Mass++ Development in 2017

Dear users, A Happy Ne

…No, no! ;-(

  • Well (calm down, calm down…), we are about two months behind the usual schedule (these two times we’ve done so far), let’s summarize the Mass++ development for 2017.

Development in 2017

  • Unfortunately, we seem to have almost no achieved advancements in 2017. Ver.3, the final form of the conventional Mass++ which was scheduled to be released earlier last year, was almost complete for implementation; however, due to malfunctions of the internal database (may be caused by the version mismatch of libraries?), we postponed the release indefinitely. As a result, bug-fixes of plug-ins have been also been halted. OMG

# Will “ver.3” ever be released…?

  • In terms of citation of the Mass++ paper published in 2014, the citation number counted in “Web of Science” is 17, of which 9 of these were cited in 2017 (and 3 cited in 2016, 4 in 2015, 1 in 2014). The citation number has therefore been recently increasing (16 citations in 3 years after “1 year after from the publish” means that the one-year average citation number is essentially over 5, which is greater the Impact Factor of Journal of Proteome Research).
  • The journals for these 9 papers in 2017 are (in reverse chronological order): Nature, Scientific Reports, Proteomes, Expert Systems with Applications, Mass Spectrometry Reviews, Gigascience, Plant Journal, Journal of Mass Spectrometry, Current Opinion in Biotechnology. Such eminent journals!

  • Hence, we conclude that Mass++ is not yet expired. Unfortunately, we have been inconveniencing our users to download ver.2.7.4 (Shimadzu version) for reading vendor raw files; we think the development based on the utilization of external software and extension of ver.2.7.5 had expired. We also concluded that we should make a transition to the development of ver.4, the UNIX compatible version.

# So… what about ver.3 … ?

# We shall keep it an open secret that this mini hackathon was held at a spa in Wakura.

  • We did not reach the final specification at that time, and continued investigating for more than half a year. Finally, from Nov. 26 to Dec. 1, some members attended the “Computational Mass Spectrometry Hackathon” hosted by “JSBi Mass Spec Informatics SIG” (joint-hosted with “Biohackathon domestic version: BH17.11” hosted by DBCLS), examined the development target and fully updated the specifications to be fixed. Based on this final specification, we will implement the new version, of which look-and-feels are very similar to ver.2.7.5.

  • Hence, we have begun to code ver.4 (long-absent development from scratch!!). The development language is Java and it will (or we EXPECT it will) run on Windows/Mac OS X/Linux.
  • Anyone interested please join! (We have lots of work other than coding; in fact I also CANNOT use Java :-P)

# In short, we decided that “it’s easier to implement from scratch than to fix bugs”!!!

Presentations in 2017

  • We originally planned to submit for a poster presentation at the annual conference of MSSJ (Mass Spectrometry Society of Japan); however, unfortunately we could not come to an agreement with MSSJ about our presentation (What the hell?!) – so we cancelled it.

  • As another presentation, the main developer (and the primary spokesman) Satoshi Tanaka gave an oral presentation entitled “The current picture of software surrounding mass spectrometry” in the BoF session “Mass Spectrometry meets Chem-informatics” of IIBMP2017 (Informatics In Biology, Medicine and Pharmacology) on Sep. 28, in Sapporo, Japan.

Agendas for 2018

  • The highest priority agenda is “the development of ver.4” for the fundamental solution to coding problems and bugs. The goal of ver..4 is a “light, quick-response viewer” and we are planning to give ver.4 the function for utilizing plug-ins of ver2.7 as “external software.”

# Crumb, excuse me, so what’s the purpose of ver.3 if ver.4 has that function …?

  • AAMOF, we will hold self-motivating mini hackathons every month (until at least June) for the DESPERATE hacking and mutual face-to-face communication. Some of these mini hackathons will be held at spas. (Dude…

  • As for the presentation about ver.4, Satoshi Tanaka will also give an oral presentation tentatively-entitled “Mass++ ver.4: Current status and the vision of open-source mass spectrometry data viewer development” in a workshop “Computational Mass Spectrometry accerates Environmental Chemistry” jointly hosted by the JSBi Mass Spec Informatics SIG and the Japan Society for Environmental Chemistry, on May 25, in Naha, Okinawa, Japan.

  • So, I’m wondering how I shall report about ver.4 in the activity report next year; I’m already worrying about it. No, excited about it!

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