[ccp4bb] OT: VectorNTI alternatives - SUMMARY
Thanks for the 38 replies, both on and off the bboard. I have tested some of them and my favorites so far are ApE and Gentle which are free and quite good. But there may be others that are also good and I missed. Darren Summary: *Firstly*, good advice from Warren DeLano: 1. Be wary of relying upon free tools not based on open-source code. 2. Be extremely wary of free tools which come with a license manager. 3. Instead favor free software tools which strictly meet the established definitions of: Open Source: http://www.opensource.org/docs/osd, Free Software: http://www.gnu.org/philosophy/free-sw.html, or Public Domain: http://en.wikipedia.org/wiki/Public_domain since it is *only* those tools that can be safely taken for granted over the long haul. But be prepared to pay good money for good software! *Secondly*, if you are going to stop using VectorNTI, export valuable files in .gb format before the program locks. If this happens, contact Invitrogen and they (might) issue a short time extension as they did for me. *Recommended programs:* *Geneious *and *CLCbio *workbench are professional polished products competing with VectorNTI – but CLC free version is just a plasmid viewer really. Sebastiano and others - much much easier than VectorNTI is *ApE *( http://www.biology.utah.edu/jorgensen/wayned/ape/), which is multi-platform and very easy to use for simple tasks. I tried ApE and was really impressed, once I got past the very simple looking format. This would do most of the things required for designing vectors and works with .gb format files – Darren *Serial cloner *(http://serialbasics.free.fr/Serial_Cloner.html) suggested by James Stroud. It works only with fasta or .xdna files – so is really a DNA editor and seems to have limited Protein analysis functions, even displaying translated ORFs above DNA sequence. But splicing DNA sequences together seems efficient. Mark Brooks - recommended *BioEdit*: http://www.mbio.ncsu.edu/BioEdit/bioedit.html It has an old fashioned cluttered interface, but does do sequence editing, translation into proteins, ClustalW alignments and contig assemblies (a bit like ContigExpress in Vector NTI). It opens ABI files for sequencing data, to view the chromatograms. It uses the external programs such as clustalw alignments or cap3 to do the contig assemblies, and its licence doesn't expire! For storing everything, I put my primers, plasmid sequences, insert sequences in a MySQL database, with an HTML front end I wrote: http://plasmidb.sourceforge.net/ *Plasmi::db *also has a homespun feel to it, and only works with Firefox, for example (not other browsers). There is a primer designer page, for traditional cloning by restriction digestion etc.. I can't pretend it's in the same league as Vector NTI, though. The data is stored in a non-proprietary format; database tables which can be viewed with either the HTML pages, or MS Excel, for example. Andy Gulick recommends the *Workbench* suite at the *San Diego Supercomputer Center*. It allows you to maintain a database of protein and DNA sequence, has many tools, and allows you to create subprojects to help organize. http://workbench.sdsc.edu Yong-Fu Li suggested *Lasergene*, but not enthusiastically due to requirement to reformat files and not very good editing functions. Roger Dodd - *PlasmaDNA *which seems pretty good for the basics http://research.med.helsinki.fi/plasmadna/ . Christian Biertümpfel recommends another free tool: *pDRAW32 *( http://www.acaclone.com/ ). It runs natively under Windows and with the emulator wine on Linux. Francis Reyes - Not sure if it's been mentioned, but I personally use *EnzymeX *(http://mekentosj.com/enzymex/) .Also recommends PDF library organizer Papers (http://mekentosj.com/papers/) to be exceptional. Juan Sanchez Weatherby - GCK2 (*GeneConstructionKit*) and another * GeneInspector*. They where pretty amazing and with lots of features for plasmid design, keeping history, sharing, and lots more. I suppose they must have improved quite a lot over the years. I can't remember what the license was like (money wise) but I think you can download a free version (doesn't let you save or print things but shows what you can actually do with them). The link you need to find them is http://www.textco.com/products/index.html Bryan Lepore – Lots can be done just with with [1] *expasy tools *and [2] *sequence manipulation suite*, which is entirely downloadable for local use. http://www.bioinformatics.org/sms2/about.html (Darren says: I agree *SMS *is very useful indeed and can be run via their website – no installation) There is *GENtle *which has a whole slew of tools associated with it. There are versions for several platforms. http://gentle.magnusmanske.de/ it is pretty similar to Vector NTI (and open source for the ambitious). For Macs: Jovine Luca - *DNA Strider *(1.4) runs just fine on both Tiger and Leopard. For more info, you can contact the author directly:
