Scott Edmunds

<figure class="wp-block-image size-large is-resized">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/ISMB2022-1024x983.jpeg"
class="wp-image-4509" loading="lazy" decoding="async"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/ISMB2022-1024x983.jpeg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/ISMB2022-300x288.jpeg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/ISMB2022-768x737.jpeg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/ISMB2022-1536x1475.jpeg 1536w"
sizes="(max-width: 768px) 100vw, 768px" width="768" height="737"
alt="ISMB2022 meets open science" />
</figure>

**Live and in-person in Madison** 
A big part of the life of a journal editor is to travel to conferences,
keeping on top of the state-of-the art of fields of interest, as well as
interacting the research community that publishes, edits and peer
reviews for your journal. The COVID-19 pandemic moving things virtual
has had the potential ([with
caveats](https://doi.org/10.1093/gigascience/giab051)) to enable many
individuals from groups that have traditionally been underrepresented to
join and participate in these events, but with an increased focus on
talks these lack the more personal interactions that occur at posters or
between and after sessions. While the curation team has attended a [few
in-person meetings](http://gigasciencejournal.com/blog/spnhc-2022/), the
Editorial team had not attended any since [PAG XXVIII in January
2020](http://gigasciencejournal.com/blog/plant-and-animal-genome/) until
this week. As we [launched at the Intelligent Systems for Molecular
Biology (ISMB)
conference](http://blogs.biomedcentral.com/bmcblog/2012/07/12/gigascience-launches-overseeing-the-transition-from-papers-to-executable-research-objects/)
in Long Beach in 2012, it has been a tradition every following year to
celebrate our birthday celebrations at the conference. And after [two
years](http://gigasciencejournal.com/blog/conferences-go-viral/) [of
virtual
attendance](http://gigasciencejournal.com/blog/ismb2021-virtual-birthday/)
and celebrations, with ISMB2022 celebrating its 30^th^ year and
*GigaScience* celebrating its 10^th^ year there was no way we could miss
the first in-person (hybrid) ISMB gathering since [ISMB 2019 in
Basel](http://gigasciencejournal.com/blog/basel-ismbeccb-and-bosc-2019/).

<figure class="wp-block-image size-large is-resized">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5889-1024x768.jpeg"
class="wp-image-4510" loading="lazy" decoding="async"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5889-1024x768.jpeg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5889-300x225.jpeg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5889-768x576.jpeg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5889-1536x1152.jpeg 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5889-2048x1536.jpeg 2048w"
sizes="(max-width: 768px) 100vw, 768px" width="768" height="576"
alt="Wisconsin Capitol from ISMB2022" />
<figcaption>The Wisconsin State Capitol building viewed from the rooftop
reception of ISMB2022</figcaption>
</figure>

Traveling to [ISMB2022](https://www.iscb.org/ismb2022) in Madison
Wisconsin there was trepidation that after 3 years would people come?
Many in the scientific community had been burned by society conferences
such as SfN [cancelling hybrid meetings at the last
minute](https://www.technologynetworks.com/neuroscience/news/sfn-2021-moves-fully-online-u-turns-on-refunds-354613)
because of COVID-19,  and anecdotally there have been a lot of shared
stories about recent conferences spreading the virus to many of the
delegates. The return of ISMB seemed to handle these worries well. With
none of the "mission accomplished" [bombast and disco
dancing](https://twitter.com/FENSorg/status/1545818678138134532) of FENS
Forum, stringent masking and social distancing protocols in the
conference venue, and an outdoor reception at the stylishly understated
Frank Lloyd Wright designed Monona Terrace Convention Centre. With
nearly 1,000 in-person attendees and 700 attending virtually it was a
good test of whether relatively larger-sized conferences could be held
safely and balanced with a hybrid/virtual format, and there were some
teething problems with the JUNO platform in some of the sessions, but
the in-person experience felt good. Making us more confident going
forward to other in-person meetings such as the [Galaxy Community
Conference](https://galaxyproject.org/events/gcc2022/) currently
underway in Minneapolis.

**Alles Gute *GigaScience*** 
ISMB2022 coincided our 10^th^ birthday, and following the success of our
previous parties we had a great turnout for Panda birthday cake and
German food and drink in the huge outdoor garden of Essen Haus
restaurant and bar. Timed for the birthday we also published a
commissioned series of [commentary
papers](https://academic.oup.com/gigascience/pages/a-decade-of-gigascience)
giving a decade long view of advances in large-scale research as Open
Science has gained momentum and become mainstream. And these were bound
alongside the many other commentary articles we have published since our
launch in a print issue that we gave out at the party alongside our
always popular t-shirts (see the [pictures on our
facebook](https://www.facebook.com/media/set/?vanity=GigaScience&set=a.5537987439547164)
page).

<figure class="wp-block-image size-large is-resized">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5964-1024x768.jpeg"
class="wp-image-4508" loading="lazy" decoding="async"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5964-1024x768.jpeg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5964-300x225.jpeg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5964-768x576.jpeg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5964-1536x1152.jpeg 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/IMG_5964-2048x1536.jpeg 2048w"
sizes="(max-width: 768px) 100vw, 768px" width="768" height="576"
alt="Birthday at ISMB2022" />
</figure>

Building upon the efforts developing the [ISMB Code of
Conduct](https://www.iscb.org/ismbeccb2017general/codeofconduct) first
adopted in the last in-person meeting, the ISMB organisers seems to have
spent some of their pandemic downtime on addressing other issues
relating to sustainability and equity. Launching a [Sustainable
Conference Travel Award](https://www.iscb.org/ismb2022-scta) to promote
sustainable travel to scientific meetings by rewarding delegates who
show environmentally friendly travel, and an ICSB Green Pledge that
includes the planting of an [ICSB grove of
trees](https://treesforlife.org.uk/groves/206760/) in the Scottish
Highlands to offset the carbon emissions of travel to the meeting. To
widen accessibility further the keynotes had qualified sign language
interpreters, and there was also a [series of Equity-focussed Research
Presentations](https://www.iscb.org/ismb2022-program/equity) hosted by
Casey Greene.

The talks at the conference were potentially more Open Science relevant
than before, with keynotes even covering Citizen Science through Tanya
Berger-Wolf presenting an amazing talk on the new field of "imageomics".
Data science and machine learning can process massive collections of
wildlife images, many citizen collected from
[iNaturalist](https://www.inaturalist.org/) and the
[wildme](http://wildme.org/) platforms, to enable scientific inquiry,
conservation, and policy decisions.

The COSI (Communities of Special Interest) tracks are usually the most
interest to us, and we started off in the
[CAMDA](http://www.camda.info/) (Critical Assessment of Mass Data
Analysis) track watching the keynote of Lynn Schriml, President of the
[Genomic Standards Consortium](https://www.gensc.org/), presenting a
talk that covered a lot of the same ground as the [recent
commentary](https://doi.org/10.1093/gigascience/giac047) she published
in our "Decade of GigaScience" series. Alongside three talks from
Serghei Mangul and his lab on the systematic assessment of metadata
completeness from fields such as omics and immunogenetics.

**BOSC and the Open Science Recommendations** 
Being advocates of everything "Open" we are regular attendees and
supporters of the [BOSC COSI: The Bioinformatics Open Source
Conference](https://www.open-bio.org/events/bosc-2021/), and this year
we and OUP were again silver sponsors of the event. On top of promoting
Open Source, the meeting also promotes Open Science, and this topic is
particularly timely with UNESCO ratifying their [Open Science
Recommendations](https://en.unesco.org/science-sustainable-future/open-science/recommendation)
since the last meeting. Having a decade experience of Open Science
publishing behind us before the field went mainstream with governmental
recognition, we felt our birthday was a good opportunity to look back at
what we have (and haven't) achieved, and use these recommendations to
guide our path into the future. Writing [an
Editorial](https://doi.org/10.1093/gigascience/giac067) timed to go out
with our birthday celebrations mapping these efforts onto the four key
pillars of Open Science highlighted by UNESCO.

