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	<title>Comments on: On Software in Astronomy</title>
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		<title>By: Home Wall Decals</title>
		<link>http://sarahaskew.net/2010/03/01/on-software-in-astronomy/comment-page-1/#comment-12930</link>
		<dc:creator>Home Wall Decals</dc:creator>
		<pubDate>Mon, 28 Mar 2011 12:41:53 +0000</pubDate>
		<guid isPermaLink="false">http://sarahaskew.net/?p=1884#comment-12930</guid>
		<description>What ever happened with the SETI thing?  My friend had the screensaver installed on his website - the one that ran through all the data in the background searching for extra-terrestrial contact.  Did they ever find anything at all?  If so, I wonder if they&#039;d reveal it.  :)</description>
		<content:encoded><![CDATA[<p>What ever happened with the SETI thing?  My friend had the screensaver installed on his website &#8211; the one that ran through all the data in the background searching for extra-terrestrial contact.  Did they ever find anything at all?  If so, I wonder if they&#8217;d reveal it.  <img src='http://sarahaskew.net/wp-includes/images/smilies/icon_smile.gif' alt=':)' class='wp-smiley' /> </p>
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		<title>By: On software in astronomy &#124; Science 3.0 Blogging Contest</title>
		<link>http://sarahaskew.net/2010/03/01/on-software-in-astronomy/comment-page-1/#comment-8773</link>
		<dc:creator>On software in astronomy &#124; Science 3.0 Blogging Contest</dc:creator>
		<pubDate>Wed, 03 Nov 2010 17:07:11 +0000</pubDate>
		<guid isPermaLink="false">http://sarahaskew.net/?p=1884#comment-8773</guid>
		<description>[...] Sarah Kendrew. Originally posted at &#8216;One Small Step&#8216;. Posted with Author&#8217;s [...]</description>
		<content:encoded><![CDATA[<p>[...] Sarah Kendrew. Originally posted at &#8216;One Small Step&#8216;. Posted with Author&#8217;s [...]</p>
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		<title>By: sarah</title>
		<link>http://sarahaskew.net/2010/03/01/on-software-in-astronomy/comment-page-1/#comment-3665</link>
		<dc:creator>sarah</dc:creator>
		<pubDate>Tue, 06 Apr 2010 10:05:00 +0000</pubDate>
		<guid isPermaLink="false">http://sarahaskew.net/?p=1884#comment-3665</guid>
		<description>OK so a few ideas seem to emerge here:
- repositories good!
- existing commercial repositories like git, sourceforge, also good.
- we should publish more papers about software and existing journals are suitable for this (I&#039;m really liking git btw)
- developing software in astronomy in terms of manpower and funding is .... a complicated issue?

Irrespective of who does it or where to host it, I&#039;m still a little stuck on my original question: what is the best way for observatories to offer their data to observers? Provide both raw and reduced (via &quot;standard but non-optimal&quot; pipeline) data? Provide only raw data plus reduction pipeline? And what is the correct balance between block-boxy pipeline and loose set of modules, transparent and flexible enough for advanced users to get the precision and insight they want? There seem to be a number of use cases for observatory archive data whose requirements are conflicting.</description>
		<content:encoded><![CDATA[<p>OK so a few ideas seem to emerge here:<br />
- repositories good!<br />
- existing commercial repositories like git, sourceforge, also good.<br />
- we should publish more papers about software and existing journals are suitable for this (I&#8217;m really liking git btw)<br />
- developing software in astronomy in terms of manpower and funding is &#8230;. a complicated issue?</p>
<p>Irrespective of who does it or where to host it, I&#8217;m still a little stuck on my original question: what is the best way for observatories to offer their data to observers? Provide both raw and reduced (via &#8220;standard but non-optimal&#8221; pipeline) data? Provide only raw data plus reduction pipeline? And what is the correct balance between block-boxy pipeline and loose set of modules, transparent and flexible enough for advanced users to get the precision and insight they want? There seem to be a number of use cases for observatory archive data whose requirements are conflicting.</p>
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		<title>By: SarahAskew &#187; Making my software open</title>
		<link>http://sarahaskew.net/2010/03/01/on-software-in-astronomy/comment-page-1/#comment-3664</link>
		<dc:creator>SarahAskew &#187; Making my software open</dc:creator>
		<pubDate>Tue, 06 Apr 2010 09:54:55 +0000</pubDate>
		<guid isPermaLink="false">http://sarahaskew.net/?p=1884#comment-3664</guid>
		<description>[...] thinking  about software development in astronomy and talking about it with friends at work and on this blog, I thought it was about time I put my money where my mouth is. I too write software &#8211; in [...]</description>
		<content:encoded><![CDATA[<p>[...] thinking  about software development in astronomy and talking about it with friends at work and on this blog, I thought it was about time I put my money where my mouth is. I too write software &#8211; in [...]</p>
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		<title>By: Rob Seaman</title>
		<link>http://sarahaskew.net/2010/03/01/on-software-in-astronomy/comment-page-1/#comment-3539</link>
		<dc:creator>Rob Seaman</dc:creator>
		<pubDate>Sat, 03 Apr 2010 07:35:58 +0000</pubDate>
		<guid isPermaLink="false">http://sarahaskew.net/?p=1884#comment-3539</guid>
		<description>No astronomy project will ever have an army of software engineers.  And that&#039;s a good thing - see Fred Brooks&#039; http://en.wikipedia.org/wiki/The_Mythical_Man-Month.  In general, with very few exceptions, development and maintenance activities for astronomical software are starved for resources.