Re: [ccp4bb] OT: VectorNTI alternatives
On Jan 28, 2009, at 3:47 AM, Darren Hart wrote: ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. My license recently expired. I had been running VectorNTI on my Mac through a Windows virtual machine. When the license ran out, I was unable to export any of the sequences that I had created. Now, if there was only a way to turn back time so that my computer thought it was still 2008 ... ehm ... ;) Jeff
Re: [ccp4bb] OT: VectorNTI alternatives
Hello, I spoke to Invitrogen (France) today and they said that, if asked, they would provide a 2 month free license so that people could do exactly this and recover their files. The also said they would send me details on a simple procedure to extract the data from a locked version which I will post on the bb. They told me they have 100,000 users - so hardly a minor specialist application! At €650-€4000 per license, that looks quite fruitful for them. An earlier poster made the point that it is a good thing to pay for good software. I agree and don't want to seem like a moaner, but I object to the strategy employed here on this occasion. Hence my original post to find out what the alternatives are. Darren 2009/1/30 Jeffrey Wilson wil...@ucmail.uc.edu On Jan 28, 2009, at 3:47 AM, Darren Hart wrote: ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. My license recently expired. I had been running VectorNTI on my Mac through a Windows virtual machine. When the license ran out, I was unable to export any of the sequences that I had created. Now, if there was only a way to turn back time so that my computer thought it was still 2008 ... ehm ... ;) Jeff -- ** Dr. Darren Hart, Team Leader High Throughput Protein Lab Grenoble Outstation European Molecular Biology Laboratory (EMBL) ** EMBL webpages: http://tinyurl.com/6xdltl http://tinyurl.com/667jrp Email: h...@embl.fr Tel: +33 4 76 20 77 68 Fax: +33 4 76 20 71 99 Skype: hartdarren Postal address: EMBL, 6 rue Jules Horowitz, BP181, 38042 Grenoble, Cedex 9, France **
Re: [ccp4bb] OT: VectorNTI alternatives
I'm not sure if it was already mentioned, but for those who use Vector NTI's ContigExpress to assemble and analyze sequencing data, the Staden package (http://staden.sourceforge.net/) is a great alternative. Cheers, Thomas
Re: [ccp4bb] OT: VectorNTI alternatives
Not sure if it's been mentioned, but I personally use EnzymeX(http://mekentosj.com/enzymex/ ) . Also, I find their PDF library organizer Papers (http://mekentosj.com/papers/ ) to be exceptional. Cheers FR On Jan 28, 2009, at 1:47 AM, Darren Hart wrote: Hello, After several years of offering the molecular biology software VectorNTI free to the academic community (their open access program) and building up a huge user base, Invitrogen have suddenly announced that they will no longer renew these free licences and the existing ones will be left to expire within the year. There are heavy renewal fees for anyone wishing to continue use of this software. Can anyone recommend decent alternative PC compatible alternatives? Main uses are construct and primer design, plus simple quick alignments, sequence data analysis etc. The database structure for storing sequences was pretty useful also. Ideally free, otherwise reasonably priced. I've seen CLCbio and Geneious have products, both free and paid. Any experience? Thanks, Darren EMBL Grenoble ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
[ccp4bb] OT: VectorNTI alternatives
Hello, After several years of offering the molecular biology software VectorNTI free to the academic community (their open access program) and building up a huge user base, Invitrogen have suddenly announced that they will no longer renew these free licences and the existing ones will be left to expire within the year. There are heavy renewal fees for anyone wishing to continue use of this software. Can anyone recommend decent alternative PC compatible alternatives? Main uses are construct and primer design, plus simple quick alignments, sequence data analysis etc. The database structure for storing sequences was pretty useful also. Ideally free, otherwise reasonably priced. I've seen CLCbio and Geneious have products, both free and paid. Any experience? Thanks, Darren EMBL Grenoble ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire.