<figure class="wp-block-image size-large">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/EditorialFigure-Final.jpg"
class="wp-image-4513" loading="lazy" decoding="async"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/EditorialFigure-Final.jpg 861w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/EditorialFigure-Final-300x274.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2022/07/EditorialFigure-Final-768x702.jpg 768w"
sizes="(max-width: 861px) 100vw, 861px" width="861" height="787"
alt="ISMB2022" />
<figcaption>Figure from <a
href="https://doi.org/10.1093/gigascience/giac067">our Editorial</a>
(adapted from the UNESCO Open Science Recommendations) mapping
GigaScience‘s efforts to the four key Open Science
pillars.</figcaption>
</figure>

As this was all fresh in our minds coming to the meeting it was great to
see many of these same issues keep coming up in the talks. With
"physical" facilities for open science being a key part of the "Open
science infrastructures" pillar [highlighted in the Open Science
Recommendations](https://unesdoc.unesco.org/ark:/48223/pf0000379949.locale=en),
BOSC is a great platform for this. Providing a space for the Open
Bioinformatics Community to meet and share experiences, as well as
hosting their
[CollaborationFest](https://www.open-bio.org/events/bosc-2021/collaborationfest/)
where participants work together to contribute code, documentation,
training materials, and challenging analysis problems and use cases.

The opening keynote from Jason Williams was on "Riding the Bicycle:
Including all Scientists on a Path to Excellence" channeling his
extensive mentoring and experience as an educator at the [DNA Learning
centre](https://dnalc.cshl.edu/) to propose and develop the new "bicycle
principles" for teaching. The proposed principles providing a
community-driven principle-based framework for improving short-format
training through two cyclic (hence "bi-cycle") and iterative processes,
and is still gathering feedback at
[bikeprinciples.org.](https://www.bikeprinciples.org/) And conveniently
also addressing UNESCO's objectives in investing in human resources,
training, education, digital literacy and capacity building for open
science.

This was followed by the "Standards and Practices for Open Science"
session which did an excellent job of fulfilling the "open" part of
BOSC's mandate, including talks on gender-based disparities and biases
in science by Rachel Torchet, providing quantitative data on the issue
by doing observational study of the French Bioinformatics communities
JOBIM conference when it went virtual (see the
[preprint](https://doi.org/10.1101/2022.03.07.483337) and our birthday
series commentary on [gender disparity in
STEM](https://doi.org/10.1093/gigascience/giac069)). Noting the
depressing finding that the improvements in gender balance gained in
virtual conferences were lost as soon as the meeting went in-person
again the following year. As well a talk from Halie Rando on the use of
Manubot to promote Open Publishing in the "Infodemic", producing very
cool updateable publications using COVID-19 data.

Continuing this Open Science theme right to the very end the final panel
chaired by Jason Williams was on Building and Sustaining Inclusive Open
Science Communities, and featured Jenea Adams, Andrew Hasley, Gary
McDowell, Monica Munoz-Torres, and Rachel Torchet. This provided a
fantastic range of perspectives and firsthand advice on community
building, as well as an interesting Q&A. Concluding with the timely
question on how we balance the advantages of virtual and in-person
conferences, as this and other recent conferences demonstrate we are at
an inflection point on whether we move from hybrid to in-person
conferencing. Allowing the virtual participation has opened it up to a
geographically and demographically more diverse audience (the technical
problems of the streaming platform not withstanding), but there has been
some vocal pushback from some of the in-person participants that they
didn't want to spend all this time and money to fly here and not be able
interact with the proportion of speakers and attendees participating
virtually. With the observation from Rachel Torchet's earlier presented
talk that hard won gains in accessibility and diversity can be lost when
conferences go back to in-person, we may need to push to retain this
rare positive from the last few years.

> [@JasonWilliamsNY](https://twitter.com/JasonWilliamsNY?ref_src=twsrc%5Etfw)
> and the panelists with
> [\#BOSC2022](https://twitter.com/hashtag/BOSC2022?src=hash&ref_src=twsrc%5Etfw)
> chair
> [@NomiHarris](https://twitter.com/NomiHarris?ref_src=twsrc%5Etfw)
> [pic.twitter.com/gis48NEajW](https://t.co/gis48NEajW)
>
> --- BOSC (@OBF_BOSC) [July 17,
> 2022](https://twitter.com/OBF_BOSC/status/1548526378928156672?ref_src=twsrc%5Etfw)

Our [newly published
mapping](https://doi.org/10.1093/gigascience/giac067) to the Open
Science pillars to look at where we need to do better has helped
*GigaScience* to focus on what we need to work on going forward, and we
would recommend others look at the efforts presented here and the UNESCO
Recommendations to inform your working practices in a similar manner. As
in-person conferences seem to be well and truly back we look forward to
ISMB and BOSC 2023 in Lyon continuing with the positive changes we've
seen here to continue to make conferences more equitable and
sustainable.

**Further Reading** 
A Decade of *GigaScience* series:
<https://academic.oup.com/gigascience/pages/a-decade-of-gigascience> 
 
Schriml LM. A decade of *GigaScience*: 10 years of the evolving genomic
and biomedical standards landscape. *GigaScience*. 2022;**11**:giac047.
doi:
[10.1093/gigascience/giac047](https://doi.org/10.1093/gigascience/giac047). 
 
Edmunds SC, Zauner H, Nogoy NA, Zhou H, Zhang H, Goodman L. A Decade of
*GigaScience*: Milestones in Open Science. *GigaScience*.
2022;**11**:giac067. doi:
[10.1093/gigascience/giac067](https://doi.org/10.1093/gigascience/giac067).

Liu L, Jovic D, Goodman L. A Decade of *GigaScience*: Women in Science:
Past, Present, and Future. *GigaScience*. 2022;**11**:giac069. doi:
[10.1093/gigascience/giac069](https://doi.org/10.1093/gigascience/giac069).

The post [Open Science Milestones and the return of in-person meetings
at
ISMB2022](http://gigasciencejournal.com/blog/birthday-at-ismb2022/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.

Live and in-person in Madison

A big part of the life of a journal editor is to travel to conferences, keeping on top of the state-of-the art of fields of interest, as well as interacting the research community that publishes, edits and peer reviews for your journal.

Open Science Milestones and the return of in-person meetings at ISMB2022

Chris Armit

Meetings In the Time of Coronavirus: Conferences go Viral

June-July usually marks peak conference season when the

 GigaScience

team is on the road, but with the COVID-19 pandemic shutting down travel and public gatherings it has been a strangely static summer.

Birthdays and Online Conferences go Viral. ISMB2020 &amp; BCC2020 in the time of COVID-19

Hans Zauner

**The year is almost over and it's time to review the highlights of
*GigaScience*'s 2017.**

::: {#attachment_2231 .wp-caption .alignright style="width: 310px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/reindeer-300x199.jpg){.size-medium
.wp-image-2231 loading="lazy" decoding="async"
aria-describedby="caption-attachment-2231" width="300" height="199"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/reindeer-300x199.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/reindeer-768x511.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/reindeer-1024x681.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/reindeer.jpg 1280w"
sizes="(max-width: 300px) 100vw, 300px"}

["Draft genome of the reindeer (Rangifer
tarandus)"](https://doi.org/10.1093/gigascience/gix102)  
Foto: [Alexandre
Buisse](https://commons.wikimedia.org/wiki/Rangifer_tarandus#/media/File:20070818-0001-strolling_reindeer.jpg)
CC-BY-SA 3.0
:::

2017 was as special year for *GigaScience*: a year of many firsts and we
celebrated our 5th birthday! An occasion to look back -- and forward, as
we did in our [anniversary
editorial](https://academic.oup.com/gigascience/article/6/9/1/4004834).
We marked the completion of our first five years in Prague, at ISMB, the
same meeting where *GigaScience* first came to life in 2012. Czech beer,
cake and our amazing guests (mainly recruited ad hoc from the BOSC
track), all coming together on a summer evening in a corner pub in
Prague: those were the ingredients for a [truly memorable birthday
party](http://gigasciencejournal.com/blog/bohemian-bashfully-baroque-birthdays-and-bingo-in-prague/).
Thanks again to all our guests for a special evening. We hope to see you
all again in 2022 for our 10th birthday party, wherever that will take
place!