Astronomy is research.  Research is exploration.  Exploration requires unprecedented approaches to problem solving - for software systems as much as or more so than any other part of the empirical exercise.

That said, there is a long history of software development in astronomy.  Entire programming languages and computing environments have been invented to solve our problems.  Modern software development is often more about logistics than algorithms.

The regular ADASS conferences and software sessions at the SPIE are joined in any given year by more than a few more targeted astronomy software related meetings.  And then there&#039;s the IVOA umbrella of activities.  As in any community, attending the right meetings is a good first step to meeting the prerequisite of comprehending the complete context of a problem.

Many of these meetings result in published volumes or online proceedings that have a shorter turnaround than the refereed literature.  The shelf life of software papers is often quite short.  Peer reviewed journal articles remain an option for projects amounting to applied computer science research, more than exercises in already established best-practice engineering.

Which is to say that there are numerous opportunities to collaborate on software projects of wide utility to the community without duplicating efforts in progress.  More traction might be gained from contacting well-established projects with suggestions for joint projects addressing missing functionality, than from undertaking a DIY program.

Production software development is not as easy as it might seem on the surface.  Robust software doesn&#039;t just follow automatically, no matter how good the initial idea is.  And unless your career goal is computer programming, somebody other than yourself has to be identified to maintain, fix and grow the software package once it is released into the wild.</description>
		<content:encoded><![CDATA[<p>No astronomy project will ever have an army of software engineers.  And that&#8217;s a good thing &#8211; see Fred Brooks&#8217; <a href="http://en.wikipedia.org/wiki/The_Mythical_Man-Month" rel="nofollow">http://en.wikipedia.org/wiki/The_Mythical_Man-Month</a>.  In general, with very few exceptions, development and maintenance activities for astronomical software are starved for resources.</p>
<p>Astronomy is research.  Research is exploration.  Exploration requires unprecedented approaches to problem solving &#8211; for software systems as much as or more so than any other part of the empirical exercise.</p>
<p>That said, there is a long history of software development in astronomy.  Entire programming languages and computing environments have been invented to solve our problems.  Modern software development is often more about logistics than algorithms.</p>
<p>The regular ADASS conferences and software sessions at the SPIE are joined in any given year by more than a few more targeted astronomy software related meetings.  And then there&#8217;s the IVOA umbrella of activities.  As in any community, attending the right meetings is a good first step to meeting the prerequisite of comprehending the complete context of a problem.</p>
<p>Many of these meetings result in published volumes or online proceedings that have a shorter turnaround than the refereed literature.  The shelf life of software papers is often quite short.  Peer reviewed journal articles remain an option for projects amounting to applied computer science research, more than exercises in already established best-practice engineering.</p>
<p>Which is to say that there are numerous opportunities to collaborate on software projects of wide utility to the community without duplicating efforts in progress.  More traction might be gained from contacting well-established projects with suggestions for joint projects addressing missing functionality, than from undertaking a DIY program.</p>
