General Licensing
Software
Support
Tips
General What are the minimum hardware requirements? Suggested requirements for Windows PCs are XP/Vista, 1GB RAM, 50 GB HD. For Intel®-based Macs, a Boot Camp created partition with Windows XP, 1GB RAM, 50GB HD.
Does Vector NTI work with Mac OSX 10.4 or 10.5? Currently Vector NTI does not work natively with Mac OS X v10.4 or 10.5. If this changes we will announce it but we do not expect this to ever change. (see above for the solution, Bootcamp, Parallels or other).
Licensing How do I install the new dynamic license for Vector NTI?
Can our lab maintain both PC and Mac versions of Vector NTI? Yes. Any combination of PC/Mac Vector NTI software and the dynamic license can be run within a group. The objects (molecule files, analysis results, etc.) within the Explorer database are completely compatible between all of these versions. Archives and Database backups are also completely compatible.
Software What are the differences between Vector NTI version 10.x and version 11? The primary difference overall is the difference in the interface between the two versions. Version 11 also has several minor new functions. These are summarized below. Clone2Seq. This is a simplified version of the Molecule Construction function available in version 10. The Molecule Construction and Design function is still accessible in version 11. VectorSelector. This is a quick way to search the Database for vectors of interest based on the vector annotations (features such as resistance markers, promoters, etc.) or restriction sites. ReGENerator. (the following is from the Invitrogen website) “As the accuracy of de novo DNA synthesis and sequencing have increased, and as the costs have decreased, designing your desired gene by building it from the ground up has become much more feasible. Indeed, this kind of “cloning” really shows its strength when the goal is to create expression constructs with a defined set of mutations: it may be significantly faster, quicker, and cheaper, to start with your desired protein sequence, mutate it as needed, attach whatever flanking sequences are required for propagation, expression, selection, purification and detection, and then synthesize your target construct chemically from individual nucleotide bases. ReGENeratorTM allows you to design such specific DNAs in silico. Simply start with your protein sequence, and if required, mutate it by substituting, adding or deleting amino acids by simply typing in new resides. Any number and type of mutation can be made in this step. Choose a codon-usage table that best reflects your experimental expression system, and ReGENeratorTM will calculate a DNA sequence that encodes your desired protein. You can add any number of flanking sequences to the 5’ and 3’ ends of the newly-created DNA—such as restriction sites, Gateway cloning sites, and expression or purification tags—then send the designed sequence electronically the secure servers at Invitrogen’s gene synthesis partner, Blue Heron® Bio. Blue Heron® will then synthesize your DNA, often in less than two weeks.” Database Backup Reminder. You can set the software to remind you to back up the local database on your computer. A summary of these and other new features can be found here: http://www.invitrogen.com/site/us/en/home/LINNEA-Online-Guides/LINNEA-Communities/Vector-NTI-Community/Vector-NTI/what-is-coming.html. Unless one of these new functions appeals to you, there is no real value in upgrading from version 10.x to version 11.
How often should I back up my Explorer Database? Ideally every day, but we suggest once a week. This process takes less than 3 minutes and will save all of the types of files within your Database. We also suggest backing up your Database in two locations; one on your computer (the default is to backup your Database to the C drive) in a folder called "VNTI Database". You should copy this folder to either your network or a CD in case your computer suffers a catastrophic failure. To back up your Database, click on the Database drop down menu within the Explorer Database, select "Database Backup..." and follow the default suggestions.
How do I connect to the Dynamic License server from home? You will need to download and install the VPN Client from one of these websites, choose the appropriate website based on your University affiliation and follow their instructions. This software is free. UNC Chapel Hill North Carolina State University East Carolina University
Are there any known bugs with Vector NTI 10.3? We know of three common problems. With AlignX after processing a sequence alignment, occasionally the graphics do not appear. This necessitates that you start your alignment over from the beginning. With ContigExpress, the program will occasionally crash; this is more common with larger assemblies >100 chromatographs and on Macs. You should occasionally save your assembly project, especially if you have made some complex editing changes that may not be easily reproducible. In addition, the Blast viewer is currently not displaying any graphics or alignments; this occurs with all PC versions of Vector NTI prior to version 10 or with 7.1 for the Mac.