Apart from celebrating, we also were one of the sponsors of the BOSC
track at ISMB, and were happy to witness that the Open Science movement
is in excellent health.

> Thanks to all the brilliant people who came and celebrated our 5th
> birthday at
> [\#ISMBECCB](https://twitter.com/hashtag/ISMBECCB?src=hash&ref_src=twsrc%5Etfw)
> tonight [pic.twitter.com/4MOMfAWfIe](https://t.co/4MOMfAWfIe)
>
> --- GigaScience (@GigaScience) [July 23,
> 2017](https://twitter.com/GigaScience/status/889266228455460865?ref_src=twsrc%5Etfw)

## **Going forward with OUP**

2017 was the first year with our new publisher, Oxford University Press.
During the transition, quite a lot of chores needed to be done behind
the scenes to continue the smooth running of the journal. We are looking
forward to further grow our radical open review, open data, open science
approach with our new publishing partner in 2018 and beyond.

## ***GigaScience* Competition and Prize Track**

::: {#attachment_2233 .wp-caption .alignright style="width: 235px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/4190569720_4b2c376c6a_z-225x300.jpg){.size-medium
.wp-image-2233 loading="lazy" decoding="async"
aria-describedby="caption-attachment-2233" width="225" height="300"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/4190569720_4b2c376c6a_z-225x300.jpg 225w, http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/4190569720_4b2c376c6a_z.jpg 375w"
sizes="(max-width: 225px) 100vw, 225px"}

["The first near-complete assembly of the hexaploid bread wheat genome,
Triticum aestivum](https://doi.org/10.1093/gigascience/gix097)"  
Foto: [D. Endresen CC-BY
2.0](https://www.flickr.com/photos/dag_endresen/4190569720)
:::

Another highly memorable event this year was the International
Conference on Genomics (ICG) meeting in Shenzhen in October. For the 7th
consecutive year we've attended our co-publisher BGI's annual meeting,
but this year we had a first: Our first ever [competition and prize
track](http://gigasciencejournal.com/blog/and-the-winner-is-our-icg12-prize-track-on-gigatv/),
to promote new, cutting edge research.

Six *GigaScience* authors were given free registration, accommodation
and travel to present their work. Among the strong contenders for the
prize was a  massively improved, [near complete wheat
genome](https://academic.oup.com/gigascience/article/6/11/1/4561661)
that made waves also beyond the wheat community. But as competitions go,
there could be only one winner, and the jury awarded the first prize to
Taras Oleksyk, who presented work on [the genome of a rather unique
mammal, *Solenodon
paradoxus*](https://www.biorxiv.org/content/early/2017/07/18/164574)
from the island of Hispaniola. Watch Oleksyk's award-winning
presentation, and all the other talks of the prize track, on our
[Youtube
channel](https://www.youtube.com/channel/UC1Xt1XQMEYqhZ002Phrpn6A).

For the prize track we also experimented with real-time open peer
review. All reviews at *GigaScience* are open after publication, but for
the ICG event we went one step further, in collaboration with our
friends at [AcademicKarma](http://academickarma.org/). Reviews could be
followed and contributed in real time via [a special
page](http://academickarma.org/conference/icg12). Transparent peer
review is a topic we are particularly interested in, of course. As [our
contribution to Peer Review
Week](http://gigasciencejournal.com/blog/peerrevwk17-update-peer-review-week-goes-transparent-and-interactive/),
we co-hosted a webinar, discussing preprints and open peer review with
AcademicKarma.

## **Some favorite articles**

::: {#attachment_2039 .wp-caption .alignleft style="width: 310px"}
![: William H. Piel and Antónia
Monteiro](http://gigasciencejournal.com/blog/wp-content/uploads/2017/05/anynana-300x256.png){.wp-image-2039
.size-medium loading="lazy" decoding="async"
aria-describedby="caption-attachment-2039" width="300" height="256"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2017/05/anynana-300x256.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2017/05/anynana.png 554w"
sizes="(max-width: 300px) 100vw, 300px"}

["A high-coverage draft genome of the mycalesine butterfly Bicyclus
anynana."](https://doi.org/10.1093/gigascience/gix035)   
foto credit: William H. Piel and Antónia Monteiro
:::

Only a subset of  articles could be presented within the timeframe of
the ICG prize track. Other highlights published last year once again
include some high quality genome assemblies. *GigaScience* continues to
be a favorite journal for advanced plant genomics, showcasing cutting
edge technology to improve assemblies; as evidenced not only by the new 
wheat assembly mentioned above, but also by a recent article on a
[ improved assembly of the wild strawberry
genome](https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/gix124/4739363?searchresult=1),
using a combination of optical maps and long reads.

In the animal department, we could not possibly write a mid-December
blog post without mentioning [the reindeer
genome](https://academic.oup.com/gigascience/article/6/12/1/4562806)
published recently, also [featured on
GigaBlog](http://gigasciencejournal.com/blog/a-christmas-gift-to-you-from-gigascience-scientists-have-unwrapped-the-reindeer-genome/).

Moving on to the insect world, we published [the genome of *Bicyclus
anynana*](http://gigasciencejournal.com/blog/the-genome-of-a-shape-shifting-butterfly/),
a charismatic butterfly and important model in evolution and ecology due
to its seasonal morphological varieties. The [data
note](https://doi.org/10.1093/gigascience/gix035) (with [supporting data
in GigaDB](http://dx.doi.org/10.5524/100280), as always) will help to
better understand this unusual developmental switch.

We also featured an arachnid species: * *The parasitic  *Tropilaelaps
mercedesae *threatens bee colonies in Asia, and the genome sequence,
[published in
*GigaScience*,](https://academic.oup.com/gigascience/article/6/3/1/3038223)
reveals some interesting features, including traces of horizontal gene
transfer from bacteria, as the authors explained in a [GigaBlog 
Q&A](http://gigasciencejournal.com/blog/getting-the-buzz-on-bee-parasites-author-qa-with-tatsuhiko-kadowaki/).

## **FAIR everything**

A certain four letter acronym was mentioned a lot wherever Open Science
was discussed in 2017, including BOSC and also the recent [FORCE
2017](http://gigasciencejournal.com/blog/force2017-in-berlin-changing-the-culture/)
meeting in Berlin:

***FAIR** -- **F**indable, **A**ccessible, **I**nteroperable,
**R**eproducible.* First drafted in 2015, there is wide agreement now
that these principles are a very good idea -- but how to
put [FAIR](https://www.force11.org/group/fairgroup/fairprinciples) into
practice? Javier Quilez and colleagues showed in a [didactical
*GigaScience*
commentary](https://academic.oup.com/gigascience/article/6/11/1/4557140)
how best practice can look like for a sequencing project (and what
errors are best avoided).

Our radical approach to openness and sharing would not have been
possible without the help of our reviewers, who agree to sign and
publish their reports and also take extra care that data and methods are
supporting the submissions. Thank you for your dedication and your
continued support!

Although we were quite busy in the first half of the year with the
transition to our new publisher OUP, we also introduced a few technical
novelties:

## **BioRxiv integration**

![](http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/Ipe-e1513672055322-168x300.jpg){.size-medium
.wp-image-2235 loading="lazy" decoding="async" width="168" height="300"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/Ipe-e1513672055322-168x300.jpg 168w, http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/Ipe-e1513672055322.jpg 387w"
sizes="(max-width: 168px) 100vw, 168px"}  
["Genome assembly of the Pink
Ipê" ](https://doi.org/10.1093/gigascience/gix125)

Not long ago posting unreviewed versions of research articles online was
seen as an avant-garde and slightly iffy thing to do as a biomedical
researcher, but preprints are becoming the new normal in the life
sciences. We always had supported preprints, we encourage our authors to
cite them and of course we never hold it against authors if they post a
preprint of their work prior to submitting to us.

