Category: Individual-based Ecology

In a Land Down Under, Pensoft joined the 11th ESP World Conference

The latest outcomes at the SELINA project and modern, open-access scholarly publishing were ‘hot’ topics we discussed with delegates in Darwin.

Official group photo of the delegates at ESP11 (Darwin, Australia).
Courtesy of the Ecosystem Services Partnership.

Between 22nd and 26th June, the 11th Ecosystem Services Partnership World Conference (ESP11) brought about 250 international delegates from diverse backgrounds: professional and demographic alike, to the Darwin Convention Centre in the capital city of the Northern Territory, Australia.

Amongst the central topics of the event were the integrations of local and indigenous values and knowledge into the understanding of ecosystem services and their sustainable management; the implementation of nature-based solutions into practice; and the collaboration of scientists with policymakers, practitioners and other stakeholders. 

Inspired by the location – curiously, Australia is the longest continuously inhabited continent on Earth – the conference had a well-pronounced focus on indigenous peoples and culture. Aptly, the conference ran under the theme: “From global to local ecosystem services: pathways to Nature-based Solutions inspired from Down Under”.

Cultural diversity was specially celebrated at both the opening and the closing ceremonies, as well as the special conference dinner. Attendees enjoyed multiple traditional performances from the region, but also from other parts of the world. They also had the chance to hear directly from members of Darwin’s indigenous communities about their own perspectives on ecosystem services and their sustainable management.

Indigenous Australian performance at the opening ceremony at ESP11 (Darwin, Australia).

During the week, each day would open with keynote speeches by renowned scientists from around the world. The programme would then continue with   a set of six parallel sessions. The conference also included poster sessions, a conference dinner and field trips meant to provide the conference participants with a face-to-face encounter with Australian natural phenomena, including close-up encounters with the signature Northern Territory fauna, such as crocodiles, birds and sea turtles.

One of the field trips took participants to the uninhabited Bare Sand Island where they got the chance to see up close a Flatback sea turtle coming out of the water, making her nest and laying her eggs before making her way back to the waves under the cover of the night.  

At the Pensoft stand, delegates met Pensoft’s Head of Journal development and PR: Iva Boyadzhieva, who would answer their questions about the various publishing opportunities and scholarly resources by the publisher, but also about the latest activities and results of the Horizon Europe-funded project SELINA (an acronym for Science for Evidence-based and Sustainable Decisions about Natural Capital).

Pensoft’s stand at the ESP11 conference in Darwin, Australia.

Having started in 2022 and set to run until 2027, SELINA comprises 50 partner organisations coordinated by the Leibniz University Hannover and Prof. Dr. Benjamin Burkhard (Leibniz University Hannover, Germany), who is also co-Chair of the ESP and Editor-in-Chief of the One Ecosystem journal. As an experienced science communicator and open-science publisher, at SELINA, Pensoft has been assigned to lead the project’s communication and dissemination activities.

The transdisciplinary project aims to provide smart, cost-effective, and nature-based solutions to historic societal challenges, such as climate change, biodiversity loss, and food security. One of the consortium’s main objectives is to identify biodiversity, ecosystem condition, and ecosystem service factors that can be successfully integrated into decision-making processes in both the public and private sectors.

Most recently, the consortium launched SELINA’s Communities of Practice initiative to promote collaborative learning and knowledge integration across Europe. This digital platform provides a forum for scientists, policymakers, practitioners, and business representatives to exchange knowledge and further engage with its real-life application. On the Communities of Practice, visitors may explore how SELINA is driving change across Europe.

Once again, all around the venue one could easily catch a glimpse of both local and exotic biodiversity that had taken cover on the laptops of the participants. The vivid stickers have become a signature Pensoft freebies that feature scientific illustration of species discussed in publications from across the publisher’s scholarly portfolio in a nod to the authors who have chosen a journal from the Pensoft scholarly portfolio. 

Besides grabbing a sticker or two from the Pensoft stand, visitors were also intrigued to learn more about Pensoft’s flagship journals fitting the scope of the conference like Nature Conservation, NeoBiota and Biodiversity Data Journal, but also about the most recently launched titles: Individual-based Ecology and Advances in Pollinator Research.

Those who have missed the opportunity to sign up for those journals’ newsletters at the stand, can do this by filling in their email address from the homepage of the journal they fancy or by updating their profiles in the Pensoft system.