Re: [ccp4bb] OT: VectorNTI alternatives
Hi Darren, much much easier than VectorNTI is ApE (http://www.biology.utah.edu/jorgensen/wayned/ape/ ), which is multi-platform and very easy to use for simple tasks. Please, could you post a summary of the answers? Thanks, ciao Sebastiano On Jan 28, 2009, at 9:47 AM, Darren Hart wrote: Hello, After several years of offering the molecular biology software VectorNTI free to the academic community (their open access program) and building up a huge user base, Invitrogen have suddenly announced that they will no longer renew these free licences and the existing ones will be left to expire within the year. There are heavy renewal fees for anyone wishing to continue use of this software. Can anyone recommend decent alternative PC compatible alternatives? Main uses are construct and primer design, plus simple quick alignments, sequence data analysis etc. The database structure for storing sequences was pretty useful also. Ideally free, otherwise reasonably priced. I've seen CLCbio and Geneious have products, both free and paid. Any experience? Thanks, Darren EMBL Grenoble ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094
Re: [ccp4bb] OT: VectorNTI alternatives
I've used serial cloner (http://serialbasics.free.fr/ Serial_Cloner.html) but not ApE, which I hope to try now that I know of it. One thing that serial cloner has going for it is a nice assembly tool that makes construct design much easier. Otherwise it could be a little less clunky in its design. editorial These days there are too many free alternatives for invitrogen to try to pilfer scientists. But I guess many companies are beginning to learn what a broken business model really means. If invitrogen were smart, they'd give their redundant NTI software away to whoever will take it and push to make it a convenient front- end ordering system for their other services which actually do have value beyond the configuration of bits on a hard-drive. (Hint: be like google.) /editorial James On Jan 28, 2009, at 1:14 AM, Sebastiano Pasqualato wrote: Hi Darren, much much easier than VectorNTI is ApE (http://www.biology.utah.edu/jorgensen/wayned/ape/ ), which is multi-platform and very easy to use for simple tasks. Please, could you post a summary of the answers? Thanks, ciao Sebastiano On Jan 28, 2009, at 9:47 AM, Darren Hart wrote: Hello, After several years of offering the molecular biology software VectorNTI free to the academic community (their open access program) and building up a huge user base, Invitrogen have suddenly announced that they will no longer renew these free licences and the existing ones will be left to expire within the year. There are heavy renewal fees for anyone wishing to continue use of this software. Can anyone recommend decent alternative PC compatible alternatives? Main uses are construct and primer design, plus simple quick alignments, sequence data analysis etc. The database structure for storing sequences was pretty useful also. Ideally free, otherwise reasonably priced. I've seen CLCbio and Geneious have products, both free and paid. Any experience? Thanks, Darren EMBL Grenoble ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094
Re: [ccp4bb] OT: VectorNTI alternatives
Hi Darren, My favourite program for editing sequences (apart from Vector NTI, which I suppose I'm going to have to delete soon), is BioEdit: http://www.mbio.ncsu.edu/BioEdit/bioedit.html It has an old fashioned cluttered interface, but does do sequence editing, translation into proteins, ClustalW alignments and contig assemblies (a bit like ContigExpress in Vector NTI). It opens ABI files for sequencing data, to view the chromatograms. It uses the external programs such as clustalw alignments or cap3 to do the contig assemblies, and its licence doesn't expire! BioEdit is quite impressive, and sometimes I use it instead of Vector NTI, even (honestly!). For storing everything, I put my primers, plasmid sequences, insert sequences in a MySQL database, with an HTML front end I wrote: http://plasmidb.sourceforge.net/ Plasmi::db also has a homespun feel to it, and only works with Firefox, for example (not other browsers). There is a primer designer page, for traditional cloning by restriction digestion etc.. I can't pretend it's in the same league as Vector NTI, though. The data is stored in a non-proprietary format; database tables which can be viewed with either the HTML pages, or MS Excel, for example. I never really believed that Vector NTI was going to stay free (even to universities etc.) for a long time, and I do think that they deserve some money for their (excellent) product. I hope that they can decide on a reasonable pricing scheme though, instead of vacillating between huge sums and nothing. They seem to be heading towards a moderate price nowadays, at least. Mark 2009/1/28 Darren Hart h...