intergalactic space\n+   traces the IR emission from PAHs. Credits:\n+   NASA/JPL-Caltech/C. Engelbracht (Steward Observatory) and the SINGS\n+   team.\n+\n+   :label:`fig:M82`\n+\n+The importance of astronomical PAHs\n+-----------------------------------\n+\n+The unique properties of PAHs, coupled with their spectroscopic\n+response to changing astrophysical conditions and their ability to convert\n+UV photons to IR radiation, makes them powerful probes of astronomical\n+objects at all stages of the stellar life cycle. Due to their low\n+ionization potentials (6-8 eV), they allow astronomers to probe\n+properties of diffuse media in regions not normally accessible. On top\n+of this, PAHs are not only witnesses to their local environment but\n+are key players in affecting ongoing astrophysical processes.\n+\n+PAHs are believed to form in the circumstellar ejecta of late-type\n+stars, after which they become part of the ISM as the material travels\n+away from the star. They are subsequently processed in the diffuse ISM\n+by the prevalent UV field, energetic particles, and strong\n+shocks. Over time, PAHs are incorporated into dense clouds, wherein\n+they participate in ongoing chemistry and are eventually brought into\n+newly-forming star and budding planetary systems. All during this\n+evolution, PAHs exert a direct influence on their environment. They\n+play important roles in circumstellar processes and the diffuse ISM by\n+modulating radiation fields and influencing charge balance. Once\n+incorporated into dense molecular clouds, they can dominate cloud\n+cooling and promote H\\ :sub:`2`\\ -formation. PAHs also control the\n+large-scale ionization balance and thereby the coupling of magnetic\n+fields to the gas. Through their influence on the forces supporting\n+clouds against gravity, PAHs also affect the process of star formation\n+itself. They are a major contributor to the heating of diffuse atomic\n+gas in the ISM and thereby the physical conditions in such\n+environments and its structure. Through their effect on the energy and\n+ionization balance of the gas, these large molecules play an important\n+role in the diffuse ISM of galaxies, photo dissociation regions (PDRs)\n+created by massive stars interacting with their environment, and in\n+protoplanetary disk surface layers.\n+\n+Thanks to their ubiquity, PAH IR emission signatures are routinely\n+used by astronomers as probes of object type and astrophysical\n+processes. For example, the PAH IR signature is used as an indicator\n+of star formation in high redshift galaxies\n+:cite:`2014ApJ...786...31R` and to differentiate between black hole\n+and starburst engines in galactic nuclei\n+:cite:`1998ApJ...498..579G`. Those astronomers who study star- and\n+planet formation use the IR PAH signature as an indicator of the\n+geometry of circumstellar disks :cite:`2001A&A...365..476M`\n+:cite:`2009A&A...502..175B`. However, the treasure trove of\n+information about an astronomical object's local conditions and its\n+evolutionary history is only accessible through detailed spectroscopic\n+analysis. This type of analysis, along with an understanding of the\n+factors that drive the these spectroscopic changes, is now possible\n+with the software developed at the NASA Ames Research Center.","path":"papers/matthew_shannon/mshannon.rst","position":125,"original_position":125,"commit_id":"3e4667b6a21d23b852f07fa054b3447b5c8cd637","original_commit_id":"3e4667b6a21d23b852f07fa054b3447b5c8cd637","user":{"login":"dalippa","id":7816645,"node_id":"MDQ6VXNlcjc4MTY2NDU=","avatar_url":"https://avatars0.githubusercontent.com/u/7816645?v=4","gravatar_id":"","url":"https://api.github.com/users/dalippa","html_url":"https://github.com/dalippa","followers_url":"https://api.github.com/users/dalippa/followers","following_url":"https://api.github.com/users/dalippa/following{/other_user}","gists_url":"https://api.github.com/users/dalippa/gists{/gist_id}","starred_url":"https://api.github.com/users/dalippa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dalippa/subscriptions","organizations_url":"https://api.github.com/users/dalippa/orgs","repos_url":"https://api.github.com/users/dalippa/repos","events_url":"https://api.github.com/users/dalippa/events{/privacy}","received_events_url":"https://api.github.com/users/dalippa/received_events","type":"User","site_admin":false},"body":"This software package? or others? If not this package, why is this comment relevant?","created_at":"2018-06-10T02:16:41Z","updated_at":"2018-06-10T02:51:11Z","html_url":"https://github.com/scipy-conference/scipy_proceedings/pull/402#discussion_r194243426","pull_request_url":"https://api.github.com/repos/scipy-conference/scipy_proceedings/pulls/402","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/scipy-conference/scipy_proceedings/pulls/comments/194243426"},"html":{"href":"https://github.com/scipy-conference/scipy_proceedings/pull/402#discussion_r194243426"},"pull_request":{"href":"https://api.github.com/repos/scipy-conference/scipy_proceedings/pulls/402"}}},"pull_request":{"url":"https://api.github.com/repos/scipy-conference/scipy_proceedings/pulls/402","id":189834973,"node_id":"MDExOlB1bGxSZXF1ZXN0MTg5ODM0OTcz","html_url":"https://github.com/scipy-conference/scipy_proceedings/pull/402","diff_url":"https://github.com/scipy-conference/scipy_proceedings/pull/402.diff","patch_url":"https://github.com/scipy-conference/scipy_proceedings/pull/402.patch","issue_url":"https://api.github.com/repos/scipy-conference/scipy_proceedings/issues/402","number":402,"state":"open","locked":false,"title":"Paper: Organic Molecules in Space: Insights from the NASA Ames Molecular Database","user":{"login":"mattjshannon","id":6873368,"node_id":"MDQ6VXNlcjY4NzMzNjg=","avatar_url":"https://avatars3.githubusercontent.com/u/6873368?v=4","gravatar_id":"","url":"https://api.github.com/users/mattjshannon","html_url":"https://github.com/mattjshannon","followers_url":"https://api.github.com/users/mattjshannon/followers","following_url":"https://api.github.com/users/mattjshannon/following{/other_user}","gists_url":"https://api.github.com/users/mattjshannon/gists{/gist_id}","starred_url":"https://api.github.com/users/mattjshannon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mattjshannon/subscriptions","organizations_url":"https://api.github.com/users/mattjshannon/orgs","repos_url":"https://api.github.com/users/mattjshannon/repos","events_url":"https://api.github.com/users/mattjshannon/events{/privacy}","received_events_url":"https://api.github.com/users/mattjshannon/received_events","type":"User","site_admin":false},"body":"If you are creating this PR in order to submit a draft of your paper,\r\nsee http://procbuild.scipy.org/ for logs generated by the build\r\nprocess.\r\n\r\nSee the [project readme](https://github.com/scipy-conference/scipy_proceedings#build-your-paper)\r\nfor more 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