<p>Production software development is not as easy as it might seem on the surface.  Robust software doesn&#8217;t just follow automatically, no matter how good the initial idea is.  And unless your career goal is computer programming, somebody other than yourself has to be identified to maintain, fix and grow the software package once it is released into the wild.</p>
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		<title>By: Ben Weiner</title>
		<link>http://sarahaskew.net/2010/03/01/on-software-in-astronomy/comment-page-1/#comment-3458</link>
		<dc:creator>Ben Weiner</dc:creator>
		<pubDate>Thu, 01 Apr 2010 01:35:40 +0000</pubDate>
		<guid isPermaLink="false">http://sarahaskew.net/?p=1884#comment-3458</guid>
		<description>Thomas, I think computational astronomy is perfectly on-topic for the existing journals.  If you think a new journal would improve matters, that&#039;s fine (I&#039;d worry about ghetto-izing the field, though).  However, I don&#039;t think you should rule out the regular journals, the scope statement of the ApJ specifically welcomes this type of paper and MNRAS also publishes computational papers.  For example here is a radiative transfer code paper in MNRAS: P. Jonsson 2006, http://adsabs.harvard.edu/abs/2006MNRAS.372....2J</description>
		<content:encoded><![CDATA[<p>Thomas, I think computational astronomy is perfectly on-topic for the existing journals.  If you think a new journal would improve matters, that&#8217;s fine (I&#8217;d worry about ghetto-izing the field, though).  However, I don&#8217;t think you should rule out the regular journals, the scope statement of the ApJ specifically welcomes this type of paper and MNRAS also publishes computational papers.  For example here is a radiative transfer code paper in MNRAS: P. Jonsson 2006, <a href="http://adsabs.harvard.edu/abs/2006MNRAS.372....2J" rel="nofollow">http://adsabs.harvard.edu/abs/2006MNRAS.372&#8230;.2J</a></p>
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		<title>By: Ben Weiner</title>
		<link>http://sarahaskew.net/2010/03/01/on-software-in-astronomy/comment-page-1/#comment-3457</link>
		<dc:creator>Ben Weiner</dc:creator>
		<pubDate>Thu, 01 Apr 2010 01:29:13 +0000</pubDate>
		<guid isPermaLink="false">http://sarahaskew.net/?p=1884#comment-3457</guid>
		<description>I don&#039;t want to promote &quot;software developer&quot; as a separate category of scientist.  That&#039;s part of our current situation, where software is an activity that is somehow distinct from doing &quot;real science.&quot;  I want us to recognize that developing good software is part of being an observer, theorist, or instrumentalist.

In my opinion, much of the really useful public software in the community&#039;s hands has been built by small numbers of scientists who needed to solve a problem they encountered in their own work, for example: DAOphot, the SDSS &quot;unofficial&quot; spectroscopic pipeline (which was essentially assembled by a few postdocs), GADGET; these are observer, instrument, theory activities respectively.

One of the major problems is that cleaning up software for release, documenting it, and/or writing a paper about it take a lot of effort, and since the rewards for it are relatively small (and there is NO way to get funding for it - even for the page charges, unless it falls under the science topic of a grant you have), few people write it up or publish.  This is one of the problems I claim that we need to change.

I agree with Kelle&#039;s comments about including software as part of instrument design/proposal.  There are still problems we discussed in the paper (even with good intentions, software comes last and the funding gets squeezed).  However, there are also people out there who think that because more or less everyone can program, reduction software is properly fobbed off on grad students or postdocs after construction, and this attitude needs to change.  Even big instruments for large telescopes in the US often have very little funding for software (Keck did not pay for the scientists who wrote the DEIMOS pipeline, for example).  I think ESO has bigger teams and takes more of the hired-programmer approach, which has its own set of drawbacks.

