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*To*: List for IMP development <>*Subject*: Re: [IMP-dev] Linear algebra*From*: Daniel Russel <>*Date*: Thu, 15 Jan 2009 21:06:01 -0800*Domainkey-signature*: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=message-id:from:to:in-reply-to:content-type :content-transfer-encoding:x-mailer:mime-version:subject:date :references; b=ioT0bq4TARWD8aBcUFlrxbGtt2Zj0g1mbi2r/kj4By1KEIgpO8L8+oIlFoTrAx7CWG 3WvHXZNjJcw7t9Qy8HpDY5V7JMLKTTfnsBqY9l32Is0EV3nQDhRBhtC2yhITp3VZNO6+ CGvtr0Z3fStfqW+SApTgfem9yGHfsg/uNsIEo=*Reply-to*: List for IMP development <>

On Jan 15, 2009, at 8:54 PM, Seung Joong Kim <> wrote:

http://math.nist.gov/~RPozo/tnt/Is this TNT that you talk about? It looks reasonable for SVD only,but it has a limited extendibility. My opinion depends on to whatextends we will use a linear algebra package. If we have any otherplans for implementing more complicated linear algebra, then I wouldlike to vote for Boost ublas's binding since it will provide morefunctionality.- Seung Joong Kim Daniel Russel wrote:I'd like to compute a SVD in IMP, so we need to revisit the question of linear algebra packages. The two main options as I see it are:1) using some big blas implementation through boost.ublas'sbindings. Theadvantages are that operations will then be really fast. Thedisadvantages are that is is a bit complicated and introduces an(easy, since basically all systems have some blas libraryinstalled) external dependency.2) use TNT. The advantages are that is is header only and has anice license so we can hide it away internally. On the flip side,we can't count on it being installed so we have to hide it awayinternally, and it isn't the best implementation of things. It isalso a bit limited (but SVD can solve all problems :-).Unless there are counter proposals, I'll stick a copy of TNT insomewhere._______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev

**Follow-Ups**:**[IMP-dev] SingeltonModifier interface***From:*Keren Lasker <>

**References**:**[IMP-dev] Linear algebra***From:*Daniel Russel <>

**Re: [IMP-dev] Linear algebra***From:*Seung Joong Kim <>

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