To make it even easier to submit bioRxiv preprints, we now offer [a
shortcut connecting bioRxiv and
*GigaScience*](http://gigasciencejournal.com/blog/shortcut-from-biorxiv-to-gigascience/).

## Code Ocean

In addition to our  integration with bioRxiv, Publons and protocols.io,
we also [experimented with the code sharing platform Code
Ocean](http://gigasciencejournal.com/blog/data-intensive-software-publishing-sailing-the-code-ocean-qa-with-ruibang-luo).
Code Ocean takes reproducible code to a new level. Authors can upload
code and data in ten programming languages and Code Ocean provides an
interactive "Compute Capsule". They also assign a Digital Object
Identifier (DOI) to the algorithm, that allows the algorithm to be cited
in the reference sections of papers. See this paper by [Ruibang Luo and
colleagues](https://academic.oup.com/gigascience/article/6/7/1/3868354),
and the [Code Ocean entry cited
therein](https://codeocean.com/2017/06/08/16gt-colon-a-fast-and-sensitive-variant-caller-using-a-16-genotype-probabilistic-model/code), 
for an example how *GigaScience*-style open data publishing ties in with
Code Ocean's reproducible software capsules.

What do our authors think of this experiment? Ruibang Luo is as excited
as we are:

> "I think Code Ocean is awesome and I would like to use it for my
> future projects and I would like to recommend my colleagues."

##  RRIDs {#rrids}

Another software-related innovation you may have come across in the
methods sections of our papers are ["Research Resource Identifiers"
(RRIDS)](https://scicrunch.org/) we are encouraging our authors to
include.

The variety of software tools and databases used in life science
projects can get bewildering, and RRIDs are a handy way to keep track of
the tool zoo. Due to the standardized format, RRIDs mentioned in our
papers are machine-readable, allowing  for example annotation bots to
enhance and extract information automatically.

::: {#attachment_2234 .wp-caption .alignright style="width: 160px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/882px-Limnoperna_fortunei-150x150.jpg){.wp-image-2234
.size-thumbnail loading="lazy" decoding="async"
aria-describedby="caption-attachment-2234" width="150" height="150"}

["A hybrid-hierarchical genome assembly strategy to sequence the
invasive golden mussel Limnoperna
fortunei."](https://doi.org/10.1093/gigascience/gix128)  
Foto:[Boltovskoy](https://commons.wikimedia.org/wiki/File:Limnoperna_fortunei.jpg)/
CC-BY-SA
:::

## Citizen Science at the UN in Nairobi

In November, our executive editor Scott Edmunds was on a diplomatic
mission in Nairobi, Kenya: Before the main UN Environment Assembly, a
Science-Policy-Business Forum on the Environment took place, and as part
of this policy forum Scott participated in [discussions around Citizen
Science](http://gigasciencejournal.com/blog/citizen-smith-goes-to-nairobi-taking-citizen-science-to-the-un/),
also representing  [Citizen Science Asia](http://citizenscience.asia).
The gathering has set aim at promoting citizen science across the globe
-- and we will continue to do our bit. Just now, we published the
[genome assembly of the golden mussel *Limnoperna
fortunei*](https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/gix128/4750781?searchresult=1),
an invasive species. Following a [Community Genomics
approach](http://gigasciencejournal.com/blog/community-genomes-from-the-peoples-parrot-to-crowdfernding/)
that we've been promoting since our [Puerto Rican "peoples" parrot
genome](https://doi.org/10.1186/2047-217X-1-14), the project was
supported in part by crowfunding and also an exercise in public
participation, [as first author Marcela Ulioano da Silva
explains](https://fellowsblog.ted.com/i-crowdfunded-my-phd-research-this-model-could-change-the-world-28a079b7a0af).

## We Love CUDDEL(s) and BYO Data & Workflow Parties {#we-love-cuddels-and-byo-data-workflow-parties}

Some of you may recall our BBSRC UK-China partnering award funded [BYO
Data](http://gigasciencejournal.com/blog/aint-no-party-like-a-bring-your-own-data-party/)
party in our Hong Kong office in 2014 and thanks to the [positive
outcome](http://gigasciencejournal.com/blog/gigametabolomics-strikes-byo-data-parties-thematic-series/),
last month we hosted another hackathon in Hong Kong made possible with a
second BBSRC grant that we've called [CUDDEL](http://cuddel.net/)
('China-UK Data Dissemination in Metabolomics'. This year the focus was
on reproducible metabolomics workflows, and 19 participants squeezed in
our office from the ISA Team at the Oxford e-Research Centre, the EBI,
the Universities of Birmingham, Manchester (Common Workflow Language),
The Sainsbury Laboratory, BGI and the University of Melbourne. The
Oxford e-Research Centre has already [blogged on
this](https://www.oerc.ox.ac.uk/news/professor-susanna-assunta-sansone-explores-open-data-hong-kong),
and follow [our blog](http://gigasciencejournal.com/blog/) to see how
things progress from this event.

## More hands on deck at GigaDB

And finally, very good news for our repository GigaDB: Our data curators
Chris and Jesse got much needed help to curate the growing volume of
data submitted to GigaDB. Please welcome our new data curators Mary Ann
Tuli and Chris Armit. The bigger *GigaScience* team is prepared for your
submissions and another exciting year of open science publishing.

We wish all our readers, authors, reviewers and editorial board members
a Happy New Year!

::: {#attachment_2242 .wp-caption .aligncenter style="width: 530px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/dragonfish.jpeg){.wp-image-2242
.size-full loading="lazy" decoding="async"
aria-describedby="caption-attachment-2242" width="520" height="178"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/dragonfish.jpeg 520w, http://gigasciencejournal.com/blog/wp-content/uploads/2017/12/dragonfish-300x103.jpeg 300w"
sizes="(max-width: 520px) 100vw, 520px"}

["Draft genome of the Antarctic dragonfish, Parachaenichthys
charcoti"](https://academic.oup.com/gigascience/article/6/8/1/4004833?searchresult=1)
:::

The post [... and a Happy New
Year](http://gigasciencejournal.com/blog/and-a-happy-new-year/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


The year is almost over and it’s time to review the highlights of
 
 GigaScience
 
 ’s 2017.

“Draft genome of the reindeer (Rangifer tarandus)”Foto: Alexandre Buisse CC-BY-SA 3.0 2017 was as special year for

 GigaScience

: a year of many firsts and we celebrated our 5th birthday! An occasion to look back – and forward, as we did in our anniversary editorial.

… and a Happy New Year

*Every summer we celebrate our birthday at the ISMB (Intelligent Systems
for Molecular Biology) conference, and this was a particularly memorable
and important one -- being the 5^th^ birthday of GigaScience, and 25^th^
edition of the ISMB.*

Having [ISMB in Prague](https://www.iscb.org/ismbeccb2017) this year,
the historic capital of old Bohemia was particularly appreciated by the
attendees, both for its beautiful baroque streets, and its reputation as
a party capital with the [highest per-capita beer
consumption](https://en.wikipedia.org/wiki/List_of_countries_by_beer_consumption_per_capita).
The five day meeting lived up to all these stereotypes and more,
attendance was up a lot compared to last years conference in DisneyWorld
(see our
[write-up](http://gigasciencejournal.com/blog/ismb16-at-disney/)), and
our party was a particularly lively and difficult one to top in the
future. The incredibly cheap beer meant our 5^th^ birthday budget went 5
times further than previous years, although the thirsty computational
biologists did a good job drinking the venue dry of dark beer. Following
last years Game of Omes theme we brought new "Data Is Coming" t-shirts
featuring our GigaPanda mascot evolving to a new "direpanda" sigil,
alongside a special 5^th^ anniversary issue that was printed for the
event. We also published a 5^th^ birthday editorial in the journal,
looking back and looking forward, that you can read
[here](https://doi.org/10.1093/gigascience/gix064).