Understandably, the highlight in the Pensoft’s journal portfolio for ESP11 delegates was One Ecosystem, which was once born in a collaboration between Pensoft, the predecessor of SELINA: ESMERALDA, and the ESP community itself.

Since its launch in 2016, the open-access peer-reviewed journal has published about 200 research papers, including field-specific research outputs typically falling outside of what traditional scientific journals would see as a publication. These include Software description, Methods, Ecosystem Services Mapping, Ecosystem Accounting Table amongst others. You can find about the origins of One Ecosystem in the 2016 launching editorial. A few years ago, the journal became part of the scholarly literature databases of both Scopus and Web of Science. In fact, the latest Scopus CiteScore of One Ecosystem places the journal in Q1 in all five categories it has been assigned to.

At a special session within the ESP11 programme, Editor-in-Chief Prof. Dr. Benjamin Burkhard welcomed various questions concerning the One Ecosystem journal.

As part of the ESP11 programme, a session dedicated on the open-science approach of One Ecosystem that relies on opening up diverse research outputs and data, in order to prompt transparency, reusability and interdisciplinary in ecological research. Together, Pensoft’s Iva Boyadzhieva, Editor-in-Chief Prof. Dr. Benjamin Burkhard and subject editor ​Dr. Paulo Pereira talked about the journal and addressed the questions of the audience, while also providing general advice on scholarly publishing and editorial work to early career researchers at the session.

The session also presented the announcement that in 2025, ESP members are eligible for a 10% discount on the APC at One Ecosystem.

As usual, the conference closed with an engaging and heart-warming ceremony, where the organisers paid another tribute to local communities and volunteers who made the event an unforgettable experience for everyone. The ceremony finished with the awards for the three best posters presented at ESP11.

Hamid Arrum Harahap was awarded first place for his poster “Ecosystem-Based Adaptation (EbA) to Climate Change for Indigenous Women in the Mentawai Islands and Aceh Singkil, Sumatra (Indonesia)”.

Hamid Arrum Harahap (Universitas Andalas, Indonesia), Nicole Boyd (Charles Darwin University) and Gail Sucharitakul (Imperial College of London, United Kingdom) were recognised for their research posters. 

“My poster highlights the climate knowledge of Indigenous women in the Mentawai Islands and Aceh Singkil. Their voices are often underrepresented in climate discourse, despite contributing the least to climate change and being among the most affected by its impacts”

said first-place sitter Hamid Arrum Harahap about his poster, titled “Ecosystem-Based Adaptation (EbA) to Climate Change for Indigenous Women in the Mentawai Islands and Aceh Singkil, Sumatra (Indonesia)”.

“In regions where downscaling climate models is difficult, intergenerational knowledge passed through indigenous women is critical. Our study highlights that while our climate models from modern science are built on numbers and projections, Indigenous women’s climate memories are rooted in stories and emotions—together, they offer complementary insights for understanding and adapting to climate change.”

In addition to the prizes handed by the ESP, he received a waiver for a free publication at One Ecosystem from the journal’s publisher Pensoft. 

“I plan to use this opportunity to publish my research on Indigenous knowledge and ecosystem services. I am currently working on two studies: one on the relational values of ecosystem services governance with Indigenous Batak communities, and the other on ecosystem-based adaptation and the vulnerability of ecosystem services to climate change, focusing on Indigenous women in Sumatra and Far North Queensland, Australia. I believe One Ecosystem is an ideal platform for this work, as it offers an innovative and accessible forum for multidisciplinary studies like mine and focusing on sustainability of the ecosystem. 

he added.

Third-placed Gail Sucharitakul received a copy of “Mapping Ecosystem Service”: a best-seller in Pensoft’s scientific book portfolio, edited by Prof. Dr. Benjamin Burkhard and Dr. Joachim Maes (European Commission DG Environment): both well-renowned in the field and the ESP community scientists. Maes is also a Deputy Editor-in-Chief at One Ecosystem. 

Now that the ESP11 World Conference has turned into a wonderful memory, we set our sights on the 2016 European conference, which will be taking place in historic Prague, Czech Republic. See you there!

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Follow One Ecosystem (BlueSky, X and Facebook), SELINA (BlueSky, X, Facebook and Linkedin) and Pensoft (BlueSky, X, Facebook, Instagram and Linkedin) on social media.