@embl.fr: Hello, After several years of offering the molecular biology software VectorNTI free to the academic community (their open access program) and building up a huge user base, Invitrogen have suddenly announced that they will no longer renew these free licences and the existing ones will be left to expire within the year. There are heavy renewal fees for anyone wishing to continue use of this software. Can anyone recommend decent alternative PC compatible alternatives? Main uses are construct and primer design, plus simple quick alignments, sequence data analysis etc. The database structure for storing sequences was pretty useful also. Ideally free, otherwise reasonably priced. I've seen CLCbio and Geneious have products, both free and paid. Any experience? Thanks, Darren EMBL Grenoble ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay CEDEX. Tel: 0169157968 Fax: 0169853715 Skype: markabrooks
Re: [ccp4bb] OT: VectorNTI alternatives
I like BioEdit too. It is PC based, downloadable, and very easy to use. It allows copy-paste of a word or text file, and does alignment, translation, back translation, etc, and more. Fabulous program. I also use Lasergene which has the long standing DNA Star, Megalign, but you have to buy a license. It also requires changing format of files to text and saving with a specific suffix such as .seq which is inconvenient. You cannot copy and paste, and when you see a good alignment, you cannot copy and paste out either. Yong-Fu Li On Wed, Jan 28, 2009 at 7:43 AM, Mark Brooks mark.x.bro...@gmail.comwrote: Hi Darren, My favourite program for editing sequences (apart from Vector NTI, which I suppose I'm going to have to delete soon), is BioEdit: http://www.mbio.ncsu.edu/BioEdit/bioedit.html It has an old fashioned cluttered interface, but does do sequence editing, translation into proteins, ClustalW alignments and contig assemblies (a bit like ContigExpress in Vector NTI). It opens ABI files for sequencing data, to view the chromatograms. It uses the external programs such as clustalw alignments or cap3 to do the contig assemblies, and its licence doesn't expire! BioEdit is quite impressive, and sometimes I use it instead of Vector NTI, even (honestly!). For storing everything, I put my primers, plasmid sequences, insert sequences in a MySQL database, with an HTML front end I wrote: http://plasmidb.sourceforge.net/ Plasmi::db also has a homespun feel to it, and only works with Firefox, for example (not other browsers). There is a primer designer page, for traditional cloning by restriction digestion etc.. I can't pretend it's in the same league as Vector NTI, though. The data is stored in a non-proprietary format; database tables which can be viewed with either the HTML pages, or MS Excel, for example. I never really believed that Vector NTI was going to stay free (even to universities etc.) for a long time, and I do think that they deserve some money for their (excellent) product. I hope that they can decide on a reasonable pricing scheme though, instead of vacillating between huge sums and nothing. They seem to be heading towards a moderate price nowadays, at least. Mark 2009/1/28 Darren Hart h...@embl.fr: Hello, After several years of offering the molecular biology software VectorNTI free to the academic community (their open access program) and building up a huge user base, Invitrogen have suddenly announced that they will no longer renew these free licences and the existing ones will be left to expire within the year. There are heavy renewal fees for anyone wishing to continue use of this software. Can anyone recommend decent alternative PC compatible alternatives? Main uses are construct and primer design, plus simple quick alignments, sequence data analysis etc. The database structure for storing sequences was pretty useful also. Ideally free, otherwise reasonably priced. I've seen CLCbio and Geneious have products, both free and paid. Any experience? Thanks, Darren EMBL Grenoble ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay CEDEX. Tel: 0169157968 Fax: 0169853715 Skype: markabrooks
Re: [ccp4bb] OT: VectorNTI alternatives - 4 Mac?
Hi Anybody have suggestions for Mac OsX alternatives? Thanks in advance, Mark
Re: [ccp4bb] OT: VectorNTI alternatives - 4 Mac?