If you read our white paper, at no time did we recommend brewing one&#039;s own repository software.  The software underlying at least some of these repositories is open source. Several people seem really energized about this particular question.  I think the choice of repository is much less important, and much less difficult, than figuring out how to get the community to reorient its funding and crediting priorities to recognize the effort that goes into writing and releasing software.  If you put all your software on sourceforge and your employers and writers of letters of recommendation are fogeys who do not understand what sourceforge is (or any other repository), it is not going to help you in the long run.  (Nothing against all you wonderful fogeys out there!  I nearly am one myself.)</description>
		<content:encoded><![CDATA[<p>I don&#8217;t want to promote &#8220;software developer&#8221; as a separate category of scientist.  That&#8217;s part of our current situation, where software is an activity that is somehow distinct from doing &#8220;real science.&#8221;  I want us to recognize that developing good software is part of being an observer, theorist, or instrumentalist.</p>
<p>In my opinion, much of the really useful public software in the community&#8217;s hands has been built by small numbers of scientists who needed to solve a problem they encountered in their own work, for example: DAOphot, the SDSS &#8220;unofficial&#8221; spectroscopic pipeline (which was essentially assembled by a few postdocs), GADGET; these are observer, instrument, theory activities respectively.</p>
<p>One of the major problems is that cleaning up software for release, documenting it, and/or writing a paper about it take a lot of effort, and since the rewards for it are relatively small (and there is NO way to get funding for it &#8211; even for the page charges, unless it falls under the science topic of a grant you have), few people write it up or publish.  This is one of the problems I claim that we need to change.</p>
<p>I agree with Kelle&#8217;s comments about including software as part of instrument design/proposal.  There are still problems we discussed in the paper (even with good intentions, software comes last and the funding gets squeezed).  However, there are also people out there who think that because more or less everyone can program, reduction software is properly fobbed off on grad students or postdocs after construction, and this attitude needs to change.  Even big instruments for large telescopes in the US often have very little funding for software (Keck did not pay for the scientists who wrote the DEIMOS pipeline, for example).  I think ESO has bigger teams and takes more of the hired-programmer approach, which has its own set of drawbacks.</p>
<p>If you read our white paper, at no time did we recommend brewing one&#8217;s own repository software.  The software underlying at least some of these repositories is open source. Several people seem really energized about this particular question.  I think the choice of repository is much less important, and much less difficult, than figuring out how to get the community to reorient its funding and crediting priorities to recognize the effort that goes into writing and releasing software.  If you put all your software on sourceforge and your employers and writers of letters of recommendation are fogeys who do not understand what sourceforge is (or any other repository), it is not going to help you in the long run.  (Nothing against all you wonderful fogeys out there!  I nearly am one myself.)</p>
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		<title>By: Thomas Robitaille</title>
		<link>http://sarahaskew.net/2010/03/01/on-software-in-astronomy/comment-page-1/#comment-3443</link>
		<dc:creator>Thomas Robitaille</dc:creator>
		<pubDate>Wed, 31 Mar 2010 15:03:03 +0000</pubDate>
		<guid isPermaLink="false">http://sarahaskew.net/?p=1884#comment-3443</guid>
		<description>The desire to have an astronomy-specific software repository is a perfect example of astronomers wanting to yet again re-invent the wheel!

Who would fund such a repository? What would happen if funding stopped? There is no reason why it would be more fail-safe than say github or sourceforge. In fact, the latter two are so widely used, that I would actually rather trust my code to them than to an astronomy specific repository. The fact that existing solutions are so popular also means that the quality of the websites is much higher than could be achieved by a couple of software developers on an astronomy grant trying to develop something &#039;from scratch&#039;.

Developers should just use whatever existing solutions there are for code hosting. I do think it would be nice to have a centralized wiki with links to the different projects on e.g. sourceforge or github, but that would be relatively simple to develop in comparison to an &#039;astronomy sourceforge&#039;.