Guest blog post: Global change, individual behaviour, and trout population persistence

New experiments reinforce that behavioural plasticity can be key for coping with environmental changes

Guest blog post by Daniel Ayllón and Steve Railsback

Early in the morning, Daniel Ayllón and his research mates at the Universidad Complutense de Madrid drive towards the mountains near Madrid. They’re out to survey streams where the endangered Southern Iberian spined-loach and Northern Iberian spined-loach used to coexist. We say “used to,” because once again they fail to find the Northern Iberian spined-loach, probably locally extinct. Such extinctions are not unusual, as freshwater fishes are one of the most threatened groups of animals in the world. There are still many brown trout there, though; the water is still cold enough for them.

Salmonids (trout, salmon and char) are especially challenged by climate change because they need cold, oxygenated and clean water. Trout populations at low altitudes or low latitudes are thus particularly at risk; many in the Iberian Peninsula have been declining for decades as rivers warm and dry. Climate models project a bleak future: such Mediterranean populations will face hotter and drier streams, with more frequent and longer droughts and heat waves, and increasing competition from warm-water fish.

A photo of a brown trout swimming over a bed of smooth pebbles in clear water.
Brown trout (Salmo trutta). Photo by J. R. Pérez (AEMS-Ríos con Vida archive)

Despite these changes, local extinctions of trout are still rare, because salmonids are among the most adaptable and resilient of freshwater fishes. They are changing their physiology and phenology, growth and reproduction patterns, and life-history strategies to adjust to the new environmental conditions, via evolutionary, plastic and behavioural mechanisms. While evolutionary ecologists typically focus on genetic adaptation to forces such as climate change, behavioural plasticity could be even more important, because it is fast, reversible and often predictable.

In fact, thermoregulatory movements seem a ubiquitous behavioural mechanism in salmonids: individuals move up and down river networks to find less-stressful temperatures and better growth potential. Behavioural plasticity in circadian activity and habitat selection (deciding when and where to feed) also help trout resist short-term environmental changes. However, we don’t know how important changes in circadian activity─or behaviours in general─are to long-term population persistence in the face of climate change. So to shed light on this question, in a recent work published in Individual-based Ecology, we ran two virtual experiments using the inSTREAM individual-based model to represent a trout population in northern Spain.

A photo of a river flowing between rocky banks, surrounded by greenery and towering mountains under a clear sky.
The Roncal study site on the River Eska (northern Spain). Photo by Benigno Elvira

Steve Railsback and his colleagues at Cal Poly Humboldt University and the US Forest Service’s Pacific Southwest Research Station in Arcata, California, have been developing, testing, and applying inSTREAM for 25 years. The central idea of individual-based models (IBMs) and of individual-based ecology in general is that a biological system can be described through its individual agents, their environment, and the interactions among agents and between agents and environment. The agents of a system (for example, all fish in a population) are modelled as unique and autonomous individuals with their own properties.

The controlled experiment of Harvey and White to quantify how trout trade off feeding vs. predation risk. The experimenters trained wild trout to feed at this dispenser, and then moved it to increasingly risky habitat. The feeding rate needed to keep the trout from leaving increases with the risk it perceives. IBMs like inSTREAM use knowledge about individual behaviour from experiments like this to predict complex population responses. Video by Jason L. White.

Agents also have behaviours: they make decisions, following simple rules or algorithms, independently of other individuals, and seek objectives such as surviving to reproduce in the future. These behaviours are adaptive: agents’ decisions depend on their state and the state of their environment. In this way, population-level results actually emerge from the behaviour of the individuals. In inSTREAM, model trout decide whether to feed vs. hide from predators at different times of day, assumed a trade-off between the need to feed and the predation risk it poses. Temperature has a strong effect on this trade-off because a fish’s metabolic rates, and thus the amount of food it needs, increase sharply with temperature.

A photo of three people wearing waders engaged in field research in a river.
Three members of the research team at the UCM conducting habitat surveys at the Roncal study site. In IBMs like inSTREAM, modelled populations and their environment are characterised by field data collected in surveys like this. Photo by Benigno Elvira.

What did we learn with our IBM? First, our simulations show what behavioural ecologists know from experiments: that during warm summers trout can meet their metabolic requirements only by feeding at multiple times of day and segregating temporally, so that fish of different size can feed at the same spot but at different times of day. Feeding during daytime is more profitable but riskier, while doing it at night is safer but less efficient, and feeding during twilight provides near-daytime growth and somewhat-reduced risk.

