BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > NMR community > News from NMR blogs
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 09-23-2017, 05:52 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 21,849
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default ELNs and the importance of life analytical data

ELNs and the importance of life analytical data

Setting the scene

Over the last 25 years, during my bachelor's degree, PhD, Post Doc, and now as director of R&D at Mestrelab, I have had the opportunity to interact with many organic chemists. Most of them, although with their own singularities, share relatively similar procedures and workflows, with their strengths and weaknesses. I have witnessed many advances in the way they conduct their research, but I also must say that there are some areas of it that remain firmly rooted in the past.

An example of the latter which I’m still seeing in many labs is the issue of data loss: In the particular case of academia, research teams are typically made up of (pre)doctoral or postdoctoral students whose residence time is usually between 3 and 8 years, roughly speaking.

During that period, they produce an enormous amount of spectroscopic data (NMR, GC/LC/MS, UV/IR, etc.) to characterize their molecules. Whilst some groups have some sophisticated IT infrastructures equipped with either in-house or third party DBs (including Mnova DB for analytical data), I think it is not unreasonable to say that most of them save their spectroscopy data on their personal computers (e. g. laptops) or in shared folders of their research group (e. g. Dropbox). Data leakage is the result as students leave.




If you're a principal investigator, I'm sure you've found yourself in the following situation: one of your students synthesized a compound some time ago. However, for some reason, you are now considering the possibility that the proposed structure may not be the right one. Obviously, to review this structure, you need to have access to the original spectroscopic data, but unfortunately, the student is no longer part of your research group and you have no way of locating the NMR spectra.

In the same plot line, some students only keep the spectroscopic data of the products that they have successfully synthesized but discard the data of those reactions that did not work in the way they had planned.

These are just two examples of what I consider to be a more general problem associated with the difficulty of efficiently managing analytical information in an organic chemistry laboratory.

Nowadays, many labs are moving from paper-based to electronic laboratory notebooks (ELNs) that offer significant benefits for long-term storage. However, most of them lack the capability to understand and handle spectroscopy data in an integrated manner. Some of them are just repository of PDFs of analytical data generated by some specialized software. This is, in my opinion, a very limited, unproductive and inefficient solution to the extent that data generated in this form has been dubbed as “dead data” where all the valuable spectroscopy information has been removed, reducing it to a series of unstructured set of images and text strings. As it is stored today, analytical data is virtually unusable and tasks like the ones listed below are simply impossible to perform:

  1. NMR data could have been processed incorrectly making a comprehensive analysis of the data unfeasible.
  2. Only some parts of the spectrum could have been reported or the resolution is too low to characterize a compound unambiguously. For instance, accurate determination of coupling constants, inspection of possible impurities or side products in a reaction would not be possible.
  3. Spectroscopic data search: Do I have any spectrum that contains a triplet at 3.5 ppm? This is a question that could not be answered with dead data.
  4. Do I have any spectrum similar to this one?
Some ELNs, in addition to PDF or plain images, also store raw data but do not offer a solution with real spectroscopy intelligence capabilities within a searchable and homogeneous environment.


Mbook 2.0: A spectroscopy-aware ELN






Our ELN, MBook 2.0 is our answer to those issues. It has been designed to take advantage of all the power of Mnova which is tightly integrated with Mbook and is responsible for processing the analytical data acquired by the chemist. The scientist only needs to send the data in a zip file and Mnova will automatically recognize the file format (NMR data such as those from Bruker, JEOL, Varian / Agilent, Magritek, Thermo picoSpin, Nanalysis as well as many LC/GC/MS and UVIR files) and process in a fully unattended way. As a result, a new Mnova document is generated on the fly and saved into the ELN.




This file can be accessed and viewed directly from within Mbook with a new spectral viewer which provides basic navigation tools such as zoom-in and out.


At this present time Mbook 2.0 does not include spectral search capabilities, but we expect to offer this feature shortly once the integration of Mbook with Mnova DB is completed





More...

