nci60submit

=Submitting Compounds to DTP=

Once you have registered as a DTP supplier you can [|submit compounds for testing] in the 60 cell line screen. Submitting a compound involves providing the structure of the compound and various other information about it via an online form. The complete structure is required. The most important consideration for accepting a compound to test is the novelty of the structure. There are classes of compounds that are considered well studied and if a submission falls in one of these classes the decision whether to test will be based on additional information that shows that this particular compound has significantly different biological properties than previous molecules in the class. The evaluation of the submission should take a few working days. If a compound is accepted for testing, the supplier is notified and can then log on to the DTP supplier page and print out a shipping list with full instructions for shipping a sample of the compound to the DTP repository. We would like to get at least 15 mg of material, but smaller amounts can be accommodated for hard to obtain compounds. The supplier is responsible for the shipping costs. Upon receipt of the material at the repository, the compound will be assigned a NSC number and the material stored until it is time for it to be shipped to the testing facility.

Some ideas for future development
Some of the things we are working on or thinking about working on.
 * 1) Removing certificates - Installation of certificates and renewal every year is a bit of work and it is not clear that the requirement results in enough extra security to justify the work. We will work on letting users choose their own username and password (so that our choices do not have to be sent out via unencrypted email) and then we wil turn certificates off.
 * 2) A submission API - There is no reason that pointing and clicking on the website should be the only way to pass us the information we need. We will work to implement a defined interface that will allow programmers to put submission functionality into programs chemists already use.
 * 3) development of software tools for chemists - work on #2 can obviously proceed in collaboration with people who are trying to develop tools for chemists to use. We are especially interested in the [|Bioclipse project]. There are a lot of things that could be useful to chemists, including tools tools that display the highest similarity scores for a given structure to structures already in the NCI repository, tools that display the biological activity of similar compounds, tools that look for common structural features of active compounds, etc.

FAQ

 * 1) can we allow batch submissions? - We don't think that making the present web page accept multiple compounds at once is a very good way of using our development resources. First, you are only allowed 15 submission per week, so there isn't much advantage in allowing batch submissions. More importantly, we think the best way to allow users more power and flexibility in submissions is to work on the software tools described above.
 * 2) can we allow users to submit other formats? - This is an important goal, but again we think that it is best addressed via the development of software tools. The best thing for a chemist is not to worry about formats at all, but have the tools they use for structure drawing and evaluation have the capability of submission built in to them.
 * 3) what about SMILES? - the problem with SMILES is that is takes the fine details of how the structure is drawn out of the hands of the chemist and puts it into the hands of a computer program. Again, the best solution is to integrate the submission tools into the drawing software. SMILES does not have any conformation information but neither does the drawing program used on the NCI site. **//The issue is that many chemists keep lists of their compounds as SMILES and having that as an additional way to input compounds would reduce the errors of redrawing complicated structures (like we had for one of our compounds recently). To avoid that in the future we'll probably use Chemsketch to import the SMILES then export as MOL and upload to the NCI site. But being able to use the SMILES directly would be more convenient.//**