• Representation of Chemical Structures
• 48 min
  1. Representation of chemical structures

  • Dr. Thomas Engel
• 35 min
  2. Chemical file formats and line notations

  • Prof. Achim Zielesny
• Visualization of Chemical Structure
• 17 min
  3. Common types of visualization of chemical structure

  • Prof. Robert M. Hanson
• Basic Algorithms in Cheminformatics
• 40 min
  4. Ring searching and aromaticity detection

  • Prof. Dr. Christoph Steinbeck
• 44 min
  5. Substructure searching, similarity calculations and fingerprints

  • Mr. Mark Rijnbeek
• 36 min
  6. Canonization, Morgan algorithm, equivalence classes

  • Dr. Markus Meringer
• Structure Databases
• 46 min
  7. Storing, searching and dissemination of chemical information

  • Prof. Achim Zielesny
• 42 min
  8. Databases, indices and structure-related queries

  • Dr. Wolf-Dietrich Ihlenfeldt
• Quantitative Structure-Activity/Property Relationships
• 40 min
  9. Overview of descriptors

  • Dr. Jörg Kurt Wegner
• Machine Learning in Cheminformatics
• 44 min
  10. Introduction to machine learning and its application in chemistry

  • Dr. Nikolas Fechner
• Cheminformatics in Drug Discovery
• 38 min
  11. Virtual screening

  • Dr. John H. Van Drie
• 47 min
  12. Pharmacophore methods in drug discovery

  • Dr. John H. Van Drie
• 65 min
  13. Pragmatic virtual fragment-based ligand design

  • Dr. Marcus Gastreich
• 44 min
  14. Chemogenomics

  • Dr. John P. Overington
• Molecular Modelling
• 62 min
  15. Molecular modelling: empirical methods

  • Prof. Tim Clark
• 59 min
  16. Molecular modelling: electronic structure methods

  • Prof. Tim Clark
• Computer-Assisted Structure Elucidation
• 53 min
  17. Methods for NMR-spectrum prediction

  • Dr. Wolfgang Robien
• 44 min
  18. Cyber-based structure elucidation

  • Prof. Morton E. Munk
• The Chemical Semantic Web
• 41 min
  19. Semantic chemistry: an overview

  • Dr. Nico Adams
• Open Notebook Science and the Open Access Movement in Chemistry
• 34 min
  20. Open research: motivation, theory, and practice

  • Dr. Cameron Neylon

Printable Handouts

PDF

Navigable Slide Index

1. Introduction
2. Acknowledgements
3. What is the web good for?
4. Publishing
5. Subscribing
6. Syndicate, remix and mashup
7. Publish, aggregate, syndicate, remix, collaborate
8. What scientists need to do
9. Publish, subscribe
10. Syndicate
11. Remix
12. So far, so good right?
13. Validate
14. Validation tools in the software world
15. Still not covered
16. Data recording in a lab notebook
17. Dead; Broken; Disconnected
18. Notebook for a fully integrated laboratory record
19. Links make the web go round
20. How do we make the web work for science?
21. Lab book as a journal
22. Blog as journal
23. Lab book vs. blog
24. A lab notebook blog
25. Automatic blogging by machines (1)
26. Integration and communication
27. Google reader
28. A closer look at a post
29. Links embedded in a post
30. Connecting up all the objects (1)
31. Connecting up all the objects (2)
32. Data objects
33. Data services
34. Variety of services
35. Embedding objects - Youtube
36. Embedding objects - ChemSpider
37. What good data services should have
38. Samples and procedures
39. Measuring solubility
40. Wikispaces
41. Spreadsheet online
42. Further analysis
43. 3D graph for solubility
44. Summary so far
45. So what we are left with?
46. The relationships between resources
47. Capturing the relationships between resources
48. Research objects on the web
49. Automatic blogging by machines (2)
50. Lightweight, natural approaches for uploading
51. Feeds of research objects
52. Integration and communication
53. The uploading process
54. Using objects from different people
55. Authoring tools for making connections
56. Connections between objects
57. Tools that will allow us to make the connections
58. Online example - PCR template
59. Other possibilities
60. 4. Semantic framework
61. We still have a problem
62. We still have two (related) problems
63. Information overload
64. Submissions to Genbank
65. Average capacity of human scientist
66. Filter failure
67. Search engines
68. People that helped (1)
69. People that helped (2)
70. If objects are locked away
71. Connect, relate and have conversations
72. If the objects are not open and available
73. Objects simply disappear
74. To exploit the web, the pieces have to be open
75. Did you open an encyclopaedia in the last 5 years?
76. Did you used Google in the last 24 hours?
77. If it isn't discoverable it doesn't exist
78. If it isn't discoverable it can't be linked to
79. Back to the open solubility project
80. The open solubility project took only four months
81. The polymath project
82. Gower's weblog
83. The synaptic leap
84. Resolution of praziquantel
85. Summary and common themes

Topics Covered

• Research works by building on the work of others
• The web as a new tool: what is it good for?
• How does this relate to the needs of researchers?
• The research record is not web enabled
• Lab notebook as blog
• Automated tools
• Using specialised services: putting research outputs where they best belong
• An example: Open Notebook Solubility
• Record is the collection of links between research outputs
• Tools to build these links and records
• Information overload
• Social filtering
• The need for open approaches
• Conclusions

Links

Series:

• Introduction to Cheminformatics

Categories:

• Methods

Talk Citation

Publication History

• Published on March 8, 2012

Financial Disclosures

• Dr. Cameron Neylon has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.