> GigaScience threw a blast of a birthday party yesterday! Happy 5
> years! Lots of love from
> [@GigaScience](https://twitter.com/GigaScience) fans
> [\#ismbeccb](https://twitter.com/hashtag/ismbeccb?src=hash)
> [pic.twitter.com/dqlQBjZ8Tk](https://t.co/dqlQBjZ8Tk)
>
> --- Fiona Nielsen (@glyn_dk) [July 24,
> 2017](https://twitter.com/glyn_dk/status/889376211029434368)

 
**Goodbye SIGs, hello COSIs. Big changes to the conference.**

Being the 25^th^ ISMB brought big changes for their milestone year, with
a major rearrangement and restructuring of the format so that the
separate SIG (special interest group) sessions that were before the main
meeting, where now integrated into the main conference, and turned into
COSIs (communities of special interest). This pushed the price up for
people that normally only attended the SIGs, but widened the audience
for the specialist communities, and also reduced the clashing between
SIGs by 50%. Generally the new format seemed to be popular, although the
big fallout from this may be our favorite SIG,
[BOSC](https://www.open-bio.org/wiki/BOSC_2017) -- the Bioinformatics
Open Source Conference, potentially leaving. It was announced that next
year BOSC and the [Galaxy Community
Conference](http://gcc2017.sciencesconf.org/) (another favourite meeting
of ours that we attended a few weeks ago) will collocate as the
Bioinformatics Community Conferences in Portland, shortly before the
main ISMB meeting in Chicago. While this is officially only a one year
experiment, depending how it goes next year the future of the meeting at
ISMB is uncertain.

As sponsors of both BOSC and GCC this year we will likely have to spend
time with both of our divided families next year. If this is a last
hurrah for BOSC at ISMB2017, it at least went with a bang. The venue was
full to bursting, and the number of new faces made up at least 30-50% of
the audience. With our open science ethos we were very happy with the
open science theme this year, and the keynotes were particularly great
(we'll update this [with the
videos](https://www.youtube.com/channel/UCNSng3q18VuQ-13RhhKJ5FA) when
they get posted online). See the storifies of [day
one](https://storify.com/pjacock/bosc-2017-day-one),
[two](https://storify.com/pjacock/bosc-2017-day-two), and the many blogs
(e.g. from [Brad
Chapman](https://github.com/chapmanb/bcbb/blob/master/posts/conferences/bosc2017_day1a.md)
and
[Biologeek](https://jonathansobel1.wordpress.com/2017/07/27/bosc-session-of-the-eccbismb-2017/)).

On top of open science, their tracks covered another of our big
interests: workflows and reproducible research. This was the third
birthday of [Common Workflow Language (CWL)](http://www.commonwl.org/)
which came out of the 2014 hackfest, and there were a number of talks
from the SevenBridges [RABIX workflow
system](https://www.sevenbridges.com/) and Galaxy. As well as Stian
Soiland-Reyes presenting the impressive [Common Workflow Language
viewer](https://view.commonwl.org/) that moves the sharing of CWL
workflows into the territory of [myExperiment](http://myexperiment.org/)
(slides [here](http://slides.com/markrobinson/cwlviewer#/)). What was
impressive this year was the organic growth of open source communities
behind many of these, the PIs and core team members of CWL and Galaxy
could sit in the audience and let others present their efforts.

We've been big promoters of citizen science, published many papers
promoting these projects and even crowdfunding our own [Bauhinia Genome
project](http://bauhiniagenome.hk/) (see Scott's [recent TEDx
talk](https://youtu.be/RcBzJI8O4j0)), so it was great to see a citizen
science track in BOSC. As a crowdfunded project travel covered by OBF
travel grants to allow Jonathon Sobel to fly from the Lausanne
[Hackuarium biohacker community](http://www.hackuarium.ch/en/),
[BeerDecoded](http://www.genome.beer/) kicked the track off talking
about their community genome project to educate people about open
science and genomics(video [here](https://youtu.be/aiIiFaocaxM)). These
were exactly the reasons we set up our own community genomics project in
Hong Kong, using the Hong Kong public's interest in their mysterious
floral emblem as a hook rather than the Swiss public's interest in beer.
Like our efforts promoting reproducible research by publishing our
[data](http://dx.doi.org/10.5524/100245) and
[protocols](https://www.protocols.io/groups/bauhinia-genome), they've
been sharing their [methods and data via
GitHub](https://github.com/beerdecoded/Beer_ITS_analysis). 
 
Both keynotes this year covered open science, Madeline Ball talking
about her work with the personal genome project and now [Open
Humans](https://www.openhumans.org/) (video
[here](https://youtu.be/PXBxZCfvMXI)). Inspired to get into open science
through being a Wikimedian, coming out of the George Church Lab she was
the manager of the original [Personal Genome
Project](http://www.personalgenomes.org/) that [recently published 174
haplotyped genomes](https://doi.org/10.1186/s13742-016-0148-z) with us,
and with open humans now provides a one-stop-shop for consent and
recruitment to donate all your medical data to medical research. Nick
Loman's talk was a love letter to ubiquitous sequencing and the Oxford
Nanopore portable sequencer (see above for [the
video](https://youtu.be/6QmITGqDvjQ)). Moving far beyond the [early work
he published with us](https://doi.org/10.1186/2047-217X-3-22) presenting
the first *E. coli* genome sequenced on the nanopore, Nick recounted us
with his adventures targeting the Ebola and Zika outbreaks armed with a
mobile sequencing lab. Described by Nick as being a bit like Top Gear,
but without the misogyny and racism, the [Zibra
project](http://www.zibraproject.org/) saw Nick drive around Brazil in a
camper van full of nanopores collecting sequencing data to determine the
natural history of the outbreak. Zika being very difficult to tackle
with amplicon sequencing, key to getting the data to work was Nick's
student Josh [sharing the protocols](https://doi.org/10.1101/098913),
getting other to adapt and share them back, and the amount of public
domain zika sequencing data has grew exponentially as a result.

> [\#BOSC2017](https://twitter.com/hashtag/BOSC2017?src=hash) final
> talk, open data keynote from
> [@pathogenomenick](https://twitter.com/pathogenomenick) "Talky
> McTalkface" <https://t.co/KnC06pXr9Q>
> [pic.twitter.com/cvoHU5QaQr](https://t.co/cvoHU5QaQr)
>
> --- Peter Cock (@pjacock) [July 23,
> 2017](https://twitter.com/pjacock/status/889133525466836992)

 
The traditional BOSC panel discussion this year covered Open Data, and
featured both keynote speakers, Andrew Su, and our Ed Board Member
Carole Goble. Nick was very gracious, highlighting our open science
efforts, and saying the crowdsourcing of the genome of the deadly 2011
*E. coli* outbreak that partly came out of the release of our [first
dataset in GigaDB](http://dx.doi.org/10.5524/100001) (see "[notes from a
tweenome"](http://gigasciencejournal.com/blog/notes-from-an-e-coli-tweenome-lessons-learned-from-our-first-data-doi/)
for the full story) was the even that first got him into Open Science.
Using our data to assemble the genome and release the results via his
blog helped him become an author of the [resulting "open source
genomics"](http://www.nejm.org/doi/full/10.1056/NEJMoa1107643) paper in
the *New England of Medicine*, and ever since he has only seen positives
rather then negative effects from early open data sharing on his career.

It was frustrating the BOSC Open Data track clashed with the BD2K Open
Data track, but this shows that even if BOSC leaves ISMB there are
plenty of other open source advocates at ISMB that can fill the gap.
Overall the new COSI schedule meant there were less clashes than
previous years, and it was the first time we could attend the
[Bio-Ontologies COSI/SIG](http://www.bio-ontologies.org.uk/) in a number
of years. In an ISMB of many birthdays, Bio-Ontologies celebrated the
milestone of it being their 20^th^ edition at ISMB, and had a [looking
forward/looking
back](https://drive.google.com/file/d/0B4y0zfdRviKsWHpQSEVhNjI1V28/view?usp=sharing)
panel covering where the field has gone. Memorable for Carole Goble's
interjection that ontologies are like underwear -- essential but if
everything is working properly then purposefully discrete -- that people
kept coming back to in the rest of the conference.