On Wed, 28 Jan 2009, Jovine Luca wrote: On 28 Jan 2009, at 16:02, Mark Collins wrote: Hi Anybody have suggestions for Mac OsX alternatives? Thanks in advance, Mark Hi Mark, The latest version of DNA Strider (1.4) runs just fine on both Tiger and Leopard. For more info, you can contact the author directly at christian.ma...@cea.fr You could also try Christian Biertuempfel's suggestion of pDRAW32: if it works under Wine on Linux, it should work under Wine (or the commercial equivalent Codeweavers Crossover) on OS X as well. Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
Re: [ccp4bb] OT: VectorNTI alternatives - 4 Mac?
Hi all, I've recently come across the program PlasmaDNA which seems pretty good for the basics - http://research.med.helsinki.fi/plasmadna/ . It works under Mac OS X and Windows... and probably Wine on Linux too. Cheers, Roger Original Message Subject: Re: [ccp4bb] OT: VectorNTI alternatives - 4 Mac? From: Mark Collins mcoll...@convex.hhmi.columbia.edu To: CCP4BB@JISCMAIL.AC.UK Date: Wed Jan 28 15:02:17 2009 Hi Anybody have suggestions for Mac OsX alternatives? Thanks in advance, Mark -- Roger Dodd PhD The Institute of Cancer Research Chester Beatty Laboratories 237 Fulham Road London SW3 6JB UK The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] OT: VectorNTI alternatives
Hello, Thanks for all the emails (only some of which reached the bb). It is clear that I am not alone in feeling aggrieved by Invitrogen suddenly introducing licence fees, having first persuaded us to put our files and time into their free product over several years. Once the thread goes quiet, I'll summarise the suggestions for everyone's benefit. I've tried several packages today but it would be good if suggestions were accompanied by brief strengths and weaknesses. From a first view, there are a number of clunky programs that do the job. And some that are really just viewers that are difficult to use for sequence manipulation. As a lab with hundreds of constructs and primers in our database, we also appreciate the file arrangement/storage as well as the sequence analysis function. Thanks Darren 2009/1/28 Darren Hart h...@embl.fr Hello, After several years of offering the molecular biology software VectorNTI free to the academic community (their open access program) and building up a huge user base, Invitrogen have suddenly announced that they will no longer renew these free licences and the existing ones will be left to expire within the year. There are heavy renewal fees for anyone wishing to continue use of this software. Can anyone recommend decent alternative PC compatible alternatives? Main uses are construct and primer design, plus simple quick alignments, sequence data analysis etc. The database structure for storing sequences was pretty useful also. Ideally free, otherwise reasonably priced. I've seen CLCbio and Geneious have products, both free and paid. Any experience? Thanks, Darren EMBL Grenoble ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. -- ** Dr. Darren Hart, Team Leader High Throughput Protein Lab Grenoble Outstation European Molecular Biology Laboratory (EMBL) ** EMBL webpages: http://tinyurl.com/6xdltl http://tinyurl.com/667jrp Email: h...@embl.fr Tel: +33 4 76 20 77 68 Fax: +33 4 76 20 71 99 Skype: hartdarren Postal address: EMBL, 6 rue Jules Horowitz, BP181, 38042 Grenoble, Cedex 9, France **
Re: [ccp4bb] OT: VectorNTI alternatives
Hi Darren, I can recommend another free tool: pDRAW32 ( http://www.acaclone.com/ ). It runs natively under Windows but I am using it with the emulator wine on Linux. Cheers, christian Darren Hart wrote: Hello, After several years of offering the molecular biology software VectorNTI free to the academic community (their open access program) and building up a huge user base, Invitrogen have suddenly announced that they will no longer renew these free licences and the existing ones will be left to expire within the year. There are heavy renewal fees for anyone wishing to continue use of this software. Can anyone recommend decent alternative PC compatible alternatives? Main uses are construct and primer design, plus simple quick alignments, sequence data analysis etc. The database structure for storing sequences was pretty useful also. Ideally free, otherwise reasonably priced. I've seen CLCbio and Geneious have products, both free and paid. Any experience? Thanks, Darren EMBL Grenoble ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. ___ Dr. Christian Biertümpfel Laboratory of Molecular Biology NIDDK/National Institutes of Health phone: +1 301 402 4647 9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201 Bethesda, MD 20892-0580 USA ___
Re: [ccp4bb] OT: VectorNTI alternatives - 4 Mac?