Source: NMR-analysis blog
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Importance of polarization transfer in reaction products for interpreting and analyzing CIDNP at low magnetic fields
From The DNP-NMR Blog: Importance of polarization transfer in reaction products for interpreting and analyzing CIDNP at low magnetic fields Pravdivtsev AN, Yurkovskaya AV, Ivanov KL, Vieth HM. Importance of polarization transfer in reaction products for interpreting and analyzing CIDNP at low magnetic fields. J Magn Reson. 2015;254(0):35-47. http://www.ncbi.nlm.nih.gov/pubmed/25797825
nmrlearner News from NMR blogs 0 05-30-2015 11:33 AM
The Importance of Characterization in Biosimilars Development - Pharmaceutical Technology Magazine
<img alt="" height="1" width="1" /> The Importance of Characterization in Biosimilars Development Pharmaceutical Technology Magazine Depending on the molecule, non-routine techniques such as protein nuclear magnetic resonance (NMR) and x-ray crystallography may also be utilized. In fact, a whole panel of methods should be employed, including orthogonal techniques to analyze ... The Importance of Characterization in Biosimilars Development - Pharmaceutical Technology Magazine More...
nmrlearner Online News 0 09-21-2013 02:52 AM
[NMRpipe Yahoo group] importance of -di command
importance of -di command Dear All, We know that in nmrDraw -di command deletes imaginary data points but we want to know why we should delete them.What is the advantage of deleting More...
NMRpipe Yahoo group news News from other NMR forums 0 12-29-2010 06:06 PM
Industrial Postdoctoral Chemist( analytical, organic or polymer) | Avomeen Analytical Services
Industrial Postdoctoral Chemist( analytical, organic or polymer) | Avomeen Analytical Services US - Ann Arbor Michigan, Ph.D. in Analytical, organic or polymer chemistry. Hands-on knowledge of following techniques Analytical instrumentation is preferred: FT-IR, NMR, GC, GC-MS, LC-MS, TGA, DSC, ICP, and SEM-EDS. Must be More...
nmrlearner Job marketplace 0 12-19-2010 01:50 AM
[NMR paper] NMR structure of the noncytotoxic alpha-sarcin mutant Delta(7-22): the importance of
NMR structure of the noncytotoxic alpha-sarcin mutant Delta(7-22): the importance of the native conformation of peripheral loops for activity. Related Articles NMR structure of the noncytotoxic alpha-sarcin mutant Delta(7-22): the importance of the native conformation of peripheral loops for activity. Protein Sci. 2004 Apr;13(4):1000-11 Authors: García-Mayoral MF, García-Ortega L, Lillo MP, Santoro J, Martínez del Pozo A, Gavilanes JG, Rico M, Bruix M The deletion mutant Delta(7-22) of alpha-sarcin, unlike its wild-type protein counterpart,...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] The importance of being ordered: improving NMR structures using residual dipolar coup
The importance of being ordered: improving NMR structures using residual dipolar couplings. Related Articles The importance of being ordered: improving NMR structures using residual dipolar couplings. C R Biol. 2002 Sep;325(9):957-66 Authors: Gronenborn AM Residual dipolar couplings arise from small degrees of alignment of molecules in a magnetic field. Most biomolecules lack sufficient intrinsic magnetic susceptibility anisotropies for practical purposes; however, alignment can be achieved using dilute aqueous phospholipid mixtures, colloidal...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] The importance of a single G in the hairpin loop of the iron responsive element (IRE)
The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study. Nucleic Acids Res. 1995 Jan 11;23(1):146-53 Authors: Sierzputowska-Gracz H, McKenzie RA, Theil EC Noncoding sequences...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] The importance of binding energy in catalysis of hydride transfer by UDP-galactose 4-
The importance of binding energy in catalysis of hydride transfer by UDP-galactose 4-epimerase: a 13C and 15N NMR and kinetic study. Related Articles The importance of binding energy in catalysis of hydride transfer by UDP-galactose 4-epimerase: a 13C and 15N NMR and kinetic study. Biochemistry. 1993 Dec 7;32(48):13220-30 Authors: Burke JR, Frey PA UDP-galactose 4-epimerase contains NAD+ irreversibly but noncovalently bound to the active site. Uridine nucleotides bind to the substrate site and induce a protein conformational change that...
nmrlearner Journal club 0 08-22-2010 03:01 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2022, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 03:00 AM.


Map