I think a &#039;Computational Astronomy &amp; Astrophysics&#039; journal is long overdue. I want to release a radiation transfer code later this year (on sourceforge), and plan to write a paper, but it&#039;s very hard to figure out what journal would accept such a paper!</description>
		<content:encoded><![CDATA[<p>The desire to have an astronomy-specific software repository is a perfect example of astronomers wanting to yet again re-invent the wheel!</p>
<p>Who would fund such a repository? What would happen if funding stopped? There is no reason why it would be more fail-safe than say github or sourceforge. In fact, the latter two are so widely used, that I would actually rather trust my code to them than to an astronomy specific repository. The fact that existing solutions are so popular also means that the quality of the websites is much higher than could be achieved by a couple of software developers on an astronomy grant trying to develop something &#8216;from scratch&#8217;.</p>
<p>Developers should just use whatever existing solutions there are for code hosting. I do think it would be nice to have a centralized wiki with links to the different projects on e.g. sourceforge or github, but that would be relatively simple to develop in comparison to an &#8216;astronomy sourceforge&#8217;.</p>
<p>I think a &#8216;Computational Astronomy &amp; Astrophysics&#8217; journal is long overdue. I want to release a radiation transfer code later this year (on sourceforge), and plan to write a paper, but it&#8217;s very hard to figure out what journal would accept such a paper!</p>
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		<title>By: Kelle Cruz</title>
		<link>http://sarahaskew.net/2010/03/01/on-software-in-astronomy/comment-page-1/#comment-3441</link>
		<dc:creator>Kelle Cruz</dc:creator>
		<pubDate>Wed, 31 Mar 2010 12:21:06 +0000</pubDate>
		<guid isPermaLink="false">http://sarahaskew.net/?p=1884#comment-3441</guid>
		<description>Software developers can (and do) publish their papers in PASP but what&#039;s missing is the respect and *incentive* factor. Writing data reduction software is just not perceived as being as important as other endeavors. I dream of a day when a department is composed of observers, theorists, instrumentalists, and software developers. The standard now seems to be that most software -- even for widely used instruments on big telescopes --  is written in someone&#039;s spare time and on the side. TripleSpecNIRES

I&#039;ve been thinking for a while that this problem needs to be addressed similar to the way NSF took on Broader Impacts.  Basically, any proposal to build a new instrument needs to also include a plan for the data reduction pipeline and will not be considered for funding without addressing the issue. It seems common for big, survey instruments to think about the pipeline from the beginning, but this does not seem true for the smaller workhorses.</description>
		<content:encoded><![CDATA[<p>Software developers can (and do) publish their papers in PASP but what&#8217;s missing is the respect and *incentive* factor. Writing data reduction software is just not perceived as being as important as other endeavors. I dream of a day when a department is composed of observers, theorists, instrumentalists, and software developers. The standard now seems to be that most software &#8212; even for widely used instruments on big telescopes &#8212;  is written in someone&#8217;s spare time and on the side. TripleSpecNIRES</p>
<p>I&#8217;ve been thinking for a while that this problem needs to be addressed similar to the way NSF took on Broader Impacts.  Basically, any proposal to build a new instrument needs to also include a plan for the data reduction pipeline and will not be considered for funding without addressing the issue. It seems common for big, survey instruments to think about the pipeline from the beginning, but this does not seem true for the smaller workhorses.</p>
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		<title>By: sarah</title>
		<link>http://sarahaskew.net/2010/03/01/on-software-in-astronomy/comment-page-1/#comment-3440</link>
		<dc:creator>sarah</dc:creator>
		<pubDate>Wed, 31 Mar 2010 11:38:24 +0000</pubDate>
		<guid isPermaLink="false">http://sarahaskew.net/?p=1884#comment-3440</guid>
		<description>Thanks for commenting Ben! 

Some astronomers do write papers about software or algorithms they develop, which in essence makes them citable, and I wonder what makes someone decide whether or not to publish. Size of the effort and the science that&#039;s being produced with it seem obvious - but there must be more subtle reasons too. I&#039;m in the process of putting a lot of my software online and the idea of opening this up to public scrutiny (although I&#039;ve never been at all secretive about it) is a little frightening....

I suppose also our traditional journals, except maybe PASP, are just not suited to a pure-software paper. Do we need a new peer-reviewed journal purely for software/methods/algorithms in astronomy? It could even be designed as a front end to a repository.</description>
		<content:encoded><![CDATA[<p>Thanks for commenting Ben! </p>
<p>Some astronomers do write papers about software or algorithms they develop, which in essence makes them citable, and I wonder what makes someone decide whether or not to publish. Size of the effort and the science that&#8217;s being produced with it seem obvious &#8211; but there must be more subtle reasons too. I&#8217;m in the process of putting a lot of my software online and the idea of opening this up to public scrutiny (although I&#8217;ve never been at all secretive about it) is a little frightening&#8230;.</p>
<p>I suppose also our traditional journals, except maybe PASP, are just not suited to a pure-software paper. Do we need a new peer-reviewed journal purely for software/methods/algorithms in astronomy? It could even be designed as a front end to a repository.</p>
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