**FAIR bingo**

Like Carole's ontology underwear comment, over the years there have been
many recurring topics and memes at ISMB. In the past these have inspired
[bioinformatics bingo cards](http://imgur.com/FAKMkXF). Where the
[NHGRI/Moore's law sequencing data
graph](https://www.genome.gov/sequencingcostsdata/) was ubiquitous in
years past, the last few years have seen the rise of docker containers,
the big trend this year was FAIR bingo -- where the speakers mentioned
the mention of [FAIR
principles](https://www.nature.com/articles/sdata201618) in nearly every
talk. Having been included on the original paper was good to see FAIR
(findable, accessible, interoperable, and reusable) moving beyond just a
mnemonic to being implemented in practice in a number of talks.
Including the [Galaxy Training Network
talk](https://bebatut-slides.github.io/bosc_07_17/#/1) for Bérénice
Batut at BOSC, as well from members of the
[GO-FAIR](https://www.dtls.nl/fair-data/go-fair/) initiative (which is a
proposal for the practical implementation of the European Open Science
Cloud), Barend Mons and Marco Roos both presenting on it and showing the
same [FAIR video](https://vimeo.com/162062013).

**Drink the ELIXIR**

The ELIXIR track on the last day was another \#FAIRbingo-heavy session,
and involved [the
launch](https://www.elixir-europe.org/news/core-data-resources) of the
new ELIXIR list of Core Data Resources and Deposition Databases.
Presented by Jo McEntyre, the [curated
list](https://www.elixir-europe.org/platforms/data/core-data-resources)
gathers together the key data resources that are of fundamental
importance to the wider life-science community and the long-term
preservation of biological data. Being ISMB old-timers we've seen
efforts such as [BioCoreDB](https://doi.org/10.1093/database/baq027)
(attending and writing about the 2011 ISMB workshop
[here](http://gigasciencejournal.com/blog/final-impressions-of-vienna-time-to-go-with-the-workflow/))
working on an information specification for biological databases, but
this goes beyond this to gather metrics and indicators to determine how
key these resources are.

The meeting ending on a high with an amazing keynote/prize lecture from
our Ed Board Member Pavel Pevzner, drawing on his incredible work moving
bioinformatics education from the classroom, to online with MOOCs
(massive open online courses) and now MAITs (massive adaptive
interactive text). It was a great note to close on, showing that
bioinformatics is getting more democratic, open and FAIR, so even if
BOSC doesn't return to ISMB in 2019, the conference will continue with
the legacy of its open source ethos.

### References

1\. Scott C. Edmunds, Nicole A. Nogoy, Hans Zauner, Peter Li,
Christopher I. Hunter, Xiao Si Zhe, Laurie Goodman; Looking back:
forward looking. *Gigascience* 2017 gix064. doi:
[10.1093/gigascience/gix064](https://doi.org/10.1093/gigascience/gix064)

UPDATE 3/8/17: now with added BOSC videos.

[Save]{style="border-radius: 2px; text-indent: 20px; width: auto; padding: 0px 4px 0px 0px; text-align: center; font: bold 11px/20px 'Helvetica Neue',Helvetica,sans-serif; color: #ffffff; background: #bd081c no-repeat scroll 3px 50% / 14px 14px; position: absolute; opacity: 1; z-index: 8675309; display: none; cursor: pointer;"}

The post [Bohemian Bashfully. Baroque birthdays and bingo in
Prague.](http://gigasciencejournal.com/blog/bohemian-bashfully-baroque-birthdays-and-bingo-in-prague/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.

Every summer we celebrate our birthday at the ISMB (Intelligent Systems for Molecular Biology) conference, and this was a particularly memorable and important one – being the 5
 
 th
 
 birthday of GigaScience, and 25
 
 th
 
 edition of the ISMB.

Bohemian Bashfully. Baroque birthdays and bingo in Prague.

**Boston 2014: More than a (Bioinformatics) Feeling**  
[![Screen shot 2014-07-31 at 4.34.01
PM](http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/Screen-shot-2014-07-31-at-4.34.01-PM-204x300.png){.alignleft
.size-medium .wp-image-1226 loading="lazy" decoding="async" width="204"
height="300"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/Screen-shot-2014-07-31-at-4.34.01-PM-204x300.png 204w, http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/Screen-shot-2014-07-31-at-4.34.01-PM.png 322w"
sizes="(max-width: 204px) 100vw, 204px"}](http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/Screen-shot-2014-07-31-at-4.34.01-PM.png)Following
from our [previous posting on BOSC, our birthday and the BMC Open Data
award party in
Boston](http://blogs.biomedcentral.com/gigablog/2014/07/17/bioinformatics-birthdays-and-booze-at-boston-bosc/ "BOSC, Boston, Birthdays and Booze in GigaBlog"){target="_blank"
rel="noopener"}, on top of having to dash between the many great talks
and sessions at ISMB, we were kept even busier than usual helping to
organize and present in a special
[Beyond-the-PDF](https://sites.google.com/site/beyondthepdf/ "BtPDF1 website"){target="_blank"
rel="noopener"} inspired ["What Bioinformaticians need to know about
digital publishing beyond the PDF"
workshop](https://www.iscb.org/cms_addon/conferences/ismb2014/workshops.php#WK06 "workshop program"){target="_blank"
rel="noopener"} at the end of the conference. Coming in the year that
Illumina are hoping to make human clinical genome sequencing affordable
with new sequencing platforms, one noticeable trend this year was a
larger number of talks dealing with a lot of the clinical implications
of this data bonanza. On top of great keynotes from Russ Altman and
Isaac Kohane (see the [write up of his
talk](http://blogs.biomedcentral.com/bmcblog/2014/07/23/national-healthcare-the-modern-biomedical-lab/ "Amye Kohane blog"){target="_blank"
rel="noopener"} from Amye), the Harnessing "Genetic Diversity to Enable
Personalized Medicine" workshop track featuring Atul Butte also covered
a lot of this area. Another highlight was the microbiome track,
particularly Eric Alm's work ([just
published](http://genomebiology.com/2014/15/7/R89 "Eric Alm paper"){target="_blank"
rel="noopener"} in *Genome Biology*) looking at the individuality of the
microbial signal from 10,000 observations of diet, health, wellness, and
behavior over a year.

On top of "big data", another hot topic that made the now traditional
[\#ISMBBingo score
sheet](https://twitter.com/jonathancairns/status/488397218203054080/photo/1 "ISMB Bingo card"){target="_blank"
rel="noopener"} was STAP cells, thanks to the continuing fall out from
the [now retracted acid bath stem
cell](http://www.nature.com/news/stap-retracted-1.15488 "STAP retraction"){target="_blank"
rel="noopener"} papers in *Nature*. With issues regarding
reproducibility of growing prominence this year, it was a good time to
take it out of its usual home as a [topic in the BOSC
program](http://www.open-bio.org/wiki/BOSC_2014_Schedule "BOSC program"){target="_blank"
rel="noopener"} to the main conference with a [second edition of our
digital publishing
workshop](https://www.iscb.org/cms_addon/conferences/ismb2014/workshops.php#WK06 "workshop program"){target="_blank"
rel="noopener"} that specifically focuses on these issues. As with last
year, the organizing committee (including our editor Scott Edmunds, Jun
Zhao from Lancaster University, Marco Roos and Barend Mons from LUMC,
our editorial board members Carole Goble and Susanna Sansone, and Amye
Kenall representing our BioMed Central publishers) put together a
fantastic line up of people at the forefront of digital publishing and
scholarly communication. Compared to [last
year](http://blogs.biomedcentral.com/gigablog/2013/08/09/more-on-our-ismb-workshop-what-bioinformaticians-need-to-know-about-digital-publishing-beyond-the-pdf/ "Last year write-up"){target="_blank"
rel="noopener"}, rather than presenting we took more of a back seat in
the workshop organization, but [topics
covered](https://www.iscb.org/cms_addon/conferences/ismb2014/workshops.php#WK06 "workshop program"){target="_blank"
rel="noopener"} many of our collaborations and key areas of interest.

