From mschofie from duke.poly.edu Fri Feb 1 10:44:35 2008 From: mschofie from duke.poly.edu (Mark Schofield) Date: Fri Feb 1 15:48:04 2008 Subject: [Bio-software] Metal Search program avail. (zinc site design) Message-ID: <4C58D438-03C2-48B0-A60A-153F2E78ECDA@duke.poly.edu> I'm trying to track down a program called Metal_Search, first described in Metal Search: A computer program that helps design tetrahedral metal-binding sites Clarke, N. D.; Yuan S.-M. (1995) Proteins Struct. Funct. Genet. 1995, 23, 256. Is it still available on-line? Thanks, Mark Schofield ----------------- Mark H. Schofield Visiting Senior Research Scientist Department of Chemical and Biological Sciences Polytechnic University 6 Metrotech Center Brooklyn, New York 11201 phone: 718-260-3288 fax: 718-260-3075 e-mail: mschofie@duke.poly.edu ----------------- From darek.kedra from gmail.com Tue Feb 5 15:39:29 2008 From: darek.kedra from gmail.com (darked) Date: Tue Feb 5 16:43:19 2008 Subject: [Bio-software] Re: Free software for motif finding References: Message-ID: On Jan 29, 5:15 am, "Aneesh Krishna" wrote: > Dear All, > > Please tell me some free software for finding motifs from a set of sequences > (both nucleotide and protein). And I want to run it in windows and command > line also. > With Regards- > Aneesh.K > krishna.ane...@gmail.com > Mob: 09999061058 If you have problems with AlignACE try following this tutorial, first with test sequences then with a set of your own: http://arep.med.harvard.edu/labgc/amcguire/IBSS/alignace_exercise.html MEME/NestedMICA shall be more user friendly IMHO. Darek Kedra http://openwetware.org/wiki/Wikiomics From darek.kedra from gmail.com Tue Feb 5 15:39:46 2008 From: darek.kedra from gmail.com (darked) Date: Tue Feb 5 16:43:26 2008 Subject: [Bio-software] Re: Free software for motif finding References: Message-ID: On Jan 29, 5:15 am, "Aneesh Krishna" wrote: > Dear All, > > Please tell me some free software for finding motifs from a set of sequences > (both nucleotide and protein). And I want to run it in windows and command > line also. > With Regards- > Aneesh.K > krishna.ane...@gmail.com > Mob: 09999061058 If you have problems with AlignACE try following this tutorial, first with test sequences then with a set of your own: http://arep.med.harvard.edu/labgc/amcguire/IBSS/alignace_exercise.html MEME/NestedMICA shall be more user friendly IMHO. Darek Kedra http://openwetware.org/wiki/Wikiomics From icuesta from cnb.uam.es Wed Feb 6 06:05:20 2008 From: icuesta from cnb.uam.es (Isabel Cuesta) Date: Wed Feb 6 09:10:31 2008 Subject: [Bio-software] HBPLUS v 3.03 - Hydrogen Bond Calculator Message-ID: <47A99470.4000106@cnb.uam.es> Good morning Mr.McDonald, My name is Isabel Cuesta and I am working as a postdoctoral researcher at CNB-CSIC-Madrid. Last week I sent to you a signed copy of the CONFIDENTIALITY AGREEMENT in order to be able to use the "HBPLUS - Hydrogen Bond Calculation" package to the following address: Ian McDonald (PG) Biological Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Gower Street LONDON WC1E 6BT UK / EC Since I didn?t here anything back I am not sure whether I sent the right document to the right place or if it didn?t arrive to you office. Please, could be very helpful if you asses me in the procedure to be able to use HBplus. Thank you very much, Sincerely, Isabel From ahmed from users.sourceforge.net Wed Feb 6 17:17:35 2008 From: ahmed from users.sourceforge.net (Ahmed Moustafa) Date: Wed Feb 6 17:27:56 2008 Subject: [Bio-software] PhyloSort - a phylogenetic sorting tool Message-ID: <4e8088e7-8a0f-452c-b91d-f844ea704503@e10g2000prf.googlegroups.com> PhyloSort (http://phylosort.sourceforge.net) is an open-source user- friendly Java tool to sort phylogenetic trees by searching for subtrees that contain a monophyletic group of interest defined by operational taxonomic units. Version 1.3 has been released and it is freely available as source code and binaries (Windows, Mac and UNIX). The manuscript that describes the implementation of PhyloSort and its application to estimate the contribution of cyanobacteria to the nuclear genome of photosynthetic eukaryotes endosymbiotic gene transfer has been published at BMC Evolutionary Biology (http:// www.biomedcentral.com/1471-2148/8/6). --ahmed From rapidrecord from yahoo.es Thu Feb 7 03:44:35 2008 From: rapidrecord from yahoo.es (MIGUEL ANGEL SEBASTIAN) Date: Thu Feb 7 13:07:03 2008 Subject: [Bio-software] New software to control the radioactive material of your facility MATRALAB Message-ID: <502676.40772.qm@web26014.mail.ukl.yahoo.com> Hello, my name is Miguel Sebastian. I have created a software called MATRALAB. Please, visit my website to know more about it: www.matralab.com MATRALAB is a radiactive material stock & inventory software, very easy to use and with very innovative features, like automatic RSO validation for radioactive request, and risk evaluation for the. I have created this program from a practical point of view, since I am also work at the area of the radiological protection (I work at the Radiation Safety Office of an University Hospital, in Barcelona). With this program you can control the whole radioactive material of a facility (with unlimited laboratories, personnel and radioisotopes authorized), the activity of the radioactive waste, control the use of the radioactive products...of course, forget decay calculations, MATRALAB calculates for you. Please, visit my website and tell me what you think. Thank you for your time. --------------------------------- ?Con Mascota por primera vez? - S? un mejor Amigo Entra en Yahoo! Respuestas. From mverghese from comentis.com Fri Feb 8 18:13:34 2008 From: mverghese from comentis.com (Mary Verghese) Date: Fri Feb 8 18:17:59 2008 Subject: [Bio-software] cytotoxicity assays Message-ID: Hi, I am trying to set up cytotoxicity assays with HepG2 cells in microwell plates. I would like to know what positive controls people have used that has worked well. Thanks Mary This message (including any attachments) is intended only for the use of the individual or entity to which it is addressed and may contain information that is non-public, proprietary, privileged, confidential, and exempt from disclosure under applicable law or may constitute as attorney work product. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this communication is strictly prohibited. If you have received this communication in error, notify us immediately by telephone (650-869-7600) or delete this message immediately. Thank you. From obyupd from yahoo.com Tue Feb 12 17:33:47 2008 From: obyupd from yahoo.com (lex) Date: Wed Feb 13 12:11:44 2008 Subject: [Bio-software] cytotoxicity assays Message-ID: <222271.66329.qm@web42110.mail.mud.yahoo.com> hi, i used standard drugs. for example, in screening my compound against cancer cells, i compared the cytotoxicity of my compound than taxol. rowena ---------------- --- Original Message ---- From: lex To: weng Sent: Monday, February 11, 2008 4:16:26 PM Subject: Fw: [Bio-software] cytotoxicity assays "No eye has seen, no ear has heard, no mind has conceived what God has prepared for those who love Him" 1 Cor. 2:9 ----- Forwarded Message ---- From: Mary Verghese To: bio-soft@magpie.bio.indiana.edu Sent: Saturday, February 9, 2008 7:13:34 AM Subject: [Bio-software] cytotoxicity assays Hi, I am trying to set up cytotoxicity assays with HepG2 cells in microwell plates. I would like to know what positive controls people have used that has worked well. Thanks Mary This message (including any attachments) is intended only for the use of the individual or entity to which it is addressed and may contain information that is non-public, proprietary, privileged, confidential, and exempt from disclosure under applicable law or may constitute as attorney work product. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this communication is strictly prohibited. If you have received this communication in error, notify us immediately by telephone (650-869-7600) or delete this message immediately. Thank you. _______________________________________________ Bio-soft mailing list Bio-soft@net.bio.net http://www.bio.net/biomail/listinfo/bio-soft Never miss a thing. Make Yahoo your homepage. Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs From scarpers from mskcc.org Fri Feb 22 01:28:16 2008 From: scarpers from mskcc.org (Stefano Scarperi) Date: Fri Feb 22 09:06:17 2008 Subject: [Bio-software] Wanted: Non-linear Reg. w/Excel (update) Message-ID: Dear colleague, I was looking for an Excel template to easily calculate ic50. Can you send me a copy of your template? Thank you. Sincerely, Stefano Scarperi MD ===================================================================== Please note that this e-mail and any files transmitted with it may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. From thulsen from gmail.com Tue Feb 26 14:33:07 2008 From: thulsen from gmail.com (thulsen@gmail.com) Date: Tue Feb 26 14:50:28 2008 Subject: [Bio-software] MyJournals.org Message-ID: Do you want to have easy access to the latest issues of your favourite journals, from all over the world, just through your web browser? Please visit http://www.myjournals.org , create a login and make your pick from the 422 journals currently available. From greatking420 from yahoo.com Tue Feb 26 19:09:11 2008 From: greatking420 from yahoo.com (ftf great) Date: Wed Feb 27 13:14:08 2008 Subject: [Bio-software] Wanted: Non-linear Reg. w/Excel (update) In-Reply-To: Message-ID: <65792.69221.qm@web65515.mail.ac4.yahoo.com> Hi, I would be interested in that as well. Thanks in advance ! Faisal Farooq PhD candidate UBCO Kelowna, BC Canada Stefano Scarperi wrote: Dear colleague, I was looking for an Excel template to easily calculate ic50. Can you send me a copy of your template? Thank you. Sincerely, Stefano Scarperi MD ===================================================================== Please note that this e-mail and any files transmitted with it may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. _______________________________________________ Bio-soft mailing list Bio-soft@net.bio.net http://www.bio.net/biomail/listinfo/bio-soft --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search. From monicaabbondi from ricercaperlavita.it Thu Feb 28 08:47:57 2008 From: monicaabbondi from ricercaperlavita.it (Abbondi) Date: Thu Feb 28 11:48:58 2008 Subject: [Bio-software] AniBio Software Message-ID: <15736690.post@talk.nabble.com> Anyone do you know AniBio Software? Have you any comments? thanks Monica -- View this message in context: http://www.nabble.com/AniBio-Software-tp15736690p15736690.html Sent from the Bio.net - Bio-soft mailing list archive at Nabble.com. From zchou from genetics.wayne.edu Thu Feb 28 09:31:18 2008 From: zchou from genetics.wayne.edu (zhuocheng Hou) Date: Thu Feb 28 11:49:06 2008 Subject: [Bio-software] about the gene tree to species tree Message-ID: <8930b34e0802280631q306c68f1xfe060304a7abe5e5@mail.gmail.com> Hi All, I want to convert the gene tree into the species tree by using some software. I don't want to infer the gene loss or gain by using the GeneTree, NOTUNG etc. I just want to use the software to convert the gene tree into species tree. If the gene number is tha same as the predefined species number, that means we can directly replace the species name with gene name, but in most situations, the gene number would be less than predefined species number. so, we need find some algorithms to find the species tree. Thanks, Zhuocheng