We then analysed how model trout change their circadian foraging behaviour under increasing climate change. As we expected, trout showed great behavioural plasticity: trout of all ages responded to warmer and drier conditions by increasing daytime feeding and overall foraging activity, although there were differences across age classes in the distribution of daily activity. Our second experiment used a great advantage of IBMs as a virtual laboratory: we can run experiments that are impossible in reality. We tested the importance of behavioural plasticity by simply turning the behaviour off. In our simulations, virtual populations of trout capable of flexible circadian feeding were more resistant to climate change─had higher biomass and a more balanced age structure─than were populations of trout that feed only during daytime.

These experiments reinforce that behavioural plasticity can be key for coping with environmental changes, so we shouldn’t minimise its relevance when predicting the persistence of salmonid populations in warming and drying rivers. This conclusion no doubt also applies to other taxa that have powerful adaptive behaviours.

This study epitomises individual-based ecology, the subject of Pensoft’s new journal: we use what we know from empirical research on individual physiology and behaviour, in an individual-based model, to study complex population responses of direct relevance to our changing world.

Research article:

Ayllón D, Railsback SF, Harvey BC, Nicola GG, Elvira B, Almodóvar A (2025) Behavioural plasticity in circadian foraging patterns increases resistance of brown trout populations to environmental change. Individual-based Ecology 1: e139560. https://doi.org/10.3897/ibe.1.e139560

Recently launched Individual-based Ecology journal publishes its first articles

IBE offers a transformative framework for addressing global challenges such as the loss of biodiversity and potential loss of ecosystem services.

Individual-based Ecology (IBE), a new open-access peer-reviewed journal by scholarly publisher and technology provider Pensoft, has now published its first articles, offering a fresh perspective on how the behaviour of individual organisms and ecological systems dynamics are linked.

The journal was launched in September 2024 with an official announcement made during the German Ecological Society’s 53rd annual conference (Freising, Germany).

Pensoft launches new journal: Individual-based Ecology

To fill a known gap in knowledge, the journal focuses on individual-based perspectives in ecology, complementing other ecological disciplines. Current approaches cannot fully capture the mechanisms underlying ecological responses to change in drivers, the journal’s editors believe, as they rarely focus on the individual organisms who directly respond to change.

Four editors-in-chief lead IBE: Prof. Dr. Volker Grimm and Prof. Dr. Karin Frank of Helmholtz Centre for Environmental Research – UFZ, Prof. Dr. Mark E. Hauber of The City University /(CUNY) of New York, and Prof. Dr. Florian Jeltsch of the University of Potsdam. “This team represents an international and collaborative group who agree on the conceptual and empirical need for this new journal”- says Dr Mark E. Hauber, from the Graduate Center of CUNY, and a former guest professor in ecology at the University of Potsdam.

The journal is published under a diamond open-access model, which makes it free of charge for both readers and authors. It publishes a wide range of articles, including empirical, experimental, and modeling studies, as well as reviews, perspectives, and methodological papers.

By blending basic and applied research, IBE offers a transformative framework for addressing global challenges such as the loss of biodiversity and potential loss of ecosystem services.

“We propose a paradigm shift in ecological science, moving from simplifying frameworks that use species, population or community averages to an integrative approach that recognizes individual organisms as fundamental agents of ecological change,” advocates write in a forum paper just published in IBE’s first issue. 

Illustration showing mouse behavior variation, predation effects, and colonization success based on boldness and size in new habitats.
Examples of individual variation and its consequences: a individual variation describes the variation in traits, including behaviour, between or within individuals resulting from various processes such as microevolution and biotic filtering. It also explicitly includes variation induced by experience, health status or microbes and microbial communities associated with the host; b simplified example showing how successful colonisation or invasion depends on inter-individual variation in morphological or behavioural traits (González-Suárez et al. 2015; Dammhahn et al. 2020; Premier et al. 2020).

“By unravelling and predicting the dynamics of biodiversity in the Anthropocene through a comprehensive study of individual organisms, their variability and their interactions, individual-based global change ecology will provide a critical foundation for a better understanding if and how we can manage individual variation and behaviour for conservation and sustainability, taking into account individual-to-ecosystem pathways and feedbacks.” 

Illustration showing the impact of individual variation on biodiversity across genes, populations, communities, and ecosystems under global change.
Hierarchical organisation from genes to ecosystems. Individuals are the elementary particles of ecological systems, meaning that variation and interactions between individuals can scale up to emergent properties at the population, community and ecosystem levels. The different ecological levels are highly interconnected through both bottom-up and top-down processes. Elucidating these feedback loops through an individual-based lens is a prerequisite for understanding ecosystem resilience and response to global change.