**Workshop 2: Further Beyond the PDF**  
[![IMG_0277](http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/IMG_0277-150x150.jpg){.alignright
.size-thumbnail .wp-image-1221 loading="lazy" decoding="async"
width="150" height="150"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/IMG_0277-150x150.jpg 150w, http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/IMG_0277-100x100.jpg 100w"
sizes="(max-width: 150px) 100vw, 150px"}](http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/IMG_0277.jpg)Being
the penultimate session of the conference it was a challenge to get
people to stick around, but we were lucky not to be the workshop that
clashed with the world cup final. The great line-up, plus the promise of
it being the last chance to get hold of our (unfortunately too) popular
Bruce Lee/Kill Bill inspired ["FREE DATA"
t-shirts](https://twitter.com/GigaScience/status/489082592541810688 "FREE DATA model"){target="_blank"
rel="noopener"} managed to draw an even bigger crowd than last year. Two
of the originally advertised participants Carole Goble and Phil Bourne
unfortunately had commitments crop up that took them away from the
conference earlier than expected, but our last minute replacement chair
(and board member) Francis Ouellette did a fantastic job keeping
everyone on time with his quacking buzzer.

As with last year, we need to thank our overqualified list of speakers,
panelists and supporters who help make it a success, and this time we
had more of a focus on peer review and software. This lead nicely into a
final discussion section expertly hosted by Mozilla Science's Kaitlin
Thaney, and was particularly topical with Mozilla Sciences "Code as a
Research Object" program seeking feedback and contributors. All of the
discussion is archived in a handy
[Storify](https://storify.com/GigaScience/what-bioinformaticians-need-to-know-about-digital "ISMB storify"){target="_blank"
rel="noopener"}, and we'll also include brief summaries and links to the
slides of the talks below.  
**  
Ciaran O'Neill & Amye Kenall: Peering into review -- Innovation, credit
& reproducibility**
\[[slides](http://www.slideshare.net/GigaScience/ciaran-oneill-amye-kenall-peering-into-review-innovation-credit-reproducibility "Peer review slides"){target="_blank"
rel="noopener"}\]  
Ciaran and Amye from BMC set the scene and gave a great overview of
current innovations and alternative models of Peer Review, both at BMC
and beyond. Ciaran covered more of the models and policy side, with Amye
getting into some technical challenges and experiments with more dynamic
papers (including our [Knitr generated electrophysiology
paper](http://blogs.biomedcentral.com/gigablog/2014/03/26/carmen-reproducible-research-and-push-button-papers/ "Push button paper blog"){target="_blank"
rel="noopener"}).

**Alejandra González-Beltrán: What was the plan? A role for data
standards, models and computational workﬂows in scholarly data
publishing**
\[[slides](http://www.slideshare.net/agbeltran/ismb-workshop-2014 "Alejandra slides"){target="_blank"
rel="noopener"}\]  
Alejandra provided an update on the talk we [presented last
year](http://www.slideshare.net/GigaScience/scott-edmunds-ismb-talk-on-big-data-publishing "Scott ISMB 2013 talk slides"){target="_blank"
rel="noopener"} on the case study that we've been carrying out with the
ISA-commons, Research Object and Nanopublication communities. Despite
having to talk over the disruption from the feeding frenzy to get hold
the last of our t-shirts, Alejandra did an excellent job presenting on
the experiments in reproducibility and improving experimental
descriptions that we have been carrying out. On top of giving great
insight into the hows and whys of these data models, some practical
tools such as the [Ontomaton
widget](http://bioinformatics.oxfordjournals.org/content/29/4/525.long "Ontomaton tool paper"){target="_blank"
rel="noopener"} for ontology annotation were presented.

**Barend Mons: Trends in data publishing**
\[[slides](http://www.slideshare.net/GigaScience/barend-mons-slides-from-ismb-2014 "Barend slides"){target="_blank"
rel="noopener"}\]  
[![www.slideshare.net/GigaScience/barend-mons-slides-from-ismb-2014](http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/Screen-shot-2014-07-31-at-4.38.31-PM-150x150.png){.alignleft
.size-thumbnail .wp-image-1228 loading="lazy" decoding="async"
width="150" height="150"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/Screen-shot-2014-07-31-at-4.38.31-PM-150x150.png 150w, http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/Screen-shot-2014-07-31-at-4.38.31-PM-100x100.png 100w"
sizes="(max-width: 150px) 100vw, 150px"}](http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/Screen-shot-2014-07-31-at-4.38.31-PM.png)Barend
followed with more on Nanopublications and Research Objects, but putting
them in context of what he is now calling "FAIR" data, making datasets:
Findable, Accessible, Interoperable, and Re-usable. With
[ELIXIR](http://www.elixir-europe.org/ "ELIXIR homepage"){target="_blank"
rel="noopener"} now promoting these principles too through the [FAIRport
initiative](http://www.datafairport.org/ "FairPort page"){target="_blank"
rel="noopener"}, Barend presented on examples of large scale datasets
they have turned into FAIR digital objects using these types of tools.
Most interesting to us was they experiments with "bring-your-own-data"
parties, as this overlaps very much with the [metabolomics
hackathon](http://gigasciencejournal.com/blog/aint-no-party-like-a-bring-your-own-data-party/)
we organised at almost the same time in Hong Kong. Watch this space for
further developments in this area, as it is an idea we are all keen to
continue with.

**Kaitlin Thaney: Software Review. Q&A and audience participation.**  
![](http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/Bsm8sRCIgAAY0161-300x224.jpeg){.alignright
.size-medium .wp-image-1967 loading="lazy" decoding="async" width="300"
height="224"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/Bsm8sRCIgAAY0161-300x224.jpeg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2014/07/Bsm8sRCIgAAY0161.jpeg 600w"
sizes="(max-width: 300px) 100vw, 300px"}The workshop was then closed
with an interactive/participative session expertly chaired by Kaitlin
Thaney. Asking questions such as "how can code be reused in a
frictionless way?", this covered themes such as code review and the lack
of career incentives and progression for software producers. With some
quite lively debate the track nicely brought a lot of the many threads
in the workshop together, and despite the cavernous dimensions of the
ballroom provided some nice feedback and contributions from the
audience.

It was encouraging to receive positive on the workshop again, and we
look forward to further Guinness fueled discussions on these topics at
ISMB2015 in Dublin. Our [next
workshop](http://australianbioinformatics.net/great-gigascience-galaxy-wkshp#.U9n8uUgUXOs "G3 workshop"){target="_blank"
rel="noopener"} covering similar open science topics will be just after
the [International Conference on Systems
Biology](http://icsb14.com/ "ICSB conference website"){target="_blank"
rel="noopener"} in Australia in September, so if you are in Melbourne on
the 19th September please come along. [Registration is
free](https://www.eventbrite.com.au/e/the-great-gigascience-and-galaxy-g3-workshop-registration-12200657495 "G3 workshop registration page"){target="_blank"
rel="noopener"}.