There is GENtle which has a whole slew of tools associated with it. There are versions for several platforms. http://gentle.magnusmanske.de/ If you're used to Vector NTI, it is pretty similar (and open source for the ambitious). _ Cynthia Kinsland, Ph. D. Director, Protein Production and Characterization Cornell University Core Lab Center Ithaca, NY 14853 On Jan 28, 2009, at 10:02 AM, Mark Collins wrote: Hi Anybody have suggestions for Mac OsX alternatives? Thanks in advance, Mark
Re: [ccp4bb] OT: VectorNTI alternatives - 4 Mac?
Hi all, Geneouis also runs on OS X. From my experience (past two years), the program works just fine. You can download the trial at http://www.apple.com/downloads/macosx/math_science/index1.html (second page). Cheers, Yann ir. Yann Sterckx Pre-doctoral student Structural Biology Brussels, Vrije Universiteit Brussel (http://www.structuralbiology.be ) Molecular and Cellular Interactions, Vlaams Instituut Biotechnologie (http://www.vib.be ) VUB - SBB Building E, 4th 5th floor Pleinlaan 2 B-1050 Brussels Belgium e-mail: yann.ster...@vub.ac.be skype: yannsterckx On 28 Jan 2009, at 16:18, Roger Dodd wrote: Hi all, I've recently come across the program PlasmaDNA which seems pretty good for the basics - http://research.med.helsinki.fi/plasmadna/ . It works under Mac OS X and Windows... and probably Wine on Linux too. Cheers, Roger Original Message Subject: Re: [ccp4bb] OT: VectorNTI alternatives - 4 Mac? From: Mark Collins mcoll...@convex.hhmi.columbia.edu To: CCP4BB@JISCMAIL.AC.UK Date: Wed Jan 28 15:02:17 2009 Hi Anybody have suggestions for Mac OsX alternatives? Thanks in advance, Mark -- Roger Dodd PhD The Institute of Cancer Research Chester Beatty Laboratories 237 Fulham Road London SW3 6JB UK The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] OT: VectorNTI alternatives
From: Darren Hart After several years of offering the molecular biology software VectorNTI free to the academic community (their open access program) and building up a huge user base, Invitrogen have suddenly announced that they will no longer renew these free licences and the existing ones will be left to expire within the year. There are heavy renewal fees for anyone wishing to continue use of this software. This is reminiscent of what happened with both MDL's Chime and Accelrys' WebLab/DSViewer, and it serves as yet another compelling anecdote for why scientists should: 1. Be wary of relying upon free tools not based on open-source code. 2. Be extremely wary of free tools which come with a license manager. 3. Instead favor free software tools which strictly meet the established definitions of: Open Source: http://www.opensource.org/docs/osd, Free Software: http://www.gnu.org/philosophy/free-sw.html, or Public Domain: http://en.wikipedia.org/wiki/Public_domain since it is *only* those tools that can be safely taken for granted over the long haul. Of course, if taking software tools for granted isn't your top priority, then please help to improve scientific software by purchasing high-quality commercial tools, by sponsoring and/or participating in open-source projects, or by becoming a developer yourself. Cheers, Warren
Re: [ccp4bb] OT: VectorNTI alternatives - 4 Mac?
For basic analysis, editing, etc, i really like ApE, A Plasmid Editor. Versions are available for OS X, linux and Windows. http://www.biology.utah.edu/jorgensen/wayned/ape/ i find it does most everything MacVector does, and a few things MacVector does not do. What VectorNTI functionality are you looking for? Mike Michael Giffin The Scripps Research Institute Department of Molecular and Experimental Medicine 10550 North Torrey Pines Road, MEM-131 La Jolla, CA 92037 email: mjgif...@scripps.edu lab: 858-784-7758 On Wed, Jan 28, 2009 at 7:02 AM, Mark Collins mcoll...@convex.hhmi.columbia.edu wrote: Hi Anybody have suggestions for Mac OsX alternatives? Thanks in advance, Mark