“By taking into account the variation, behaviours, and interactions of individual organisms, individual-based ecology links the responses of organisms to the responses of ecosystems: if we understand enough about individuals, we can predict complex system dynamics, even under novel conditions,” the editors and colleagues write in a “manifesto” for individual-based ecology that they published in the new journal. “We intend the journal to show how the individual-based perspective, in empirical, theoretical, and computational studies, benefits all branches of ecology.”

IBE’s first published research articles provide excellent examples of the individual-based perspective of the journal. Church et al. explore, using an established model of brown trout, how the uptake of microplastics by fish with different personalities affects population size. Ayllón et al. use the same model to explore to what extent behavioural plasticity allows this species to cope with environmental change, in particular increasing temperatures. Railsback and Harvey argue that in many models the representation of mortality risk is too simple. They present a new method, “survival increase functions”, which is more realistic but still straightforward to calibrate. 

Guest blog post: Global change, individual behaviour, and trout population persistence

The journal is supported by the Helmholtz Centre for Environmental Research (UFZ, Germany) and the City University of New York (CUNY, USA).

The journal utilises Pensoft’s innovative ARPHA platform, which offers a seamless end-to-end publishing experience, encompassing all stages between manuscript submission and article publication, indexation, dissemination and permanent archiving. As a journal of Pensoft, IBE joins a number of open-access scholarly outlets in ecology  by the publisher.

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You can keep up with updates from the journal on Bluesky, X and Facebook.

Here’s to a year of growing and succeeding together!

Within and beyond our Pensoft team, we celebrate a year of well-nourished partnerships and excitement for the future

Yet another hectic year has passed for our team at Pensoft, so it feels right to look back at the highlights from the last 12 months, as we buckle up for the leaps and strides in 2025.

In the past, we have used the occasion to take you back to the best moments of our most popular journals (see this list of 2023 highlights from ZooKeys, MycoKeys, PhytoKeys and more!); share milestones related to our ARPHA publishing platform (see the new journals, integrations and features from 2023); or let you reminisce about the coolest research published across our journals during the year (check out our Top 10 new species from 2021).

In 2022, when we celebrated our 30th anniversary on the academic scene, we extended our festive spirit throughout the year as we dived deep into those fantastic three decades. We put up Pensoft’s timeline and finished the year with a New Species Showdown tournament, where our followers on (what was back then) Twitter voted twice a week for their favourite species EVER described on the pages of our taxonomic journals.

Spoiler alert: we will be releasing our 2024 Top 10 New Species on Monday, 23 December, so you’d better go to the right of this screen and subscribe to our blog!

As we realised we might’ve been a bit biased towards our publishing activities over the years, this time, hereby, we chose to present you a retrospection that captures our best 2024 moments from across the departments, and shed light on how the publishing, technology and project communication endeavours fit together to make Pensoft what it is.

In truth, we take pride in being an exponentially growing family of multiple departments that currently comprises over 60 full-time employees and about a dozen freelancers working from all corners of the world, including Australia, Canada, Belgium and the United Kingdom. Together, we are all determined to make sure we continuously improve our service to all who have trusted us: authors, reviewers, editors, client journals, learned societies, research institutions, project consortia and other external collaborators.


After all, great deeds are only possible when you team up with great like-minded people!

Pensoft as an open-access academic publisher 

Pensoft’s stand at the 2024 TDWG-SPNHC joint conference (September, Japan).

In 2024, at Pensoft, we were hugely pleased to see a significant growth in the published output at almost all our journals, including record-breaking numbers in both submissions and publications at flagship titles of ours, including the Biodiversity Data Journal, PhytoKeys and MycoKeys. 

Other fantastic news came in June from our Indexing team, who confirmed that One Ecosystem: a quite unique and novel academic outlet we launched in collaboration with the Ecosystem Services Partnership in 2016 – received its first Impact Factor. 

Later in 2024, our colleagues, who work together with our clients to ensure their journals comply with the requirements of the top scholarly databases before they apply for indexation, informed us that another two journals in our portfolio have had their applications to Clarivate’s Web of Science successfully accepted. These are the newest journal of the International Association of Vegetation Science: Vegetation and Classification, and Metabarcoding and Metagenomics: a journal we launched in 2017 in collaboration with a team of brilliant scientists working together at the time within the DNAquaNet COST Action.

In 2024, we also joined the celebrations of our long-time partners at the Museum für Naturkunde Berlin, whose three journals: Zoosystematics and Evolution, Deutsche Entomologische Zeitschrift and Fossil Record are all part of our journal portfolio. This year marked the 10th Open Access anniversary of the three journals.

