parts.igem.org:Feature requests

Revision as of 21:18, 12 June 2006 by WingZero (Talk | contribs)

• Add bug report • Add a note on Registry organization •

  1. Jkm 10:11, 12 Jul 2005 (EDT): Not sure if this is feasible, but automated sequence matching would be helpful. Similar to blast, but let me upload a set of sequence files (tagged as forward or reverse) and a BB part, and the Registry should align the sequences to verify the part. It would also be nice to save those sequence files, linked to the BB part, for future reference.
    • Ilya: A primitive version of such tool lives on my machine: http://habanero.mit.edu/cgi-bin/biobricks.pl
  2. Download the sequence with annotated features of a part or assembly in genbank format.
  3. Reshma 05:22, 14 Jul 2005 (EDT): Blast against the entire database (ideally such that BioBrick ends could automatically be ignored).
  4. Endy 11:35, 29 Jul 2005 (EDT): It would be great if there was a clear interface, or links to the already existing interface, for ordering (i) parts and (ii) parts assembly.
  5. Jkm 14:38, 29 Jul 2005 (EDT): It would be nice to have a single page that allowed editing of all the parts of a BB. For making single small changes, the current page is great. To make multiple changes (particularly when creating new parts), having to open and save each part individually is irritating.
  6. Jkm 16:44, 8 Aug 2005 (EDT): Propagate changes in basic parts through their derived parts. See, for instance, I13457 (bases 76-85 reading ...ttactatctc...) and I13528 (bases 76-86 reading ...ttactactctc...). I13457 was created first, then modified with the sequence came back with a (minor) change. I13528 remains unchanged, though it explicitly derives from I13457.
  7. BC 11:34, 26 Sep 2005 (EDT): There seems to be some difficulties currently in renaming a part in the registry. In addition while editing the different sections of a part page independently has some advantages, there is also benefit in being able to rapidly create parts that are very similar or analagous by just copying and pasting all the data about one part. Currently, this has to be done in several steps.
    • BC 15:06, 26 Sep 2005 (EDT): A related feature that might be desirable in the long term would be to allow the parallel creation of a family of composite parts that only vary in one of the parts. For example, a family of reporters each with a slightly different promoter. I'd like to be able to say, create ten parts simultaneously with each of the promoters R008X preceding E0240. X=1:10.
  8. Reshma 19:39, 3 Oct 2005 (EDT): More powerful searching of the registry. For instance, I want all parts of the form promoter.Q04400 where promoter can be any promoter. It would also be nice to specify whether you want any parts, just available parts or available and working parts. Perhaps this could be implemented via regular expression matching?
  9. BC 15:35, 8 Nov 2005 (EST): Primer design tools - It would be nice if I could enter a part number and specify two enzymes and the registry would generate sets of primers ready to PCR that part from an arbitrary piece of DNA with BioBrick ends that could be cut with the specified enzymes.
  10. Reshma 13:58, 16 Nov 2005 (EST): Enter features on the opposite strand.
    • Done. Put a 1 in the Reverse column when editing the features of a particular part.
  11. Reshma 13:58, 16 Nov 2005 (EST)]: Enter features by simply pasting the sequence of the feature into a box. Then the registry would find that feature in the part sequence (on either strand) and auto-calculate the coordinates for you. You then enter the name of the feature separately. Ideally, it would be sophisticated enough to be able to cope with multiple instances of a feature sequence.
  12. Reshma 13:58, 16 Nov 2005 (EST): Blast results should include links from matches back to their registry page.
  13. BC 16:24, 22 February 2006 (EST): A forum to ask a question such as "Does anybody have sequencing primers for BBa_R00xx?" - a registry mailing list of all users might be the best way to do this?
  14. RS 13:03, 11 March 2006 (EST): Creation of a duplicate part in the reverse orientation. This would save a person from having to reenter all the features.
  15. DE 15:28, 4 April 2006 (EDT): A recent changes feature (a la' most wikis) so that Registry users can see what's changing in near real time / real time.
    • Done. See [http://parts.mit.edu/d/parts/partsdb/changes.cgi Recent part changes].
  16. RS 17:52, 30 April 2006 (EDT): Creation of a duplicate part with a new part number. This would save the user from having to reenter features when they create a new variant of an existing part.
  17. RS 15:17, 5 June 2006 (EDT): The [http://openwetware.org/wiki/OpenWetWare:Biblio Biblio] extension for ease and standardization of entering references. I am already making use of the extension in certain parts even though the extension is not currently implemented.
  18. Bcanton 16:45, 5 June 2006 (EDT):Getting sequence information out of the registry is really awkward. I should be able to copy and paste the forward sequence, the reverse sequence, and the double stranded sequence easily. Right now, I can only get the forward strand sequence. On a related note, I know its been brought up by others but enabling the export/import of annotated genbank files would make the registry a significantly more useful tool.
    • Bcanton 17:02, 6 June 2006 (EDT): A useful feature would be to export the sequence of a part inserted into a BioBrick plasmid. This could then be annotated in your favorite sequence manipulation software.
  19. Bcanton 17:49, 6 June 2006 (EDT):It take more characters to write <partinfo>J01008</partinfo> than to write [[Part:BBa_J01008|J01008]]. Could the <partinfo> tags be renamed to <bb> maybe?
  20. Bcanton 18:05, 6 June 2006 (EDT): It would be nice if the name in the part designed field was a link to that users page or to a page listing all the parts designed by that person. Not critical by any means but it would be helpful in some situations.
  21. Drew 15:51, 7 June 2006 (EDT): This isn't a bug so much as an important new feature... the ability to export sequence information including annotation features in some standard format (e.g., genbank). Otherwise, it doesn't make sense for folks to use the Registry as a tool for annotating sequences (as the annotation information isn't exportable).
  22. WingZero 21:08, 11 June 2006 (EDT): I've noticed that many people have a fondness for the JPEG format. I would ask that you please start using the PNG format. Refer to [http://en.wikipedia.org/wiki/Wikipedia:Image_use_policy#Format Wikipedia Policy] if you don't know which format to use. As an example, take Image:Show more parts.jpg. There are hideous artifacts from the compression process. It's just plain blurry. I have uploaded Image:Show more parts.png which, not only looks better, but is smaller too.
    • Smelissali 9:40, 12 June 2006 (EDT): Apologies. Many of those are put down as placeholders until i get to a computer with photoshop or fireworks. Thanks for fixing that one for me
    • WingZero 16:55, 12 June 2006 (EDT): In that case, I fixed the others, but I don't know where Image:Availability and usefulness.jpg came from (edit:never mind, found that one). It seems many people don't know when to use JPEG, because Image:800px-TermDotPLot.JPG should never have been one in the first place (but there's nothing you can do about that without the original data). You don't need Photoshop, just use [http://www.gimp.org/ The GIMP]. It's easy and free.