**Further Reading**  
Storify of the Workshop:
[https://storify.com/GigaScience/what-bioinformaticians-need-to-know-about-digital](https://storify.com/GigaScience/what-bioinformaticians-need-to-know-about-digital "ISMB workshop storify"){target="_blank"
rel="noopener"}

[Save]{style="border-radius: 2px; text-indent: 20px; width: auto; padding: 0px 4px 0px 0px; text-align: center; font: bold 11px/20px 'Helvetica Neue',Helvetica,sans-serif; color: #ffffff; background: #bd081c  no-repeat scroll 3px 50% / 14px 14px; position: absolute; opacity: 1; z-index: 8675309; display: none; cursor: pointer; top: 1820px; left: 476px;"}

The post [Continuing the push beyond static documents. ISMB, and more on
our "What Bioinformaticians need to know about digital publishing beyond
the PDF2"
workshop](http://gigasciencejournal.com/blog/continuing-the-push-beyond-static-documents-ismb-and-more-on-our-second-what-bioinformaticians-need-to-know-about-digital-publishing-beyond-the-pdf2-workshop/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


Boston 2014: More than a (Bioinformatics) Feeling

Following from our previous posting on BOSC, our birthday and the BMC Open Data award party in Boston, on top of having to dash between the many great talks and sessions at ISMB, we were kept even busier than usual helping to organize and present in a special Beyond-the-PDF inspired “What Bioinformaticians need to know about digital publishing beyond the PDF” workshop at the end

Continuing the push beyond static documents. ISMB, and more on our “What Bioinformaticians need to know about digital publishing beyond the PDF2” workshop

**GigaScience reaches its first anniversary of publication, and achieves
several milestones in changing how life science research is published**

[![](http://gigasciencejournal.com/blog/wp-content/uploads/2013/07/IMG_3396-300x225.jpg){.alignleft
.size-medium .wp-image-684 decoding="async" width="300" height="225"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2013/07/IMG_3396-300x225.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2013/07/IMG_3396-768x576.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2013/07/IMG_3396-1024x768.jpg 1024w"
sizes="(max-width: 300px) 100vw, 300px"}](http://gigasciencejournal.com/blog/wp-content/uploads/2013/07/IMG_3396.jpg)One
year on from our launch, we are unveiling new features and functionality
at the [Intelligent Systems for Molecular
Biology](http://www.iscb.org/ismbeccb2013 "ISMB 2013 conference website"){target="_blank"
rel="noopener"} (ISMB) meeting at the ICC in Berlin (pictured) this
week. As well as a print issue celebrating the best of the last year, we
are announcing new features and tools, along with a new data analysis
platform, [GigaGalaxy](http://galaxy.cbiit.cuhk.edu.hk/){target="_blank"
rel="noopener"}.
[GigaGalaxy](http://galaxy.cbiit.cuhk.edu.hk/ "GigaGalaxy"){target="_blank"
rel="noopener"} is an online platform that supports the reproducibility
of data analyses. It provides a means to share computational tools and
workflows that further document and reproduce data analyses reported in
papers published in the journal. Through GigaGalaxy, *GigaScience*
offers method publishing and sharing workflows and analyses in a
transparent, executable manner:
[http://galaxy.cbiit.cuhk.edu.hk/](http://galaxy.cbiit.cuhk.edu.hk/ "GigaGalaxy"){target="_blank"
rel="noopener"}

[GigaDB](http://gigadb.org/ "GigaDB"){target="_blank" rel="noopener"} is
a repository to host data and tools associated primarily with articles
in *GigaScience*. The database recently relaunched with a new look, new
functionality, and updated browsing options. GigaDB also offers
[Aspera](http://asperasoft.com/ "Aspera website"){target="_blank"
rel="noopener"} data transfer (see our recent posting on our [Aspera
functionality](http://blogs.biomedcentral.com/gigablog/2013/06/07/faster-dataset-kill-kill/ "Aspera write-up"){target="_blank"
rel="noopener"}), which can be up to 100x faster than FTP, and a clear
benefit for academics handling huge datasets. Through an association and
[associate
membership](http://www.datacite.org/node/75 "membership blog"){target="_blank"
rel="noopener"} with DataCite, datasets and methods in
[GigaDB](http://gigadb.org/ "GigaDB"){target="_blank" rel="noopener"}
will be assigned a DOI that can be used as a standard citation for
future use of these data in other articles by the authors and other
researchers.
[http://gigadb.org/](http://gigadb.org/ "GigaDB homepage"){target="_blank"
rel="noopener"}

GigaDB has over 50 datasets, and more than 25TB of data, to date. Much
of it unpublished data from the BGI. As well as extending to a broader
range of fields producing mega-datasets such as
[proteomics](http://dx.doi.org/10.5524/100047 "proteomics data 1"){target="_blank"
rel="noopener"} and
[neuroimaging](http://blogs.biomedcentral.com/gigablog/2013/05/09/the-difficulties-sharing-neuroscience-data-can-data-publishing-help/ "GIgaScience Neuroimaging commentary"){target="_blank"
rel="noopener"}, the journal is able to track how datasets have been
used. Many of the previously unpublished datasets released on the
platform have been used by other projects, and this has not prevented
publication of genome papers at a later date. The pigeon genome was
[released](http://dx.doi.org/10.5524/100007 "Pigeon DOI"){target="_blank"
rel="noopener"} in July 2011, and with its main genome only [published
in
Science](http://www.sciencemag.org/content/339/6123/1063 "Pigeon Science paper"){target="_blank"
rel="noopener"} in early 2013. Between these dates it has enabled other
researchers to use it without restriction and publish work on the genes
involved in [pigeon
milk](http://www.biomedcentral.com/1471-2164/14/169 "Pigeon milk paper"){target="_blank"
rel="noopener"}. Several groups have also used released but unpublished
[polar bear
genome](http://dx.doi.org/10.5524/100008 "Polar bear genome DOI"){target="_blank"
rel="noopener"} data in comparative and [population
genetics](http://www.sciencemag.org/content/336/6079/344.short "Science Polar bear paper"){target="_blank"
rel="noopener"} studies for various bear species.

Executive Editor Scott Edmunds is on hand at the ISMB in Berlin for our
birthday this week. You can talk to him at BioMed Central's booth (#18)
and also coordinating and speaking in a workshop on July 22, on '[What
Bioinformaticians need to know about digital publishing beyond the
PDF](http://www.iscb.org/cms_addon/conferences/ismbeccb2013/workshops.php#WK03 "ISMB workshop"){target="_blank"
rel="noopener"}'. This is our 3rd year at ISMB (see the write-ups from
[2011](http://blogs.biomedcentral.com/gigablog/2011/07/20/final-impressions-of-vienna-time-to-go-with-the-workflow/ "2011 GigaBlog on ISMB"){target="_blank"
rel="noopener"} and
[2012](http://blogs.biomedcentral.com/gigablog/2012/07/25/1-2-3-4-get-with-the-wiki/ "ISMB 2012 blog"){target="_blank"
rel="noopener"}), so look out for forthcoming postings here in
[GigaBlog](http://blogs.biomedcentral.com/gigablog/){target="_GigaBlog homepage"
rel="noopener"}. You can also follow the tweets from
[\#BOSC2013](http://www.open-bio.org/wiki/BOSC_2013 "BOSC 2013 homepage"){target="_blank"
rel="noopener"} and tomorrows \#AFP13 SIG (of which we are publishing a
[series](http://blogs.biomedcentral.com/gigablog/2013/07/01/automated-function-prediction-call-for-papers-for-a-special-series/ "AFP series CfP"){target="_blank"
rel="noopener"}), and the main meeting from the \#ISMBECCB hashtag.

The post [GigaBirthday at
ISMB](http://gigasciencejournal.com/blog/gigabirthday-at-ismb/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


GigaScience reaches its first anniversary of publication, and achieves several milestones in changing how life science research is published

One year on from our launch, we are unveiling new features and functionality at the Intelligent Systems for Molecular Biology (ISMB) meeting at the ICC in Berlin (pictured) this week.

Messages de Rogue Scholar

Open Science Milestones and the return of in-person meetings at ISMB2022

Birthdays and Online Conferences go Viral. ISMB2020 & BCC2020 in the time of COVID-19

… and a Happy New Year

Bohemian Bashfully. Baroque birthdays and bingo in Prague.

Continuing the push beyond static documents. ISMB, and more on our “What Bioinformaticians need to know about digital publishing beyond the PDF2” workshop

GigaBirthday at ISMB