10 years of Open Access: Museum für Naturkunde Berlin and Pensoft celebrate a decade of partnership

In the meantime, we also registered a record in new titles either joining the Pensoft portfolio or opting for ARPHA Platform’s white-label publishing solution, where journal owners retain exclusivity for the publication of their titles, yet use ARPHA’s end-to-end technology and as many human-provided services as necessary.

Pensoft’s CEO and founder Prof. Dr. Lyubomir Penev with Prof. Dr. Marc Stadler, Editor-in-Chief of IMA Fungus and President of the International Mycological Association at the Pensoft booth at the 12th International Mycological Congress (August, the Netherlands). 

Amongst our new partners are the International Mycological Association who moved their official journal IMA Fungus to ARPHA Platform. As part of Pensoft’s scholarly portfolio, the renowned journal joins another well-known academic title in the field of mycology: MycoKeys, which was launched by Pensoft in 2011. The big announcement was aptly made public at this year’s 12th International Mycological Congress where visitors of the Pensoft stand could often spot newly elected IMA President and IMA Fungus Chief editor: Marc Stadler chatting with our founder and CEO Lyubomir Penev by the Pensoft/MycoKeys booth.

Other partners who chose the services of ARPHA Platform for their journals in 2024 include the International Biogeography Society, United Arab Emirates University and Medical University Pleven.

On our end, we did not stop supporting enthusiastic and proactive scientists in their attempt to bridge gaps in scientific knowledge. In January, we launched the Estuarine Management and Technologies journal together with Dr. Soufiane Haddout of the Ibn Tofail University, Morocco. 

Later on, Dr. Franco Andreone (Museo Regionale di Scienze Naturali, Italy) sought us with the idea to launch a journal addressing the role of natural history museums and herbaria collections in scientific progress. This collaboration resulted in the Natural History Collections and Museomics journal, officially announced at the joint TDWG-SPNHC conference in Okinawa, Japan in August.

Natural History Collections and Museomics launches with its inaugural editorial

Around this time, we finalised our similarly exciting journal project in partnership with Prof. Dr. Volker Grimm (UFZ, Germany), Prof. Dr. Karin Frank (UFZ, Germany), Prof. Dr. Mark E. Hauber (City University of New York) and Prof. Dr. Florian Jeltsch (University of Potsdam, Germany). The outcome of this collaboration is called Individual-based Ecology: a journal that aims to promote an individual-based perspective in ecology, as it closes the knowledge gap between individual-level responses and broader ecological patterns.

ARPHA Platform welcomes new journal launched by Pensoft: Individual-based Ecology

The three newly-launched journals are all published under the Diamond Open Access model, where neither access, nor publication is subject to charges.

As you can see, we have a lot to be proud of in terms of our journals. This is also why in 2024 our team took a record number of trips to attend major scientific events, where we got the chance to meet face-to-face with long-time editors, authors, reviewers and readers of our journals. Even more exciting was meeting the new faces of scientific research and learning about their own take on scholarship and academic journals.

Pensoft’s CEO and founder Prof. Dr. Lyubomir Penev welcomed editors at PhytoKeys to the Pensoft-PhytoKeys-branded booth at the XX International Botanical Congress in July 2024 (Spain).

In 2024, we presented our journals and publishing opportunities at about 20 scientific forums, including the XX International Botanical Congress (July, Spain), the 12th International Mycological Congress (August, the Netherlands), the 10th World Congress of Herpetology (August, Malaysia) and the XXVII International Congress of Entomology (August, Japan).

Pensoft as a scientific technology provider

We cannot possibly comment on Pensoft’s tech progress in 2024 without mentioning the EU-funded project BiCIKL (acronym for Biodiversity Community Integrated Knowledge Library) that we coordinated for three years ending up last April. 

This 36-month endeavour saw 14 member institutions and 15 research infrastructures representing diverse actors from the biodiversity data realm come together to improve bi-directional links between different platforms, standards, formats and scientific fields. 

Following these three years of collaborative work, we reported a great many notable research outputs from our consortium (find about them in the open-science project collection in the Research Ideas and Outcomes journal, titled “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective”) that culminated in the Biodiversity Knowledge Hub: a one-stop portal that allows users to access FAIR and interlinked biodiversity data and services in a few clicks; and also a set of policy recommendations addressing key policy makers, research institutions and funders who deal with various types of data about the world’s biodiversity, and are thereby responsible to ensuring there findability, accessibility, interoperability and reusability (FAIR-ness).