Support How do I join the Vector NTI users mailing list? This mailing list is used to facilitate discussion concerning generally available bioinformatics resources as well as to being the medium for announcements of system maintenance and downtime schedules for the dynamic license version of Vector NTI. We also post tips to common Vector NTI problems and use this list to announce upcoming workshops and training sessions for Vector NTI. You can join by emailing to: tarandal@email.unc.edu and asking to be added to the list. You do not have to be a Vector NTI user to join this list but you must submit a request with an academic email address.
Are there workshops available for Vector NTI? Yes, these sessions are posted at the following website (http://bioinformatics.unc.edu/education/). The types and frequency of sessions depend on the demand, and any newly posted sessions are announced through the Vector NTI mailing list (see above question). Course descriptions for our regularly scheduled sessions can be found at the same site. These will only be offered for UNC-CH, NCSU and ECU researchers.
What kind of training sessions (levels) are offered for Vector NTI? Both Introductory and advanced levels of training are available (http://bioinformatics.unc.edu/education/). Our Introductory session is an overview of all of the components that make up Vector NTI and requires no previous experience using this software package. Our advanced sessions focus on a specific feature of Vector NTI (such as ContigExpress or Molecule Construction and Design, but not limited to those). The advanced sessions require competence with Vector NTI. We suggest that those new to Vector NTI attend an Introductory session first. All of our scheduled Introductory and advanced sessions are 2 hrs; the frequency and type of sessions depend on demand. We can arrange lab-oriented sessions for research groups, individual training and guest lectures/demos for any bioinformatics-oriented class. Any customized session can be requested by emailing tarandal@email.unc.edu. We are currently are only offering workshops at UNC-CH, NCSU, and ECU.
Who can attend/request Vector NTI training sessions? Currently Vector NTI sessions are available only at UNC-CH, NCSU and ECU, but anyone within the UNC System is free to attend these workshops. We request that any individual signing up for our regularly scheduled sessions use a UNC System email address.
Can I request a custom/individual session for how to do "X" with Vector NTI? Yes, in addition to the sessions posted on our website, we offer lab-oriented sessions for groups and individual training. Any customized session can be requested by emailing tarandal@email.unc.edu..
Do you provide paid support for Vector NTI? No. The support we provide is funded by the UNC School of Medicine (Program in Molecular Biology and Biotechnology) and is provided without charge.
What is the "UNC Shared Bioinformatics Resource"? The UNC Shared Bioinformatics Resource was originally set up by the UNC General Administration (GA) to support and train biologists within the UNC 16 Campus System in the bioinformatics tools supported by the UNC Center for Bioinformatics. Funding for this from the GA has been discontinued so we are continuing this program on a more limited basis, any inquires about this should be addressed to tarandal@email.unc.edu.
Who should I contact for help with Vector NTI related queries? Thomas Randall, Ph.D.
Tips How do I use the camera function to copy a sequence alignment? A sequence alignment cannot be directly pasted into PowerPoint without losing the color and font; this has to be done indirectly. Click once within the sequence alignment pane. Click on the camera button, select "Text" format to select the entire alignment, and click on OK. Open a Microsoft Word document and paste the alignment into an empty document. If the alignment is skewed, then repeat the process with a smaller word wrap of 30-40. Once the alignment is copied into a Word file it can then be selected and copied and the "Paste Special" function in PowerPoint can be used to move the alignment into PowerPoint.
Can my molecule files be transferred between PC and Mac versions of Vector NTI? Yes. Any molecule in your Database can be transferred between PC/Mac versions and/or static/dynamic versions of Vector NTI. Place the files into a subset (sub-base for Macs) in your Explorer Database. Archive the subset by clicking once on the subset then opening the Table dropdown menu and going to Export>Subset into archive. This archive can then be placed into the Explorer Database of a separate copy of Vector NTI by dragging.
How do I import oligonucleotides into my database? Detailed instructions on how to import oligonucleotides into your Oligo Database
How do I export oligonucleotides from my database? Detailed instructions on how to export oligonucleotides from your Oligo Database
How do I perform sequence searches of the Vector NTI database? Detailed instructions on how to perform sequence searches of the Vector NTI database |