Reach out to potential users

jonrkarr commented 5 years ago

Topdown proteomics -- ProteoForm nomenclature
- Richard LeDuc: Richard.leduc@northwestern.edu
- Veit Schwammle: veits@bmb.sdu.dk
- Michael Shortreed: mshort@chem.wisc.edu
- Stefan Solntsev: solntsev@wisc.edu
Maintainers of DNAmod, MODOMICS, RESID, etc.
- DNAmod: Michael Hoffman: michael.hoffman@utoronto.ca
- MODOMICS
- Janusz Bujnicki: iamb@genesilico.pl
- Henri Grosjean: henri.grosjean@cgm.cnrs-gif.fr
- Magdalena Machnicka: mmika@genesilico.pl
- Kaja Milanowska: kaja@genesilico.pl
- Pietro Boccaletto: pietro.boccaletto@gmail.com
- RESID: John Garavelli: jsgarave@udel.edu
- MethDB: Christoph Grunau: christoph.grunau@univ-perp.fr
- MethSMRT: Zhi Xie: xiezhi@gmail.com
- RMBase: Jian-Hua Yang: yangjh7@mail.sysu.edu.cn
- RNA Modification DB
- Paul Agris: pagris@albany.edu
- Daniele Fabris: fabris@albany.edu
- Srivathsan V. Ranganathan: svranganathan@albany.edu
- PSI-MOD:
- Pierre-Alain Binz, pierre-alain.binz@chuv.ch
- Sylvie Ricard-Blum, sylvie.ricard-blum@univ-lyon1.fr
- dbPTM:
- Tzong-Yi Lee: francis@saturn.yzu.edu.tw
- Hsien-Da Huang: huanghsienda@cuhk.edu.cn
- PIR
  - Cathy Wu: wuc@dbi.udel.edu
  - Darren Natale: dan5@georgetown.edu
  - Cecilia Arighi: arighi@dbi.udel.edu
  - Judith Blake: Judith.blake@jax.org
- UniMod: John Cottrell: jcottrell@matrixscience.com
Maintainers of SBOL (expanded amino acid code)
- Herbert Sauro: hsauro@uw.edu
- Chris Meyers: myers@ece.utah.edu
- Curtis Madsen: ckmadsen@bu.edu
- Nicholas Roehner: nicholasroehner@gmail.com
Epigenetics: ask Gang Fang for advice
Synthetic genetic code: ask Stephen Fried for advice

jonrkarr commented 5 years ago

To: {{ email }} Subject: BpForms notation and software tools for describing and calculating properties of modified DNA, RNA, and proteins

Dear {{ name }},

We're reaching out to share BpForms (https://www.bpforms.org), a new toolkit for concretely describing and calculating properties of modified DNA, RNA, and protein, which we think would be helpful to {{ research }}. By unambiguously communicating the structures of modified DNA, RNA, and proteins, BpForms aims to help researchers integrate data and model epigenetic, post-transcriptional and post-translational modification.

We developed BpForms to help us describe the DNA, RNA, and proteins represented by our whole-cell models (see https://wholecell.org for more information). We think that BpForms would also be a valuable tool for your work.

The BpForms toolkit includes four components:

A simple FASTA-like notation for describing the primary structures of modified DNA; RNA, and proteins, including any uncertainty in their structures;
Three alphabets of hundreds of non-canonical nucleic and amino acids curated from DNAmod, MODOMICS, and RESID, as well as the ability to extend these alphabets and/or create additional alphabets;
Web, command line, and Python tools for calculating properties of modified DNA, RNA, and proteins such as their major protonation state, formula, molecular weight, and charge; and
A brief tutorial and detailed documentation.

BpForms is available open-source under the MIT License.

We hope BpForms is helpful to your work. Please reach out for any help using BpForms.

Regards, Jonathan Karr Yassmine Chebaro Paul Lang

ychebaro commented 5 years ago

What do you think of : Huillin Li, mass spectrometry scientist, (https://www.nature.com/articles/nchem.2908), we shared the same office when she was in Strasbourg and I think this could interest her. She is currently a professor in the School of Pharmaceutical Sciences, Sun Yat-sen University.

jonrkarr commented 5 years ago

Sure. This isn't an exhaustive list. Feel free to add more.

We can use the template message about and mail merge. Feel free to add more people to this table:

jonrkarr commented 5 years ago

Done

KarrLab / bpforms

Reach out to potential users #38