The Biodiversity Knowledge Hub
Visit the Biodiversity Knowledge Hub: the main product of the BiCIKL consortium at: https://biodiversityknowledgehub.eu/.

Apart from coordinating BiCIKL, we also worked side-by-side with our partners to develop, refine and test each other’s tools and services, in order to make sure that they communicate efficiently with each other, thereby aligning with the principles of FAIR data and the needs of the scientific community in the long run.

During those three years we made a lot of refinements to our OpenBiodiv: a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System, and our ARPHA Writing Tool. The latter is an XML-based online authoring environment using a large set of pre-formatted templates, where manuscripts are collaboratively written, edited and submitted to participating journals published on ARPHA Platform. What makes the tool particularly special is its multiple features that streamline and FAIRify data publishing as part of a scientific publication, especially in the field of biodiversity knowledge. In fact, we made enough improvements to the ARPHA Writing Tool that we will be soon officially releasing its 2.0 version!

OpenBiodiv – The Open Biodiversity Knowledge Management System
ARPHA Writing Tool 2.0

Amongst our collaborative projects are the Nanopublications for Biodiversity workflow that we co-developed with KnowledgePixels to allow researchers to ‘fragment’ their most important scientific findings into machine-actionable and machine-interpretable statements. Being the smallest units of publishable information, these ‘pixels of knowledge’ present an assertion about anything that can be uniquely identified and attributed to its author and serve to communicate a single statement, its original source (provenance) and citation record (publication info).

Nanopublications for Biodiversity

In partnership with the Swiss-based Text Mining group of Patrick Ruch at SIB and the text- and data-mining association Plazi, we brought the SIB Literature Services (SIBiLS) database one step closer to solidifying its “Biodiversity PMC” portal and working title.

Towards the “Biodiversity PMC”: a literature database supporting advanced content queries

Understandably, we spent a lot of effort, time and enthusiasm in raising awareness about our most recent innovations, in addition to our long-standing workflows, formats and tools developed with the aim to facilitate open and efficient access to scientific data; and their integration into published scholarly work, as well as receiving well-deserved recognition for their collection.

We just can’t stress it enough how important and beneficial it is for everyone to have high-quality FAIR data, ideally made available within a formal scientific publication!    

Pensoft’s CTO Teodor Georgiev talks about innovative methods and good practices in the publication of biodiversity data in scholarly papers at the First national meeting of the Bulgarian Barcode of Life (BgBOL) consortium (December, Bulgaria).
Pensoft’s CEO and founder Prof. Dr. Lyubomir Penev presenting his “Data papers on biodiversity” talk at the “Biodiversity data in montane and arid Eurasia” symposium jointly organized by GBIF and by the Institute of Zoology of Republic of Kazakhstan (November, Kazakhstan).

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Pensoft’s CTO Teodor Georgiev presents new features and workflows currently in testing at the ARPHA Writing Tool 2.0 at the EASE Autumn Symposium 2024 (online event).

Pensoft’s Head of Journal development, Marketing and PR Iva Boyadzhieva talks about Pensoft’s data publishing approach and innovations at the German Ecological Society 53rd Annual Conference (September, Germany).

Pensoft as a science communicator

At our Project team, which is undoubtedly the fastest developing department at Pensoft, science communicators are working closely with technology and publishing teams to help consortia bring their scientific results closer to policy actors, decision-makers and the society at large.

Ultimately, bridging the notorious chasm between researchers and global politics boils down to mutual understanding and dialogue. 

Pensoft’s communication team attended COP16 (November 2024, Colombia) along with partners at the consortia of CO-OP4CBD, BioAgora and RESPIN: three Horizon Europe projects, whose communication and dissemination is led by Pensoft.

Throughout 2024, the team, comprising 20 science communicators and project managers, has been working as part of 27 EU-funded project consortia, including nine that have only started this year (check out all partnering projects on the Pensoft website, ordered from most recently started to oldest). Apart from communicating key outcomes and activities during the duration of the projects, at many of the projects, our team has also been actively involved in their grant proposal drafting, coordination, administration, platform development, graphic and web design and others (see all project services offered by Pensoft to consortia).

Naturally, we had a seat on the front row during many milestones achieved by our partners at all those 27 ongoing projects, and communicated to the public by our communicators. 

