Date: Sat, 27 Oct 2012 03:42:09 -0700 (PDT) From: Tim te Beek <timteb...@gmail.com> To: cytoscape-discuss@googlegroups.com Message-Id: <6222d563-45f3-41a6-9650-037709e444cd@googlegroups.com> In-Reply-To: <afc8141e-1809-4e52-a955-2d6cb2eb3b42@googlegroups.com> References: <1f17bbc3-b3cd-4d7a-9ad7-b5d5cd495c8c@t36g2000prj.googlegroups.com> <4F05E22B.1000902@cgl.ucsf.edu> <afc8141e-1809-4e52-a955-2d6cb2eb3b42@googlegroups.com> Subject: Re: [Cytoscape-discuss] how to import a Large size text file MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_Part_1323_19426714.1351334530023" ------=_Part_1323_19426714.1351334530023 Content-Type: multipart/alternative; boundary="----=_Part_1324_20169494.1351334530023" ------=_Part_1324_20169494.1351334530023 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Marco, Not sure how it will respond to such large input files, but for delimited= =20 files input I've written an alternative input plugin:=20 http://apps.cytoscape.org/apps/alternativetableimport Let me know if it solves your problem, or if you run into trouble using=20 this alternate import plugin. Best, Tim On Saturday, October 20, 2012 12:34:10 PM UTC+2, Marco Baglivo wrote: > > Hi all, > there are some news? i'm very interested. > I've imported a dot file of 19M but i have not output, "please wait..."= =20 > indefinitely > > Il giorno gioved=C3=AC 5 gennaio 2012 18:47:23 UTC+1, Scooter Morris ha s= critto: >> >> On 12/26/2011 12:07 AM, xiangs wrote: >> > I'm new to Cytoscape and trouble to import large text file.my text >> > file have more than16000 nodes and 23370311 edges(size 1.5G). >> > i use macbook pro with i7cpu,8G memory.Also i have edited the >> > cytoscape.sh file and >> > change: >> > java -Dswing.aatext=3Dtrue -Xss10M -Xmx8G -jar cytoscape.jar >> > cytoscape.CyMain -p plugins "$@" >> > then i ran cytoscape.sh->file->import->network from table.then wait >> > wait wait.cytoscape load file 3 days and looks like will not stop.oh >> > my gold.how can i import lage size text file?can cytoscape deal this >> > large size file. >> > >> > another question: >> > i try to import a small size file(70M).load successful and the no >> > action,no network view.i had to click edit->create view then wait wait >> > wati,unfortunately no network visualization.then again edit->create >> > view and then again and then again.I gave up >> > >> > have anyone successful like this.can you tell me how to use cytoscape >> > import large file and create view.many many many thanks. >> > >> Greetings, >> Yes, I have successfully imported large networks (I don't think=20 >> I've ever imported 23M edges, though). If you want to give me a pointer= =20 >> to your 70M file, I'm happy to investigate as to why you can't visualize= =20 >> it. As I suggested previously, though, setting your java size to be=20 >> equal to the amount of memory you have is a very bad idea. The -Xmx=20 >> parameter is the heap size (the amount of memory Java can allocate for= =20 >> data), not the total footprint. By setting the heap to 8G when you only= =20 >> have 8G of memory, you are going to induce significant paging, which is= =20 >> extremely slow on a macbook (or any laptop for that matter). On an MBP= =20 >> with 8G, I would never recommend setting your heap to larger than 6G. = =20 >> 23M edges is a lot of edges, and I'm not sure any kind of visualization= =20 >> is going to be useful. Is there a way to filter the edges down a little= ? >> >> -- scooter >> >> ------=_Part_1324_20169494.1351334530023 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Marco,<div><br></div><div>Not sure how it will respond to such large inp= ut files, but for delimited files input I've written an alternative input p= lugin: <a href=3D"http://apps.cytoscape.org/apps/alternativetableimpor= t">http://apps.cytoscape.org/apps/alternativetableimport</a></div><div>Let = me know if it solves your problem, or if you run into trouble using this al= ternate import plugin.</div><div><br></div><div>Best,</div><div>Tim</div><d= iv><br>On Saturday, October 20, 2012 12:34:10 PM UTC+2, Marco Baglivo wrote= :<blockquote class=3D"gmail_quote" style=3D"margin: 0;margin-left: 0.8ex;bo= rder-left: 1px #ccc solid;padding-left: 1ex;">Hi all,<div>there are some ne= ws? i'm very interested.</div><div>I've imported a dot file of 19M but i ha= ve not output, "please wait..." indefinitely<br><br>Il giorno gioved=C3=AC = 5 gennaio 2012 18:47:23 UTC+1, Scooter Morris ha scritto:<blockquote class= =3D"gmail_quote" style=3D"margin:0;margin-left:0.8ex;border-left:1px #ccc s= olid;padding-left:1ex">On 12/26/2011 12:07 AM, xiangs wrote:<br>> I'm ne= w to Cytoscape and trouble to import large text file.my text<br>> file h= ave more than16000 nodes and 23370311 edges(size 1.5G).<br>> i use macbo= ok pro with i7cpu,8G memory.Also i have edited the<br>> cytoscape.sh fil= e and<br>> change:<br>> java -Dswing.aatext=3Dtrue -Xss10M -Xmx8G -ja= r cytoscape.jar<br>> cytoscape.CyMain -p plugins "$@"<br>> then= i ran cytoscape.sh->file->import-><wbr>network from table.then wa= it<br>> wait wait.cytoscape load file 3 days and looks like will not sto= p.oh<br>> my gold.how can i import lage size text file?can cytoscape dea= l this<br>> large size file.<br>><br>> another question:<br>> i= try to import a small size file(70M).load successful and the no<br>> ac= tion,no network view.i had to click edit->create view then wait wait<br>= > wati,unfortunately no network visualization.then again edit->create= <br>> view and then again and then again.I gave up<br>><br>> have = anyone successful like this.can you tell me how to use cytoscape<br>> im= port large file and create view.many many many thanks.<br>><br>Greetings= ,<br> Yes, I have successfully imported large networks (= I don't think <br>I've ever imported 23M edges, though). If you want = to give me a pointer <br>to your 70M file, I'm happy to investigate as to w= hy you can't visualize <br>it. As I suggested previously, though, set= ting your java size to be <br>equal to the amount of memory you have is a v= ery bad idea. The -Xmx <br>parameter is the heap size (the amount of = memory Java can allocate for <br>data), not the total footprint. By s= etting the heap to 8G when you only <br>have 8G of memory, you are going to= induce significant paging, which is <br>extremely slow on a macbook (or an= y laptop for that matter). On an MBP <br>with 8G, I would never recom= mend setting your heap to larger than 6G. <br>23M edges is a lot of e= dges, and I'm not sure any kind of visualization <br>is going to be useful.= Is there a way to filter the edges down a little?<p>-- scooter</p><p= ></p><p></p></blockquote></div></blockquote></div> ------=_Part_1324_20169494.1351334530023-- ------=_Part_1323_19426714.1351334530023--
Message from discussion how to import a Large size text file
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