Amongst those are the release of the InsectsCount web application developed within the Horizon 2020 project SHOWCASE. Through innovative gamification elements, the app encourages users to share valuable data about flower-visiting insects, which in turn help researchers gain new knowledge about the relationship between observed species and the region’s land use and management practices (learn more about InsectsCount on the SHOWCASE prroject website). 

Another fantastic project output was the long-awaited dataset of maps of annual forest disturbances across 38 European countries derived from the Landsat satellite data archive published by the Horizon Europe project ForestPaths in April (find more about the European Forest Disturbance Atlas on the ForestPaths project website).

In a major company highlight, last month, our project team participated in COP29 in Baku, Azerbaijan with a side event dedicated to the role of open science and science communication in climate- and biodiversity-friendly policy.

Pensoft’s participation at COP29 – as well as our perspective on FAIR data and open science – were recently covered in an interview by Exposed by CMD (a US-based news media accredited to cover the event) with our science communicator Alexandra Korcheva and project manager Boris Barov. 

You see, A LOT of great things worth celebrating happened during the year for us at Pensoft: all thanks to ceaselessly flourishing collaboration based on transparency, trust and integrity. Huge ‘THANK YOU!’ goes to everyone who has joined us in our endeavours!

Here’s to many more shared achievements coming up in 2025!

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Pensoft launches new journal: Individual-based Ecology

IBE joins a number of open-access ecology journals published by Pensoft

Scholarly publisher and technology provider Pensoft has launched Individual-based Ecology (IBE), a new peer-reviewed, diamond open-access journal established to promote an individual-based perspective in ecology.

IBE aims to bridge the gap between individual-level responses and broader ecological patterns. In the face of global challenges, the journal is looking to contribute to both a better understanding and new sets of predictions of how ecological systems will respond to anthropogenic change. It aims to support the development of appropriate mitigation and restoration measures by focusing on the entities that actually and directly respond to change, i.e. individual organisms.

The journal embraces basic and applied, theoretical and empirical research in terrestrial and aquatic ecology. It welcomes contributions that incorporate data or novel insights about individual organisms and their interactions that are relevant to explaining system-level dynamics. IBE will publish a wide range of articles, including empirical, experimental, and modeling studies, as well as reviews, perspectives, and methodological papers.

As a diamond open-access journal, IBE is currently free to publish and free to read, ensuring that all published research is freely accessible to the global community.

The journal will utilise Pensoft’s innovative ARPHA platform, known for its robust support of academic publishing and efficient dissemination of research. Thanks to its fast-track publishing solution, the new journal offers a seamless, end-to-end publishing experience, encompassing all stages between manuscript submission and article publication, indexation, dissemination and permanent archiving. The publishing services provided by ARPHA also include a variety of human-provided services and integrations with third-party providers, intended to maximise the reach and usability of scholarly knowledge published in IBE.

A banner of IBE presented at the German Ecological Society’s 53rd annual conference (9-13 September 2024, Freising, Germany).

IBE will be led by four editors-in-chief: Prof. Dr. Volker Grimm and Prof. Dr. Karin Frank of Helmholtz Center for Environmental Research – UFZ, Prof. Dr. Mark E. Hauber of The City University of New York, and Prof. Dr. Florian Jeltsch of the University of Potsdam.

„We are excited to launch Individual-based Ecology, a new, promising journal that will contribute to a better understanding of ecological systems and how we interact with them,” said Prof Lyubomir Penev, founder and CEO of ARPHA and Pensoft.

“The time has come to establish individual-based ecology as an important complement to all other branches of ecology, both because we need it to fully understand and predict the response of ecological systems to change, and because empirical and modelling approaches have reached a level where the collection and use of individual-based data has become possible,” says Prof Volker Grimm, one of the editors-in-chief.

“It is exciting to be able to launch a journal that embraces ecological principles at the level of individuals across any and all lineages of life on our planet”, notes Prof. Mark E. Hauber, also an editor-in-chief. 

“This new journal will promote nothing less than a paradigm shift in ecological thinking from averaging approaches to a science focused on the fundamental agents of change, i.e. individual organisms. Systematically recognising the importance of individual variation in ecological systems will transform our fundamental understanding of how biodiversity and its components emerge from individual responses and interactions, and how the emerging levels of organisation will respond to changing environments,” said Prof Florian Jeltsch from the editorial team.  

IBE joins a number of open-access ecology journals published by Pensoft.

For more information on the journal’s focus and scope and guidelines to authors, visit IBE’s website and follow it on BlueSky, X and Facebook.